Contacts of the helix formed by residues 13 - 37 (chain B) in PDB entry 3HMX
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with PHE 13 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B MET* 1.3 80.1 + - - +
14B PRO* 1.3 74.6 - - + +
15B CYS* 3.6 18.8 + - + -
16B LEU* 3.7 21.9 + - + +
17B HIS* 3.8 14.6 + - - +
88B CYS* 3.4 28.5 - - + -
89B LEU 3.7 1.6 - - - -
90B ALA* 3.1 44.6 - - + -
94B THR* 4.9 3.1 - - + -
191B MET* 4.0 11.4 - - + -
194B LEU* 4.2 26.9 - - + -
195B ASN* 2.9 36.3 + - + +
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Residues in contact with PRO 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B MET 4.4 3.1 - - - +
13B PHE* 1.3 103.1 - - + +
15B CYS* 1.3 63.5 - - - +
17B HIS* 3.0 24.2 + - + +
18B HIS* 3.6 13.0 + - + +
87B SER 4.5 4.0 - - - +
88B CYS* 3.6 22.0 - - - -
89B LEU 4.8 3.4 - - - +
147B ALA* 6.1 0.9 - - + -
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Residues in contact with CYS 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B PHE* 3.5 11.7 - - + -
14B PRO* 1.3 74.8 - - - +
16B LEU* 1.3 69.3 + - - +
17B HIS 3.0 1.6 - - - -
18B HIS* 2.7 10.4 + - - +
19B SER* 2.7 23.2 + - - -
87B SER* 5.0 0.2 - - - -
88B CYS* 2.0 45.9 - - - -
144B LEU* 4.7 3.0 - - + +
147B ALA* 4.7 5.4 - - - -
148B LEU* 3.7 28.7 - - - -
191B MET* 3.6 24.0 - - + -
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Residues in contact with LEU 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B PHE* 3.7 17.8 - - + +
15B CYS* 1.3 75.9 - - - +
17B HIS* 1.3 55.4 + - - +
19B SER* 4.0 1.1 - - - +
20B GLN* 2.7 67.8 + - + +
188B ASP* 3.8 8.1 - - - +
191B MET* 3.3 24.7 - - + +
192B SER* 3.4 38.1 - - - +
195B ASN* 3.8 26.9 - - + +
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Residues in contact with HIS 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B PHE 3.8 5.9 + - - +
14B PRO* 3.0 17.4 + - + +
15B CYS 2.9 0.8 + - - -
16B LEU* 1.3 79.7 - - - +
18B HIS* 1.3 76.2 + + - +
20B GLN* 3.9 9.3 - - - +
21B ASN* 3.1 54.9 + - - +
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Residues in contact with HIS 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B PRO* 3.9 17.2 + - + +
15B CYS* 2.7 12.1 + - - +
17B HIS* 1.3 90.8 + + - +
19B SER* 1.3 58.9 + - - +
21B ASN* 3.1 11.0 + - - +
22B LEU* 2.8 30.8 + - - +
140B VAL* 5.0 4.8 - - + +
143B GLU* 3.6 47.8 + - + +
144B LEU* 3.7 20.6 - - + -
147B ALA* 3.8 19.1 - - + +
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Residues in contact with SER 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B CYS 2.7 18.5 + - - -
16B LEU* 3.6 3.8 + - - +
18B HIS* 1.3 74.0 - - - +
20B GLN* 1.3 56.2 + - - -
22B LEU* 3.3 6.2 + - - +
23B LEU* 3.0 28.9 + - - +
144B LEU* 4.3 5.5 - - - +
184B ALA 5.1 0.7 - - - +
187B ILE* 3.9 16.8 - - - +
188B ASP* 3.0 35.9 + - - +
191B MET* 3.7 22.7 - - - +
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Residues in contact with GLN 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A ARG* 4.6 18.1 - - - +
16B LEU* 2.7 59.1 + - + +
17B HIS* 3.9 8.2 - - - +
19B SER* 1.3 69.4 - - - +
21B ASN* 1.3 65.0 - - - +
23B LEU* 3.5 2.6 + - - +
24B ARG* 3.0 41.9 + - - +
188B ASP* 3.5 20.3 + - - +
192B SER* 5.2 1.0 + - - -
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Residues in contact with ASN 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B HIS* 3.1 52.9 + - - +
18B HIS* 3.5 13.2 + - - +
20B GLN* 1.3 76.6 - - - +
22B LEU* 1.3 57.6 + - - +
24B ARG* 2.7 36.4 + - - +
25B ALA* 3.1 28.8 + - - +
140B VAL* 4.3 18.1 - - + +
143B GLU* 5.1 5.7 + - - -
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Residues in contact with LEU 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B HIS 2.8 16.4 + - - +
19B SER* 3.5 5.4 - - - +
20B GLN 3.1 0.2 - - - -
21B ASN* 1.3 73.6 - - - +
23B LEU* 1.3 69.1 + - - +
24B ARG 3.0 1.1 - - - -
25B ALA* 2.9 13.0 + - - +
26B VAL* 2.9 28.8 + - + +
109B LEU* 4.0 15.5 - - + -
137B MET 4.7 0.7 - - - +
140B VAL* 3.7 30.7 - - + +
141B ILE* 3.9 18.6 - - + -
144B LEU* 3.5 28.9 - - + -
180B PHE* 4.1 7.4 - - + -
184B ALA* 4.5 13.7 - - + -
187B ILE* 4.5 12.1 - - + -
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Residues in contact with LEU 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A TYR* 4.9 9.6 - - + +
19B SER 3.0 16.7 + - - +
20B GLN* 3.9 4.5 - - - +
22B LEU* 1.3 75.6 - - - +
24B ARG* 1.3 59.2 + - - +
26B VAL* 3.9 1.3 - - - +
27B SER* 2.9 36.6 + - - +
181B ARG* 3.8 26.2 - - + +
184B ALA* 3.8 16.3 - - + +
185B VAL* 3.5 48.5 - - + +
188B ASP* 4.1 15.3 - - + +
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Residues in contact with ARG 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B GLN* 3.0 37.6 + - - +
21B ASN* 2.7 40.2 + - - +
23B LEU* 1.3 80.8 - - + +
25B ALA* 1.3 56.9 - - - +
27B SER* 3.3 6.3 + - - -
28B ASN* 2.9 43.5 + - - +
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Residues in contact with ALA 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ASN 3.1 18.1 + - - +
22B LEU 2.9 4.6 + - - +
24B ARG* 1.3 78.6 - - - +
26B VAL* 1.3 57.6 - - - +
28B ASN* 3.4 5.3 + - - +
29B MET* 2.9 29.0 + - - +
32B LYS* 5.6 0.3 + - - -
134B ASP* 5.6 1.7 - - - +
136B ASN* 5.0 6.1 - - + +
137B MET* 4.1 17.4 - - + +
140B VAL* 3.8 24.0 - - + -
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Residues in contact with VAL 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B LEU* 2.9 26.1 + - + +
23B LEU* 4.1 4.0 - - - +
25B ALA* 1.3 73.8 - - - +
27B SER* 1.3 58.3 + - - +
28B ASN 3.1 0.2 - - - -
29B MET* 4.3 5.6 - - - +
30B LEU* 2.7 34.2 + - + +
137B MET* 3.8 12.6 - - + -
177B LEU* 3.8 15.7 - - + +
180B PHE* 3.4 34.5 - - + -
181B ARG* 3.7 38.8 - - + +
184B ALA* 4.9 2.9 - - + -
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Residues in contact with SER 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B LEU* 2.9 23.3 + - - +
24B ARG* 3.3 7.6 + - - -
26B VAL* 1.3 77.0 - - - +
28B ASN* 1.3 65.0 + - - +
30B LEU* 3.9 2.6 - - - +
31B GLN* 3.2 33.4 + - - +
181B ARG* 2.7 44.3 + - - +
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Residues in contact with ASN 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ARG* 2.9 32.9 + - - +
25B ALA* 3.4 5.8 + - - +
27B SER* 1.3 83.7 + - - +
29B MET* 1.3 63.5 + - - +
31B GLN* 3.7 8.7 + - - +
32B LYS* 3.3 37.6 + - - +
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Residues in contact with MET 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ALA 2.9 17.0 + - - +
26B VAL* 3.9 2.9 - - - +
28B ASN* 1.3 75.2 - - - +
30B LEU* 1.3 67.1 + - - +
32B LYS* 3.0 27.5 + - + +
33B ALA* 3.0 12.3 + - + +
131B ILE* 4.1 17.5 - - + -
132B PHE 3.3 24.0 - - - +
133B LEU* 3.7 19.7 - - + -
134B ASP* 3.6 27.4 - - + +
137B MET* 4.0 27.8 - - + -
173B LEU* 4.7 4.3 - - + -
177B LEU* 3.8 22.3 - - + +
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Residues in contact with LEU 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B VAL 2.7 22.3 + - - +
27B SER 3.9 4.0 - - - +
29B MET* 1.3 74.9 - - - +
31B GLN* 1.3 71.3 + - + +
33B ALA* 3.3 4.8 + - + +
34B ARG* 3.2 28.8 + - + +
174B CYS* 4.6 2.9 - - - +
177B LEU* 3.4 43.4 - - + +
178B HIS* 3.6 43.3 - - + +
181B ARG* 4.1 25.6 - - + -
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Residues in contact with GLN 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B SER 3.2 19.7 + - - +
28B ASN* 3.9 10.3 - - - +
29B MET 3.2 0.8 - - - -
30B LEU* 1.3 86.7 - - - +
32B LYS* 1.3 62.0 + - + +
34B ARG* 3.9 19.3 + - - +
35B GLN* 2.9 53.0 + - - +
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Residues in contact with LYS 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B ALA 5.6 0.2 + - - -
28B ASN* 3.3 29.6 + - - +
29B MET* 3.0 24.8 + - - +
31B GLN* 1.3 75.7 - - - +
33B ALA* 1.3 65.8 + - - +
35B GLN* 3.0 6.3 + - - -
36B THR* 3.0 33.3 + - + +
131B ILE* 4.5 14.6 - - + -
132B PHE 5.4 1.8 - - - +
134B ASP* 3.4 31.4 + - + +
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Residues in contact with ALA 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B MET* 3.0 7.0 + - + +
30B LEU* 3.3 9.6 + - + +
32B LYS* 1.3 77.5 - - - +
34B ARG* 1.3 55.7 + - - +
35B GLN 2.8 2.4 + - - -
36B THR* 2.9 6.3 + - - -
37B LEU* 2.7 44.5 + - + +
131B ILE* 4.8 6.4 - - + +
173B LEU* 5.2 6.1 - - + -
174B CYS* 4.3 17.9 - - - -
177B LEU* 3.8 24.5 - - + -
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Residues in contact with ARG 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B LEU* 3.2 24.7 + - + +
31B GLN* 4.2 24.5 - - - +
33B ALA* 1.3 76.5 - - + +
35B GLN* 1.3 59.2 + - + +
36B THR 3.7 0.2 - - - -
37B LEU 4.5 12.4 - - - +
42B CYS* 4.0 30.4 + - + +
43B THR* 4.2 24.6 - - - +
44B SER 5.1 3.8 - - - +
174B CYS* 5.4 0.4 - - - -
178B HIS* 5.1 13.9 + - + +
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Residues in contact with GLN 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B GLN* 2.9 45.7 + - - +
32B LYS* 3.0 6.1 + - - +
33B ALA 2.9 1.4 - - - -
34B ARG* 1.3 82.4 - - + +
36B THR* 1.3 66.7 + - + +
37B LEU 3.7 1.1 - - - -
38B GLU* 5.8 0.2 - - - +
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Residues in contact with THR 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B LYS* 3.0 18.5 + - + +
33B ALA* 2.9 4.3 + - - -
35B GLN* 1.3 87.2 - - + +
37B LEU* 1.3 65.7 + - - +
38B GLU* 3.8 12.3 + - - +
130B GLN* 4.7 14.5 + - - +
131B ILE* 3.6 30.2 - - + +
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Residues in contact with LEU 37 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ALA* 2.7 22.8 + - + +
34B ARG* 4.5 6.8 - - - +
35B GLN 5.4 0.7 - - - -
36B THR* 1.3 88.5 - - - +
38B GLU* 1.3 63.3 + - - +
39B PHE 4.0 0.2 - - - -
40B TYR* 4.3 28.6 - - + +
42B CYS* 4.4 13.4 - - - +
130B GLN* 3.7 29.6 - - + +
131B ILE* 4.4 20.9 - - + -
170B LYS* 3.6 34.5 - - + +
173B LEU* 5.4 3.4 - - + -
174B CYS* 3.9 14.8 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il