Contacts of the helix formed by residues 18 - 39 (chain B) in PDB entry 3DH1
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 SER 18 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A ILE* 4.1 1.8 - - - -
156A PRO* 3.2 27.1 - - - -
157A GLY* 4.7 5.6 - - - -
16B PHE 3.5 2.2 + - - -
17B GLN* 1.3 72.9 - - - +
19B MET* 1.3 57.4 + - - +
20B GLU* 3.3 9.1 + - - +
21B GLU* 3.0 36.9 + - - +
22B THR* 2.7 31.0 + - - -
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Residues in contact with MET 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A MET* 3.5 44.4 - - + +
22A THR* 3.7 28.7 - - + -
23A GLU* 5.1 5.6 - - + +
123A VAL* 4.9 4.9 - - + -
155A ILE* 3.8 24.5 - - + +
156A PRO 3.2 10.1 + - - +
157A GLY* 5.1 1.8 - - - -
158A TYR* 4.4 37.5 - - + +
18B SER* 1.3 75.1 - - - +
20B GLU* 1.3 63.4 + - + +
22B THR* 3.3 7.3 + - - -
23B GLU* 3.1 37.4 + - - +
155B ILE* 6.3 0.2 - - + -
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Residues in contact with GLU 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B SER* 3.3 8.3 + - - +
19B MET* 1.3 76.4 - - + +
21B GLU* 1.3 63.8 + - + +
23B GLU* 3.4 17.0 + - - +
24B LYS* 3.0 26.5 + - - +
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Residues in contact with GLU 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B TYR* 2.8 31.1 + - - -
16B PHE 4.1 0.2 - - - +
17B GLN* 3.4 28.8 - - + +
18B SER* 3.0 35.5 + - - +
19B MET 3.3 0.2 - - - -
20B GLU* 1.3 80.5 - - + +
22B THR* 1.3 54.8 + - - +
24B LYS* 3.2 22.6 + - - +
25B TRP* 2.9 37.2 + - - +
52B ASN* 4.4 5.4 + - - +
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Residues in contact with THR 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A MET* 3.6 26.0 - - + -
155A ILE* 4.7 9.3 - - + +
17B GLN* 4.4 5.0 + - - +
18B SER 2.7 21.3 + - - -
19B MET* 3.3 10.9 + - - -
20B GLU 3.2 0.4 - - - -
21B GLU* 1.3 72.9 - - - +
23B GLU* 1.3 65.8 + - - +
25B TRP* 3.1 4.1 + - - +
26B MET* 2.9 24.5 + - + +
101B TYR* 3.4 34.9 + - + -
123B VAL* 4.0 17.0 - - + -
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Residues in contact with GLU 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A MET* 5.2 4.0 - - + -
23A GLU* 5.4 3.8 - - - +
19B MET* 3.1 24.7 + - + +
20B GLU* 3.5 17.2 - - - +
22B THR* 1.3 80.0 - - - +
24B LYS* 1.3 62.5 + - - +
26B MET 3.5 0.5 + - - -
27B GLU* 3.0 27.2 + - - +
158B TYR* 3.2 45.4 + - + +
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Residues in contact with LYS 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B GLN* 5.0 0.2 + - - -
20B GLU 3.0 14.5 + - - +
21B GLU* 3.4 23.7 + - - +
22B THR 3.1 0.2 - - - -
23B GLU* 1.3 76.5 - - - +
25B TRP* 1.3 110.7 + - + +
27B GLU* 3.2 24.3 + - - +
28B GLU* 3.3 19.7 + - - +
52B ASN* 5.4 2.0 + - - -
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Residues in contact with TRP 25 (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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17B GLN* 2.9 30.0 + - + -
21B GLU 2.9 24.1 + - - -
22B THR 3.1 3.8 + - - +
24B LYS* 1.3 115.3 - - + +
26B MET* 1.3 56.7 + - - +
28B GLU* 3.1 16.5 + - - +
29B ALA* 3.0 22.9 + - - +
47B LEU* 3.0 24.7 - - + +
49B VAL* 3.6 24.4 - - + +
52B ASN* 4.6 11.2 - - - -
54B VAL* 3.5 31.4 - - + -
101B TYR* 3.7 41.3 - + + -
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Residues in contact with MET 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B THR* 2.9 18.4 + - + +
25B TRP* 1.3 72.5 - - - +
27B GLU* 1.3 63.4 + - - +
29B ALA* 3.5 6.1 + - + +
30B MET* 3.1 33.9 + - + +
101B TYR* 3.7 17.0 - - + -
102B VAL 3.6 24.2 - - - +
103B THR* 5.0 3.1 - - - -
123B VAL* 3.6 34.3 - - + +
124B TYR 3.8 2.5 - - - -
125B GLY* 3.8 12.3 - - - +
158B TYR* 3.3 62.4 - - + +
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Residues in contact with GLU 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B GLU* 3.0 19.0 + - - +
24B LYS* 3.2 19.0 + - - +
26B MET* 1.3 75.0 - - - +
28B GLU* 1.3 61.0 - - - +
30B MET* 3.2 5.5 + - - +
31B HIS* 3.1 36.5 + - + +
158B TYR* 4.7 3.3 - - - +
159B ARG* 3.1 27.2 + - - +
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Residues in contact with GLU 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B LYS* 3.3 14.7 + - - +
25B TRP* 3.1 30.2 + - - +
27B GLU* 1.3 77.2 - - - +
29B ALA* 1.3 63.8 + - - +
31B HIS* 3.4 13.5 + - + +
32B MET* 3.1 29.6 + - + +
47B LEU* 3.6 12.7 - - + +
54B VAL* 5.3 1.6 - - - +
57B LYS* 3.4 26.9 + - - +
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Residues in contact with ALA 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B TRP 3.0 14.3 + - - +
26B MET* 4.0 10.5 - - + +
28B GLU* 1.3 77.1 - - - +
30B MET* 1.3 58.3 + - + +
32B MET* 3.3 6.4 + - - +
33B ALA* 2.9 27.5 + - - +
45B GLY* 3.5 28.1 - - - +
46B CYS* 4.2 7.9 - - - +
47B LEU* 3.7 7.1 - - + +
101B TYR 4.2 11.4 - - - +
102B VAL 4.9 0.9 - - - +
103B THR* 3.6 10.7 + - - +
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Residues in contact with MET 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B MET* 3.1 20.2 + - + +
27B GLU 3.3 9.4 - - - +
29B ALA* 1.3 75.8 - - - +
31B HIS* 1.3 65.6 + - - +
33B ALA* 3.2 5.5 + - - +
34B LYS* 3.0 36.8 + - - +
103B THR* 4.3 11.9 - - - +
158B TYR* 5.7 1.3 - - + +
159B ARG* 3.9 32.5 - - + +
162B GLU* 2.9 47.8 - - + +
163B ALA* 4.2 12.3 - - - +
166B MET* 3.8 24.3 - - + +
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Residues in contact with HIS 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B GLU* 3.1 25.8 + - + +
28B GLU* 3.4 16.1 + - + +
30B MET* 1.3 75.6 - - + +
32B MET* 1.3 62.6 + - + +
34B LYS* 2.9 33.8 + - - +
35B GLU* 3.0 26.1 + - - +
159B ARG* 6.1 2.9 - - - -
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Residues in contact with MET 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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28B GLU* 3.1 18.1 + - + +
29B ALA* 3.5 8.1 - - - +
31B HIS* 1.3 77.3 - - + +
33B ALA* 1.3 58.5 + - - +
35B GLU* 3.0 18.4 + - - +
36B ALA 2.9 23.7 + - - -
45B GLY* 4.0 4.0 - - - -
46B CYS 4.0 17.5 - - - +
47B LEU* 4.8 5.6 - - - -
57B LYS* 3.8 28.7 - - + +
58B GLY* 3.4 38.1 - - - +
59B ARG* 3.2 39.0 - - + +
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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 ALA 2.9 9.6 + - - +
30B MET 3.2 5.8 + - - +
32B MET* 1.3 74.7 - - - +
34B LYS* 1.3 63.4 + - - +
36B ALA* 3.5 1.2 + - - -
37B LEU* 3.2 16.8 + - - +
43B PRO* 3.5 28.0 - - - +
44B VAL 4.2 3.4 - - - +
45B GLY 3.7 13.8 - - - +
103B THR* 3.5 24.7 - - - +
166B MET* 4.1 16.1 - - + +
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Residues in contact with LYS 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 MET* 3.0 29.3 + - - +
31B HIS* 2.9 45.4 + - - +
33B ALA* 1.3 75.4 - - - +
35B GLU* 1.3 63.0 + - + +
37B LEU* 3.2 21.5 + - + +
38B GLU* 3.0 27.8 + - - +
159B ARG* 5.4 5.7 - - - +
166B MET* 4.0 22.6 - - - -
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Residues in contact with GLU 35 (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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31B HIS* 3.0 16.4 + - - +
32B MET* 3.0 26.8 + - - +
34B LYS* 1.3 76.4 - - + +
36B ALA* 1.3 60.5 + - - +
38B GLU* 3.4 10.5 + - - +
39B ASN* 2.9 32.7 + - - +
59B ARG* 2.9 35.3 + - - +
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Residues in contact with ALA 36 (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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32B MET 2.9 12.2 + - - +
33B ALA 3.8 8.5 - - - +
34B LYS 3.2 0.2 - - - -
35B GLU* 1.3 73.9 - - - +
37B LEU* 1.3 64.0 + - - +
39B ASN* 3.1 11.1 + - - +
41B GLU* 2.9 36.7 + - + +
42B VAL 3.4 24.5 - - - +
43B PRO* 3.9 2.0 - - + -
44B VAL 4.1 5.6 - - - +
59B ARG* 4.1 18.7 - - + +
60B ASN 4.8 0.9 - - - +
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Residues in contact with LEU 37 (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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33B ALA 3.2 10.2 + - - +
34B LYS* 3.2 18.3 + - + +
36B ALA* 1.3 76.8 - - - +
38B GLU* 1.3 67.2 + - + +
40B THR* 3.2 18.7 + - - -
41B GLU 3.8 7.9 + - - +
43B PRO* 4.1 15.0 - - + +
166B MET* 3.8 37.9 - - + +
169B THR* 4.0 14.6 - - + +
170B PHE* 4.2 14.5 - - + -
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Residues in contact with GLU 38 (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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34B LYS* 3.0 32.8 + - - +
35B GLU* 3.4 9.2 + - - +
36B ALA 3.2 0.6 - - - -
37B LEU* 1.3 86.1 - - + +
39B ASN* 1.3 63.8 + - - +
40B THR* 3.3 3.9 + - - -
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Residues in contact with ASN 39 (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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35B GLU* 2.9 23.4 + - - +
36B ALA* 3.1 9.3 + - - +
38B GLU* 1.3 82.3 - - - +
40B THR* 1.3 71.6 + - - +
41B GLU* 3.1 17.6 + - + +
59B ARG* 4.9 9.3 - - - +
63B ASN* 5.2 2.3 - - - +
64B GLN* 4.2 23.3 + - + +
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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) + - + + + + + -
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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