Contacts of the helix formed by residues 11 - 32 (chain B) in PDB entry 3U9J
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 11 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ASP* 3.1 3.4 + - - +
10B VAL* 1.3 106.1 - - + +
12B THR* 1.3 68.0 + - - +
13B ALA 3.4 2.0 - - - -
14B PRO* 3.2 5.6 - - - +
15B HIS* 2.9 40.4 + + + +
57B HIS* 5.4 0.2 - + - -
61B GLU* 3.3 32.8 - - + -
65B ILE* 4.1 23.1 - - + -
66B ILE* 4.7 2.0 - - + -
130B GLU* 3.5 50.9 - - + -
131B GLU* 4.0 10.3 - - + -
134B PHE* 3.9 18.6 - + + -
135B GLN* 3.8 15.9 - - + -
138B LEU* 4.1 3.8 - - + -
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Residues in contact with THR 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ASP* 2.5 34.1 + - - -
11B PHE* 1.3 76.2 - - - +
13B ALA* 1.3 59.9 + - - +
15B HIS* 3.4 4.7 + - - +
16B TRP* 2.9 29.1 + - + +
131B GLU* 4.9 12.8 - - - +
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Residues in contact with ALA 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ASP 5.4 1.6 + - - -
12B THR* 1.3 75.3 - - - +
14B PRO* 1.3 76.5 - - + +
16B TRP* 3.1 21.2 + - + +
17B ARG* 3.2 11.8 + - - +
151B LYS* 5.6 7.0 - - - +
155B ILE* 4.2 17.7 - - + -
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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
----------------------------------------------------------
9B ASP 5.6 1.3 - - - +
10B VAL 3.9 17.5 - - - +
11B PHE* 3.2 13.2 - - - +
13B ALA* 1.3 93.7 - - + +
15B HIS* 1.3 57.0 + - - +
17B ARG* 3.2 8.5 + - + +
18B MSE 2.9 36.5 + - + +
57B HIS* 3.6 22.9 - - + -
154B VAL* 4.3 4.9 - - + -
155B ILE* 4.5 9.6 - - + -
158B HIS* 3.7 33.7 - - + +
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Residues in contact with HIS 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B PHE* 2.9 34.1 + + + +
12B THR* 3.8 3.4 - - - +
14B PRO* 1.3 73.6 - - - +
16B TRP* 1.3 61.2 + - - +
18B MSE 3.9 1.7 - - + +
19B LYS* 2.8 41.3 + - + +
57B HIS* 3.4 15.5 + + - -
61B GLU* 3.5 2.2 + - - -
127B MSE 3.5 44.0 - - + +
130B GLU* 3.0 16.8 - - - -
131B GLU* 2.6 29.0 + - - +
203B FE 2.2 28.1 - - - -
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Residues in contact with TRP 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B THR* 2.9 16.8 + - + +
13B ALA* 3.1 16.4 + - + +
15B HIS* 1.3 76.0 - - - +
17B ARG* 1.3 81.1 + - + +
19B LYS* 3.5 7.8 + - - +
20B GLN* 2.9 65.5 + - + +
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Residues in contact with ARG 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B ALA 3.2 6.8 + - - +
14B PRO* 3.2 10.9 + - + +
15B HIS 3.2 0.2 - - - -
16B TRP* 1.3 92.0 - - + +
18B MSE 1.3 76.1 + - + +
20B GLN* 3.1 28.8 + - - +
21B LEU* 2.9 47.3 + - + +
24B LEU* 5.2 3.4 - - - +
53B GLU* 2.9 42.0 + - - +
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Residues in contact with MSE 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B PRO* 2.9 27.0 + - + +
15B HIS* 3.3 5.8 + - - +
17B ARG* 1.3 91.6 - - + +
19B LYS* 1.3 58.3 + - - +
21B LEU* 3.2 6.2 + - - +
22B VAL* 2.9 32.5 + - - +
53B GLU* 4.3 22.0 - - + +
54B PHE* 3.6 27.3 - - + -
57B HIS* 3.7 44.2 - - + +
123B PHE* 4.0 12.3 - - + -
127B MSE 4.0 15.5 - - - -
158B HIS* 3.8 20.9 - - + -
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Residues in contact with LYS 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B HIS* 2.8 23.7 + - - +
16B TRP* 3.8 6.3 - - - +
18B MSE 1.3 72.6 - - - +
20B GLN* 1.3 67.0 + - - +
22B VAL* 3.3 8.0 + - - +
23B GLY* 3.0 20.3 + - - -
124B LEU* 5.3 13.5 - - + -
127B MSE 3.9 31.4 - - + +
131B GLU* 4.3 20.3 + - - -
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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
----------------------------------------------------------
16B TRP* 2.9 49.4 + - + +
17B ARG* 3.1 39.6 + - - +
19B LYS* 1.3 76.8 - - - +
21B LEU* 1.3 57.9 + - - +
23B GLY* 3.3 3.2 + - - -
24B LEU* 3.0 46.6 + - + +
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Residues in contact with LEU 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B ARG* 2.9 58.5 + - + +
18B MSE 3.2 8.9 + - - +
20B GLN* 1.3 74.7 - - - +
22B VAL* 1.3 64.7 + - - +
24B LEU* 3.2 15.1 + - + +
25B TYR* 3.0 28.4 + - - +
50B THR* 3.9 32.5 + - + +
53B GLU* 3.7 27.1 - - + +
54B PHE* 3.9 16.2 - - + -
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Residues in contact with VAL 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B MSE 2.9 20.4 + - - +
19B LYS* 3.3 11.4 + - - +
21B LEU* 1.3 74.9 - - - +
23B GLY* 1.3 65.6 + - - +
25B TYR* 3.3 21.9 + - + +
26B CYS* 3.0 31.0 + - - -
54B PHE* 3.9 15.5 - - + -
120B THR* 3.7 26.9 - - + -
123B PHE* 4.0 19.7 - - + -
124B LEU* 4.9 9.9 - - + -
127B MSE 5.2 0.2 - - + -
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Residues in contact with GLY 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B LYS 3.0 14.3 + - - -
20B GLN 3.6 3.8 - - - -
22B VAL* 1.3 77.9 - - - +
24B LEU* 1.3 62.4 + - - +
26B CYS* 3.5 5.8 + - - +
27B ASP* 3.1 32.8 + - - +
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Residues in contact with LEU 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B ARG* 5.2 2.9 - - - +
20B GLN* 3.0 36.7 + - + +
21B LEU* 3.6 22.9 - - + +
22B VAL 3.2 0.2 - - - -
23B GLY* 1.3 76.2 - - - +
25B TYR* 1.3 57.9 + - - +
27B ASP* 3.4 14.0 + - + +
28B LYS* 3.0 28.5 + - - +
50B THR* 6.2 0.2 - - - +
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Residues in contact with TYR 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B LEU 3.0 22.2 + - - +
22B VAL* 3.5 23.6 - - + +
24B LEU* 1.3 75.5 - - - +
26B CYS* 1.3 77.7 + - - +
28B LYS* 3.8 7.4 - - + +
29B LEU* 2.8 34.4 + - + +
43B LEU* 4.8 2.3 - - + +
46B SER* 5.5 5.6 - - - +
47B LEU* 3.6 26.0 - - + +
50B THR* 4.0 19.3 - - + +
51B PHE* 3.8 20.9 - + - -
54B PHE* 3.9 11.0 - + - -
116B LEU* 4.2 20.8 + - + -
119B PHE* 3.6 16.6 - - - -
120B THR* 2.7 27.9 + - - -
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Residues in contact with CYS 26 (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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22B VAL* 3.0 31.6 + - - +
23B GLY* 3.7 7.2 - - - +
25B TYR* 1.3 95.3 - - - +
27B ASP* 1.3 64.5 + - - +
29B LEU* 3.7 9.9 - - - +
30B SER* 3.1 24.4 + - - -
120B THR* 5.0 7.2 - - - -
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Residues in contact with ASP 27 (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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23B GLY 3.1 19.1 + - - +
24B LEU* 3.5 16.8 - - + +
26B CYS* 1.3 76.1 - - - +
28B LYS* 1.3 62.8 + - - +
30B SER* 2.7 24.2 + - - -
31B LYS* 3.2 17.8 + - + +
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Residues in contact with LYS 28 (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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24B LEU 3.0 18.1 + - - +
25B TYR* 3.8 7.2 - - + +
27B ASP* 1.3 75.8 - - - +
29B LEU* 1.3 59.3 + - - +
31B LYS* 3.2 5.3 + - - +
32B THR* 2.7 37.6 + - - +
42B ALA* 4.7 4.5 - - + +
43B LEU* 3.9 24.2 - - + -
46B SER* 3.5 35.9 - - - +
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Residues in contact with LEU 29 (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 TYR* 2.8 25.3 + - + +
26B CYS* 3.7 11.2 - - - +
28B LYS* 1.3 73.2 - - - +
30B SER* 1.3 62.7 + - - +
31B LYS 3.3 0.9 + - - -
32B THR* 3.3 17.8 + - - +
34B PHE* 3.6 36.5 - - + -
43B LEU* 3.8 15.7 - - + +
112B LEU* 4.3 4.7 - - + -
113B LYS* 4.3 27.0 - - + +
116B LEU* 4.1 32.3 - - + -
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Residues in contact with SER 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B CYS 3.1 13.6 + - - -
27B ASP* 2.7 22.7 + - - -
29B LEU* 1.3 78.8 - - - +
31B LYS* 1.3 72.8 + - - +
32B THR 4.7 1.9 - - - +
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Residues in contact with LYS 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B ASP* 3.4 19.8 - - + +
28B LYS* 3.2 6.5 + - - +
30B SER* 1.3 85.6 - - - +
32B THR* 1.3 64.7 + - - +
33B ASN* 3.5 2.9 + - - +
39B ASP* 4.1 4.0 - - - +
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Residues in contact with THR 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B LYS* 2.7 26.1 + - - +
29B LEU 3.3 9.6 + - - +
30B SER 4.7 2.1 - - - +
31B LYS* 1.3 79.1 - - - +
33B ASN* 1.3 71.4 + - - +
34B PHE* 3.5 33.8 + - + -
39B ASP* 3.7 30.0 + - + +
40B PHE* 4.5 0.7 - - - +
43B LEU* 3.9 23.7 - - + +
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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