Contacts of the helix formed by residues 36 - 52 (chain B) in PDB entry 3C3C
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 ASN 36 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B VAL* 4.8 1.1 - - - -
33B ILE* 3.9 16.2 - - + -
35B ASN* 1.3 73.2 + - - +
37B GLN* 1.3 62.1 + - - +
38B ARG 3.4 2.5 - - - -
39B ILE* 3.4 11.7 + - + +
40B LYS* 3.2 32.1 + - - +
83B GLU* 2.7 40.9 + - + +
87B LEU* 4.1 13.1 - - + +
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Residues in contact with GLN 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B ASN* 3.2 25.5 + - - +
36B ASN* 1.3 75.7 + - - +
38B ARG* 1.3 62.8 + - - +
40B LYS* 3.4 10.7 + - + +
41B ALA* 3.0 29.8 + - + +
372B GLY 4.6 6.2 + - - +
391B VAL* 3.3 46.5 + - - +
392B SER 4.1 7.2 + - - +
393B THR* 3.8 25.4 - - - +
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Residues in contact with ARG 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B ASP* 3.4 40.3 + - + +
24B PHE* 3.8 5.9 - - - -
25B ASN 2.9 27.9 + - - -
26B VAL* 3.9 16.3 - - + +
27B PRO* 5.6 5.5 - - - +
35B ASN 5.1 0.2 + - - -
36B ASN* 3.4 0.8 - - - +
37B GLN* 1.3 81.5 - - - +
39B ILE* 1.3 61.3 + - - +
41B ALA* 3.7 10.6 - - - +
42B ALA* 3.9 3.3 + - - +
166B GLY* 4.5 1.6 - - - -
188B LEU* 5.1 2.8 - - - +
372B GLY 4.3 7.8 + - - -
393B THR* 3.0 46.7 + - + +
394B GLY 3.3 14.5 + - - -
417B 3PG 2.9 45.4 + - - -
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Residues in contact with ILE 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B PHE* 3.8 24.7 - - + -
26B VAL* 3.8 23.1 - - + -
33B ILE* 4.0 17.3 - - + -
36B ASN* 3.4 10.3 + - + +
37B GLN 3.2 0.4 - - - -
38B ARG* 1.3 76.3 - - - +
40B LYS* 1.3 66.6 + - - +
41B ALA 3.3 0.3 + - - -
42B ALA* 3.4 12.1 + - - +
43B VAL* 3.6 10.9 + - - +
80B VAL* 4.1 13.5 - - + +
83B GLU* 4.0 25.8 - - + -
84B LEU* 3.9 30.1 - - + -
87B LEU* 3.6 17.5 - - + -
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Residues in contact with LYS 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LYS* 6.1 2.4 - - - +
36B ASN* 3.2 25.7 + - - +
37B GLN* 3.8 13.2 - - + +
39B ILE* 1.3 77.0 - - - +
41B ALA* 1.3 63.4 + - - +
43B VAL* 3.1 28.0 + - - +
44B PRO* 3.7 4.2 - - - +
87B LEU* 3.9 26.7 - - + +
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Residues in contact with ALA 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B GLN* 3.0 19.7 + - + +
38B ARG 3.7 6.5 - - - +
39B ILE 3.2 0.2 - - - -
40B LYS* 1.3 75.8 - - - +
42B ALA* 1.3 60.3 + - - +
44B PRO* 3.2 13.0 - - - +
45B SER 5.3 0.2 + - - -
163B ASP* 4.5 0.9 - - - +
188B LEU* 3.5 46.5 + - + +
393B THR* 3.8 10.5 - - + -
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Residues in contact with ALA 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B VAL* 3.8 21.3 - - + -
24B PHE* 3.7 33.2 - - + -
38B ARG 3.9 2.6 + - - +
39B ILE 3.4 2.5 + - - +
40B LYS 3.3 1.0 - - - -
41B ALA* 1.3 76.8 - - - +
43B VAL* 1.3 65.8 + - - +
44B PRO 3.3 0.4 - - - -
45B SER* 3.0 19.8 + - - -
46B ILE* 3.6 15.1 + - + +
163B ASP* 3.6 13.2 - - + +
188B LEU* 4.6 3.3 - - + +
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Residues in contact with VAL 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B ILE 3.6 16.2 - - - +
40B LYS* 3.1 17.2 + - - +
42B ALA* 1.3 77.6 - - - +
44B PRO* 1.4 67.8 - - + +
46B ILE* 3.2 10.4 + - - +
47B LYS* 3.1 46.1 + - + +
84B LEU* 4.0 22.0 - - + -
87B LEU* 4.3 25.4 - - + +
88B LEU* 4.5 7.2 - - + -
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Residues in contact with PRO 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A SER* 4.4 18.7 - - - +
416A ILE* 5.8 5.2 - - + -
40B LYS 3.7 4.7 - - - +
41B ALA* 3.2 17.7 - - - +
42B ALA 3.4 0.4 - - - -
43B VAL* 1.4 97.8 - - + +
45B SER* 1.3 60.6 + - - +
47B LYS* 4.0 7.8 - - + +
48B PHE* 3.1 23.9 + - - +
187B PHE* 4.3 15.6 - - + -
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Residues in contact with SER 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B LEU* 3.8 17.7 - - - +
20B MET* 4.0 13.9 - - - -
42B ALA 3.0 5.7 + - - -
44B PRO* 1.3 77.8 - - - +
46B ILE* 1.3 61.4 + - - +
48B PHE* 3.5 2.8 + - - +
49B CYS* 3.1 31.2 + - - -
163B ASP* 2.8 30.4 + - - -
186B GLY* 3.9 0.6 - - - -
187B PHE* 3.1 31.5 + - - +
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Residues in contact with ILE 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B MET* 4.2 19.7 - - - -
24B PHE* 5.0 1.1 - - + -
42B ALA* 3.8 26.7 - - + +
43B VAL* 3.2 10.7 + - - +
44B PRO 3.1 0.2 - - - -
45B SER* 1.3 75.8 - - - +
47B LYS* 1.3 64.4 + - - +
49B CYS* 3.3 6.3 + - - +
50B LEU* 3.2 35.6 + - + +
57B VAL* 4.6 11.4 - - + +
59B LEU* 3.9 30.3 - - + -
84B LEU* 4.6 14.8 - - + -
88B LEU* 4.2 22.7 - - + -
115B VAL* 4.5 8.3 - - + -
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Residues in contact with LYS 47 (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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3A SER* 4.1 16.2 - - - -
43B VAL* 3.1 32.9 + - + +
44B PRO* 4.0 6.5 - - + +
46B ILE* 1.3 77.3 - - - +
48B PHE* 1.3 59.0 + - - +
50B LEU* 3.4 6.9 + - - +
51B ASP* 2.8 40.7 + - - +
87B LEU 5.3 1.7 + - - -
88B LEU* 3.8 33.9 + - + +
90B LYS* 5.3 9.4 - - - +
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Residues in contact with PHE 48 (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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3A SER* 3.8 14.1 - - - +
4A ASN* 3.7 39.0 - - + -
8B LEU* 3.5 41.1 - - + -
9B ASP* 4.2 13.9 - - + -
11B LEU 5.1 3.1 - - - -
13B VAL* 4.9 5.4 - - + -
44B PRO 3.1 19.8 + - - +
45B SER 3.7 4.9 - - - +
46B ILE 3.2 0.2 - - - -
47B LYS* 1.3 76.3 - - - +
49B CYS* 1.3 62.3 + - - +
51B ASP* 4.3 0.2 - - - -
52B ASN* 2.8 73.0 + - + +
187B PHE* 3.7 12.8 - + + -
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Residues in contact with CYS 49 (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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8B LEU* 4.1 21.8 - - - -
13B VAL* 4.2 7.7 - - + +
18B VAL* 4.3 16.6 - - + -
20B MET* 3.9 20.6 - - - -
45B SER 3.1 20.4 + - - -
46B ILE 3.7 7.2 - - - +
47B LYS 3.3 0.6 - - - -
48B PHE* 1.3 82.2 - - - +
50B LEU* 1.3 60.5 + - - +
52B ASN 3.6 1.0 + - - -
53B GLY 3.3 5.2 + - - -
54B ALA* 2.9 36.5 + - + +
57B VAL* 3.7 16.8 - - + -
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Residues in contact with LEU 50 (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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46B ILE* 3.2 23.3 + - + +
47B LYS* 3.9 5.2 - - - +
49B CYS* 1.3 79.3 - - - +
51B ASP* 1.3 63.8 + - - +
53B GLY* 3.6 9.5 + - - -
54B ALA* 4.7 11.2 - - + +
56B SER 5.3 0.7 - - - -
57B VAL* 4.5 16.6 - - + +
88B LEU* 4.9 3.1 - - + -
90B LYS* 3.8 32.1 - - + -
113B GLY* 3.9 32.8 - - - +
114B SER 5.0 1.3 - - - +
115B VAL* 3.7 26.2 - - + -
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Residues in contact with ASP 51 (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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1A SER* 4.6 21.2 - - - -
2A LEU 4.6 0.2 + - - -
3A SER* 2.7 36.4 + - - +
47B LYS* 2.8 29.4 + - - +
48B PHE 3.2 3.8 + - - +
50B LEU* 1.3 76.6 - - - +
52B ASN* 1.3 63.2 + - - +
53B GLY 3.4 2.5 + - - -
90B LYS* 5.5 6.2 + - - -
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Residues in contact with ASN 52 (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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1A SER* 5.8 4.0 - - - -
3A SER* 5.0 0.6 + - - -
13B VAL* 3.6 17.7 - - + -
14B LYS* 3.4 29.1 + - - +
48B PHE* 2.8 67.0 + - - +
51B ASP* 1.3 82.9 - - - +
53B GLY* 1.3 56.1 + - - +
54B ALA 3.6 1.3 - - - -
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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
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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