Contacts of the helix formed by residues 31 - 42 (chain B) in PDB entry 3IIV
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 ASP 31 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16B ARG* 4.1 5.2 - - - +
17B VAL* 4.1 0.7 - - - -
28B ASP* 3.1 33.9 + - + +
29B SER 3.5 0.2 - - - -
30B GLY* 1.3 76.0 - - - +
32B PRO* 1.4 65.7 - - - +
33B VAL* 2.9 21.1 + - - +
34B GLU* 3.5 22.4 + - + +
35B LEU* 2.9 30.7 + - - +
65B LEU* 5.8 0.2 - - - +
68B LYS* 5.1 6.5 + - - -
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Residues in contact with PRO 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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10B LEU* 4.0 4.6 - - + +
12B LEU* 3.6 29.4 - - + -
15B GLY 3.1 29.4 - - - +
17B VAL* 3.6 11.0 - - + -
30B GLY 3.5 6.9 - - - +
31B ASP* 1.4 88.3 - - - +
33B VAL* 1.3 58.4 + - - +
36B GLY* 2.9 26.2 + - - -
49B PHE* 3.8 19.6 - - + -
65B LEU* 4.1 25.8 - - + -
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Residues in contact with VAL 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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31B ASP* 2.9 10.8 + - - +
32B PRO* 1.3 75.4 - - - +
34B GLU* 1.3 60.9 + - - +
37B LYS* 2.9 33.9 + - + +
65B LEU* 3.5 28.5 - - + -
68B LYS* 3.8 29.8 - - + +
69B VAL* 3.9 17.9 - - + -
72B GLN* 3.2 43.1 - - + +
73B ILE* 4.1 3.2 - - + +
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Residues in contact with GLU 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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26B LEU* 3.4 22.9 - - + +
27B ARG* 2.9 32.9 + - - +
28B ASP* 2.8 31.9 + - - +
31B ASP* 3.3 22.1 + - + +
33B VAL* 1.3 82.1 - - - +
35B LEU* 1.3 57.3 + - - +
37B LYS* 3.8 5.1 - - + +
38B PHE* 3.0 29.1 + - - +
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Residues in contact with LEU 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B LEU* 3.8 20.0 - - + -
17B VAL* 4.1 17.3 - - + -
21B SER* 3.8 24.7 - - - +
23B PHE* 3.6 26.5 - - + -
26B LEU* 4.0 16.0 - - + +
29B SER 4.2 5.2 - - - +
31B ASP 2.9 17.5 + - - +
32B PRO 4.2 1.6 - - - +
34B GLU* 1.3 75.8 - - - +
36B GLY* 1.3 59.6 + - - +
38B PHE* 3.3 5.5 + - + +
39B TYR* 2.9 55.6 + - + -
228B HIS* 4.2 8.1 - - + -
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Residues in contact with GLY 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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10B LEU* 4.2 5.8 - - - +
32B PRO 2.9 18.8 + - - -
33B VAL 3.9 0.4 - - - -
35B LEU* 1.3 77.4 - - - +
37B LYS* 1.3 63.7 + - - +
39B TYR* 3.2 2.6 + - - +
40B SER* 3.0 18.7 + - - -
47B LEU* 3.4 32.4 - - - +
49B PHE* 4.6 1.3 - - - -
73B ILE* 3.7 10.1 - - - -
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Residues in contact with LYS 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 VAL* 2.9 22.6 + - + +
34B GLU* 3.8 5.6 - - - +
36B GLY* 1.3 75.1 - - - +
38B PHE* 1.3 65.2 + - - +
40B SER* 2.6 29.6 + - - +
41B GLU* 3.0 42.8 + - - +
72B GLN* 3.1 35.8 + - + +
73B ILE* 3.6 10.0 - - + +
74B ASP* 5.4 7.5 + - - +
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Residues in contact with PHE 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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23B PHE* 3.3 48.0 - + - -
25B ASN* 3.3 27.6 - - - -
26B LEU* 3.8 17.3 - - + -
34B GLU 3.0 18.6 + - - +
35B LEU* 3.5 7.6 - - + +
37B LYS* 1.3 76.6 - - - +
39B TYR* 1.3 64.5 + + - +
41B GLU* 2.9 22.4 + - - +
42B ILE* 3.2 39.0 + - + +
256B LEU* 3.7 28.5 - - + -
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Residues in contact with TYR 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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8B ALA* 4.3 10.1 - - + -
10B LEU* 4.4 3.8 - - + -
23B PHE* 3.3 28.7 - + - -
35B LEU* 2.9 37.3 + - + -
36B GLY 3.6 6.3 - - - +
38B PHE* 1.3 75.9 - + - +
40B SER* 1.3 62.8 + - - +
41B GLU 3.2 0.5 + - - -
42B ILE* 3.2 20.1 + - + +
43B GLY 3.4 0.5 + - - -
44B ILE* 3.1 52.1 + - + -
47B LEU* 4.1 12.1 - - + -
227B PHE* 3.2 18.1 - + + +
228B HIS* 2.7 54.6 + + - -
234B VAL* 4.3 8.5 - - + -
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Residues in contact with SER 40 (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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36B GLY 3.0 11.8 + - - -
37B LYS* 2.6 32.7 + - - +
39B TYR* 1.3 76.9 - - - +
41B GLU* 1.3 60.3 + - - +
42B ILE 3.4 0.2 - - - -
43B GLY* 4.4 3.8 + - - -
44B ILE 4.4 4.1 - - - +
73B ILE* 3.8 17.0 - - - +
74B ASP 4.9 1.9 + - - -
75B ILE* 3.6 39.7 - - - +
252B GLY* 4.7 7.8 - - - +
255B SER* 5.0 1.0 + - - -
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Residues in contact with GLU 41 (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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37B LYS* 3.0 46.0 + - + +
38B PHE* 2.9 24.7 + - - +
40B SER* 1.3 81.8 - - - +
42B ILE* 1.3 61.3 + - - +
43B GLY 3.8 0.7 - - - -
252B GLY 3.4 6.5 - - - +
254B GLY 4.4 0.3 + - - -
255B SER* 3.3 33.3 + - - -
256B LEU* 3.5 41.7 + - + +
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Residues in contact with ILE 42 (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 PHE* 4.7 5.8 - - + -
38B PHE* 3.5 53.6 - - + +
39B TYR* 3.5 32.1 - - + +
41B GLU* 1.3 85.1 - - - +
43B GLY* 1.3 56.8 + - - +
233B ASP* 5.7 3.8 - - - +
234B VAL* 4.1 23.6 - - + +
235B ARG* 4.4 9.4 + - + +
252B GLY 3.8 5.8 - - - -
253B LEU* 3.3 18.1 - - - +
254B GLY 4.7 3.9 + - - +
256B LEU* 4.3 7.4 - - + -
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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
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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