Contacts of the strand formed by residues 5 - 13 (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 ARG 5 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B ALA 4.1 6.3 - - - +
4B LYS* 1.3 73.7 - - - +
6B ILE* 1.3 62.4 + - - +
7B ASP* 2.7 35.1 + - - +
45B ASP* 3.4 5.8 - - + +
46B GLU* 3.3 35.9 + - - -
99B LYS* 3.8 2.0 - - - +
167B GLU* 3.0 38.2 + - - -
197B PRO* 5.2 5.3 - - - +
199B ILE* 3.7 13.1 - - - +
214B PHE* 3.6 6.4 - - - -
219B ASP* 3.1 12.6 + - - +
220B ALA* 3.1 15.3 - - + +
221B ALA 2.9 26.7 + - - -
249B ARG* 3.4 22.7 - - - +
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Residues in contact with ILE 6 (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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4B LYS 5.1 2.5 - - - +
5B ARG* 1.3 79.6 - - - +
7B ASP* 1.3 63.2 + - - +
43B GLY 5.2 0.2 - - - +
44B ILE* 3.8 12.3 - - + +
45B ASP* 2.8 41.1 + - - +
210B PHE* 3.8 19.5 - - + -
214B PHE* 3.8 19.7 - - + -
221B ALA* 3.6 4.5 - - + +
227B PHE* 3.6 33.4 - - + -
234B VAL* 5.2 3.6 - - + -
237B LEU* 4.1 11.0 - - + -
238B LYS* 4.0 25.1 - - + -
241B LEU* 3.8 19.5 - - + -
248B VAL* 5.3 1.6 - - + -
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Residues in contact with ASP 7 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B ARG* 2.7 47.8 + - - +
6B ILE* 1.3 80.0 - - - +
8B ALA* 1.3 61.5 + - - +
44B ILE* 4.4 2.7 - - - -
46B GLU* 3.3 23.6 + - - +
47B LEU 6.0 0.9 - - - -
48B SER* 6.4 0.7 - - - -
199B ILE* 4.2 8.7 - - - +
220B ALA* 4.5 6.7 - - - -
221B ALA 2.9 11.8 + - - +
222B LYS* 3.3 21.3 + - + +
223B ALA 3.1 22.5 + - - +
227B PHE* 3.8 5.7 - - - -
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Residues in contact with ALA 8 (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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7B ASP* 1.3 73.5 - - - +
9B ALA* 1.3 61.0 + - - +
10B LEU* 4.3 2.0 - - + -
39B TYR* 4.3 16.4 - - + -
44B ILE* 3.8 29.3 - - + +
46B GLU 3.1 7.3 + - - -
47B LEU* 3.4 16.3 - - + +
48B SER* 3.0 23.5 + - - +
222B LYS* 4.8 1.3 - - - -
223B ALA 3.4 7.0 - - - +
227B PHE* 4.2 7.9 - - + -
228B HIS* 4.9 2.0 - - - +
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Residues in contact with ALA 9 (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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7B ASP 4.2 0.2 - - - -
8B ALA* 1.3 74.1 - - - +
10B LEU* 1.3 61.8 + - - +
11B ILE* 4.2 7.0 - - + -
48B SER* 3.2 21.5 - - - +
50B TRP* 6.3 0.9 - - + -
201B HIS* 4.9 1.3 - - + +
222B LYS* 3.7 23.3 - - + +
223B ALA 2.9 10.1 + - - +
224B ASP* 3.2 18.0 - - - +
228B HIS* 2.9 24.3 - - - -
264B MG 4.3 5.4 - - - -
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Residues in contact with LEU 10 (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 4.1 4.5 - - - +
9B ALA* 1.3 81.2 - - - +
11B ILE* 1.3 63.2 + - - +
12B LEU* 3.9 11.6 + - + +
17B VAL* 4.1 13.2 - - + -
32B PRO* 4.0 13.2 - - + +
35B LEU* 3.8 25.4 - - + -
36B GLY* 4.2 4.3 - - - +
39B TYR* 4.4 6.5 - - + -
47B LEU* 4.0 24.9 - - + -
48B SER 2.9 12.6 + - - +
49B PHE* 3.4 26.0 - - + -
50B TRP* 2.9 25.5 + - - +
228B HIS* 3.8 21.5 - - + +
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Residues in contact with ILE 11 (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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9B ALA* 5.3 9.9 - - + +
10B LEU* 1.3 75.9 - - - +
12B LEU* 1.3 59.9 - - - +
17B VAL* 3.3 10.0 - - - +
18B VAL* 2.8 54.7 + - + +
50B TRP* 3.5 32.5 - - + +
52B ILE* 4.0 22.0 - - + -
202B ARG* 6.3 1.6 - - - +
224B ASP* 5.6 10.3 - - + +
228B HIS* 5.2 1.4 - - - -
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Residues in contact with LEU 12 (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* 4.1 18.2 - - + +
11B ILE* 1.3 83.6 - - - +
13B LYS* 1.3 61.8 - - - +
15B GLY 5.3 2.7 - - - +
16B ARG 3.2 12.8 - - - +
17B VAL* 4.1 8.3 - - + -
18B VAL* 3.9 2.7 - - - -
32B PRO* 3.6 25.1 - - + -
49B PHE* 4.0 24.0 - - + -
50B TRP 2.9 12.3 + - - +
51B ASP* 3.3 10.0 - - + +
52B ILE* 2.8 31.5 + - - +
62B MET* 4.2 12.1 - - + -
65B LEU* 3.5 31.9 - - + -
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Residues in contact with LYS 13 (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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12B LEU* 1.3 76.4 - - - +
14B ASP* 1.3 90.1 + - - +
15B GLY 3.1 1.6 - - - -
16B ARG* 2.9 25.3 + - - +
18B VAL* 3.7 16.3 - - + +
52B ILE* 3.9 22.0 - - + +
53B THR* 3.3 15.5 - - - +
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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