Contacts of the helix formed by residues 10 - 25 (chain B) in PDB entry 2VR1
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 10 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B ASN* 1.3 83.4 + - - +
11B GLY* 1.3 79.4 + - - +
12B GLU 3.5 0.5 + - - -
13B ILE* 3.3 10.7 - - - +
14B ALA* 3.3 18.9 + - - +
36B ASP* 2.8 40.4 + - - +
39B LEU* 3.7 18.3 - - + +
60B TYR* 3.9 11.7 - - + +
84B PHE* 3.7 33.7 - - + -
370B HIS* 4.8 6.5 + - - -
375B TYR* 3.9 16.0 + - - -
378B PRO* 4.2 6.7 - - - +
381B TYR* 3.3 40.1 - - - +
382B ASP* 5.1 8.5 + - - +
384B MET 5.5 3.4 + - - -
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Residues in contact with GLY 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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10B ARG* 1.3 84.3 - - - +
12B GLU* 1.3 65.3 + - - -
14B ALA* 3.8 1.5 - - - +
15B LEU* 3.2 21.0 + - - +
39B LEU* 3.7 13.8 - - - +
41B HIS* 4.5 2.6 + - - -
370B HIS* 3.3 35.6 - - - +
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Residues in contact with GLU 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B ARG 3.5 0.2 + - - -
11B GLY* 1.3 72.1 - - - -
13B ILE* 1.3 64.8 + - - +
15B LEU* 3.3 6.3 + - - +
16B ARG* 2.9 25.6 + - - +
19B ARG* 5.8 0.2 + - - -
82B TYR* 2.7 32.0 + - - +
368B GLU* 3.9 30.2 - - - +
369B SER* 4.1 6.0 + - - +
370B HIS* 3.1 23.0 + - + +
384B MET* 3.5 18.1 + - + +
385B ILE 4.7 3.6 - - - +
386B GLY* 4.9 0.4 - - - -
387B LYS* 2.6 43.5 + - + +
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Residues in contact with ILE 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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9B ASN* 3.2 35.7 - - + +
10B ARG 3.3 5.2 - - - +
12B GLU* 1.3 86.5 - - - +
14B ALA* 1.3 65.1 + - - +
16B ARG* 3.2 10.9 + - + +
17B ILE* 3.0 37.4 + - + +
81B GLY* 4.3 7.4 - - - -
82B TYR* 3.4 46.9 - - + +
293B ILE* 4.5 8.3 - - + -
297B HIS* 4.0 25.1 - - + -
309B ILE* 4.9 1.3 - - + -
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Residues in contact with ALA 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B ILE* 3.9 18.6 - - + +
9B ASN* 3.9 4.3 - - - +
10B ARG* 3.3 23.6 + - - +
13B ILE* 1.3 82.5 - - - +
15B LEU* 1.3 56.7 + - - +
17B ILE* 3.3 4.2 + - - +
18B LEU* 2.9 27.2 + - - +
41B HIS* 3.4 39.7 - - + +
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Residues in contact with LEU 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A GLU* 5.4 0.2 - - - -
11B GLY 3.2 9.5 + - - +
12B GLU* 3.5 9.9 - - - +
14B ALA* 1.3 77.7 - - - +
16B ARG* 1.3 63.6 + - - +
18B LEU* 3.0 18.0 + - + +
19B ARG* 3.0 50.4 + - + +
40B LYS* 4.3 9.6 - - + -
41B HIS* 3.7 28.6 - - + +
44B LEU* 3.9 25.6 - - + -
369B SER 3.5 29.8 - - - +
370B HIS* 4.1 8.5 - - + -
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Residues in contact with ARG 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A PHE* 4.5 8.9 - - - +
12B GLU* 2.9 15.4 + - - +
13B ILE* 3.2 17.5 - - + +
15B LEU* 1.3 77.7 - - - +
17B ILE* 1.3 62.2 + - - +
19B ARG* 3.4 14.9 + - - +
20B ALA* 3.3 22.1 + - - +
23B GLU* 5.5 2.2 + - - -
297B HIS* 3.3 23.8 + - + +
301B GLU* 2.9 29.3 + - - -
307B ASP* 3.1 25.3 + - - -
309B ILE* 3.5 23.3 - - + +
366B ARG* 3.3 19.8 - - - +
368B GLU* 3.3 26.7 - - - +
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Residues in contact with ILE 17 (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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5B ILE* 4.2 4.5 - - + -
7B ILE* 3.8 34.5 - - + -
9B ASN* 5.4 0.9 - - + -
13B ILE* 3.0 29.1 + - + +
14B ALA* 3.7 5.8 - - - +
16B ARG* 1.3 73.2 - - - +
18B LEU* 1.3 66.4 + - - +
20B ALA* 3.2 3.1 + - - +
21B CYS* 2.9 32.5 + - - -
79B HIS* 3.6 50.7 - - + +
81B GLY* 4.1 14.6 - - - +
309B ILE* 4.2 16.4 - - + -
313B LEU* 5.2 0.9 - - + -
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Residues in contact with LEU 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A GLU* 5.8 0.4 - - - +
7B ILE* 4.0 11.4 - - + +
14B ALA 2.9 13.4 + - - +
15B LEU* 3.0 15.9 + - + +
17B ILE* 1.3 76.3 - - - +
19B ARG* 1.3 63.8 + - + +
21B CYS* 3.2 6.0 + - - +
22B LYS* 2.9 45.8 + - + +
28B THR* 4.0 13.7 - - + +
41B HIS* 3.4 34.5 - - + +
44B LEU* 4.0 27.1 - - + +
45B ALA* 3.7 23.8 - - + +
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Residues in contact with ARG 19 (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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358A HIS* 6.0 1.4 + - - -
361A GLY* 3.2 29.9 + - - +
362A GLY* 3.8 19.1 - - - +
363A PHE 5.6 0.4 - - - +
404A ASN* 3.9 8.2 + - + +
408A GLU* 3.0 42.5 + - - +
12B GLU 5.8 0.2 + - - -
15B LEU* 3.0 49.7 + - + +
16B ARG* 3.7 15.9 - - - +
18B LEU* 1.3 82.1 - - + +
20B ALA* 1.3 65.4 + - - +
22B LYS* 3.3 6.8 + - + +
23B GLU* 3.0 37.4 + - - +
367B TRP 4.7 3.0 + - - -
368B GLU* 4.2 18.0 + - - +
369B SER 4.9 4.0 + - - +
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Residues in contact with ALA 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ARG* 3.3 11.7 + - - +
17B ILE 3.2 5.9 + - - +
19B ARG* 1.3 78.6 - - - +
21B CYS* 1.3 63.1 + - - +
23B GLU* 3.3 7.9 + - - +
24B LEU* 3.1 26.9 + - - +
307B ASP* 5.5 0.2 - - - -
309B ILE* 3.5 34.5 - - + -
310B LYS* 3.9 19.2 - - + +
313B LEU* 3.9 10.8 - - + -
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Residues in contact with CYS 21 (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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5B ILE* 3.7 35.7 - - - -
7B ILE* 4.8 0.4 - - - -
17B ILE* 2.9 23.7 + - - -
18B LEU 3.4 8.5 - - - +
20B ALA* 1.3 75.8 - - - +
22B LYS* 1.3 62.3 + - - +
24B LEU* 3.0 3.6 + - - -
25B GLY 3.0 4.9 + - - -
26B ILE* 3.0 46.9 + - + +
28B THR* 3.5 22.4 - - + -
313B LEU* 4.3 9.9 - - - -
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Residues in contact with LYS 22 (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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400A ALA* 5.5 0.9 - - - +
403A LYS* 5.2 0.6 - - - +
404A ASN* 2.6 51.7 + - + +
407A GLN* 4.1 24.1 - - + +
18B LEU* 2.9 39.7 + - + +
19B ARG* 3.8 2.5 - - + +
21B CYS* 1.3 76.7 - - + +
23B GLU* 1.3 61.0 + - - +
25B GLY* 3.4 11.6 + - - +
26B ILE 4.6 3.6 - - - +
28B THR* 5.4 5.6 - - + +
44B LEU* 5.0 12.6 - - + +
46B ASP* 5.5 8.7 - - - +
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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
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363A PHE* 5.0 2.4 - - - +
397A VAL* 4.4 2.0 - - + +
400A ALA* 4.1 22.0 - - + +
401A ARG* 3.3 46.1 + - + +
404A ASN* 3.7 13.2 - - - +
16B ARG* 5.5 1.7 + - - -
19B ARG* 3.0 29.6 + - - +
20B ALA* 3.6 8.2 + - - +
22B LYS* 1.3 76.4 - - - +
24B LEU* 1.3 63.0 + - + +
25B GLY 3.5 0.5 + - - -
307B ASP* 4.6 2.5 - - - +
310B LYS* 3.0 40.0 + - + +
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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
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1B MET* 4.3 34.1 - - + +
20B ALA 3.1 10.9 + - - +
21B CYS 3.0 2.4 + - - +
23B GLU* 1.3 78.7 - - - +
25B GLY* 1.3 61.2 + - - +
26B ILE* 3.6 22.1 + - + +
310B LYS* 3.9 35.0 - - + +
313B LEU* 3.7 35.2 - - + -
314B ARG* 4.1 18.6 - - + +
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Residues in contact with GLY 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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2B LEU 4.7 2.1 - - - +
3B ASP* 4.6 2.3 - - - +
21B CYS 3.0 3.7 + - - -
22B LYS* 3.4 9.4 + - - -
23B GLU 3.2 4.6 + - - -
24B LEU* 1.3 79.3 - - - +
26B ILE* 1.3 61.6 + - - +
27B LYS* 3.9 7.0 + - - +
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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