Contacts of the helix formed by residues 34 - 46 (chain B) in PDB entry 1V1A
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 GLY 34 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B GLU 4.1 17.7 - - - -
11B LEU* 4.3 2.9 - - - +
33B GLY* 1.3 72.6 - - - -
35B ALA* 1.3 67.9 + - - -
36B GLU* 3.2 3.8 - - - -
37B VAL* 2.7 17.5 + - - +
38B ASN* 2.7 15.5 + - - +
1302B KDG 3.2 26.1 + - - +
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Residues in contact with ALA 35 (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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34B GLY* 1.3 68.9 - - - +
36B GLU* 1.3 67.8 + - - +
38B ASN* 3.5 3.9 + - - +
39B VAL* 2.8 32.1 + - - +
130B HIS* 6.2 0.2 - - - +
132B SER* 3.9 22.2 - - - +
134B ILE* 4.2 15.5 - - + -
165B ASN* 4.2 3.1 - - - +
251B ASP* 3.5 28.8 - - - +
1302B KDG 3.3 13.9 + - - +
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Residues in contact with GLU 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B THR* 2.7 24.5 + - - +
7B ALA 2.9 26.4 - - - +
8B GLY* 4.1 8.7 - - - -
9B GLU 4.6 4.9 + - - +
34B GLY 4.3 1.2 - - - -
35B ALA* 1.3 79.6 + - - +
37B VAL* 1.3 56.5 + - - +
39B VAL* 3.0 4.7 + - - +
40B ALA* 2.6 38.1 + - - +
52B PHE* 3.8 17.5 - - + -
130B HIS* 4.3 8.5 - - + +
131B LEU* 4.6 0.7 - - - -
132B SER* 2.7 41.9 + - - +
134B ILE* 5.3 2.1 - - - +
135B THR* 3.6 11.0 + - - -
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Residues in contact with VAL 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B GLU 5.2 0.4 - - - -
10B PRO* 3.4 35.2 - - + -
32B VAL* 3.9 18.6 - - + -
33B GLY 3.4 21.5 - - - +
34B GLY* 2.7 14.0 + - - +
36B GLU* 1.3 73.2 - - + +
38B ASN* 1.3 53.3 + - - +
40B ALA* 3.0 8.1 + - - +
41B VAL* 2.8 35.8 + - + +
52B PHE* 3.9 14.1 - - + -
65B VAL* 5.0 0.7 - - + -
69B LEU* 3.8 21.5 - - + -
288B HIS* 4.3 11.0 - - + -
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Residues in contact with ASN 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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33B GLY* 3.9 4.5 - - - -
34B GLY 2.7 19.6 + - - +
35B ALA 3.5 6.3 - - - +
37B VAL* 1.3 72.7 - - - +
39B VAL* 1.3 56.2 + - - +
41B VAL* 3.6 1.2 + - - +
42B ALA* 3.0 30.3 + - - +
248B GLY 5.1 0.9 - - - +
251B ASP* 2.9 32.0 + - + +
252B ALA* 5.6 0.6 + - - +
287B ASP* 3.6 22.1 + - - +
288B HIS* 2.8 44.9 + - + +
1302B KDG 3.1 27.7 + - - -
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Residues in contact with VAL 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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6B THR* 4.4 4.9 - - + +
35B ALA 2.8 26.0 + - - +
36B GLU* 3.0 7.3 + - - +
38B ASN* 1.3 74.3 - - - +
40B ALA* 1.3 65.1 + - - +
42B ALA* 3.2 1.6 + - - +
43B LEU* 2.9 49.3 + - + +
130B HIS* 3.7 36.1 - - + +
251B ASP* 3.9 20.0 - - + +
254B ALA* 5.2 0.9 - - + -
255B ALA* 4.1 17.7 - - + +
258B LEU* 4.3 9.9 - - + -
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Residues in contact with ALA 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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6B THR* 3.7 20.4 - - + +
36B GLU 2.6 19.5 + - - +
37B VAL* 3.4 6.7 - - - +
39B VAL* 1.3 73.4 - - - +
41B VAL* 1.3 61.7 + - - +
43B LEU 3.5 0.2 + - - -
44B ALA* 3.2 9.2 + - - +
50B VAL* 3.2 27.4 - - + +
52B PHE* 4.1 12.1 - - + -
69B LEU* 4.7 2.9 - - + -
74B VAL* 4.0 23.8 - - + -
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Residues in contact with VAL 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B VAL* 2.8 24.1 + - + +
38B ASN 4.2 2.2 - - - +
40B ALA* 1.3 70.3 - - - +
42B ALA* 1.3 60.9 + - - +
44B ALA* 3.3 2.9 + - - +
45B ARG* 2.9 39.5 + - - +
68B ARG* 4.4 5.6 - - + -
69B LEU* 4.0 20.4 - - + -
72B GLU* 3.5 44.6 - - + +
74B VAL* 4.3 5.6 - - + -
288B HIS* 3.9 29.4 - - + +
291B ALA* 5.3 0.2 - - + -
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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
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38B ASN 3.0 19.5 + - - +
39B VAL 3.2 0.4 + - - +
41B VAL* 1.3 77.0 - - - +
43B LEU* 1.3 62.4 + - - +
45B ARG* 3.4 3.7 + - - +
46B LEU* 3.2 27.1 + - - +
252B ALA* 4.8 8.7 - - + -
255B ALA* 3.6 23.1 - - + -
277B LEU* 4.7 8.7 - - + +
288B HIS* 5.8 0.6 - - + +
291B ALA* 4.1 24.4 - - + +
292B PRO 4.5 0.9 - - - +
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Residues in contact with LEU 43 (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 VAL* 3.7 27.6 - - + -
6B THR* 4.6 1.1 - - + -
39B VAL* 2.9 41.2 + - + +
40B ALA* 3.8 3.8 - - - +
42B ALA* 1.3 76.1 - - - +
44B ALA* 1.3 58.9 + - - +
46B LEU* 2.9 24.2 + - - +
48B VAL* 3.1 27.0 + - + +
50B VAL* 3.7 29.2 - - + -
255B ALA* 3.4 34.8 - - + +
258B LEU* 4.3 11.7 - - + -
259B ALA* 4.5 9.0 - - + +
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Residues in contact with ALA 44 (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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40B ALA 3.2 15.4 + - - +
41B VAL* 3.6 4.9 - - - +
43B LEU* 1.3 79.9 - - - +
45B ARG* 1.3 61.4 + - - +
47B GLY* 3.0 14.0 + - - -
48B VAL 3.6 12.7 + - - +
50B VAL* 3.9 5.8 - - + +
72B GLU* 3.4 27.4 - - + +
73B GLY 4.3 5.2 - - - +
74B VAL* 3.8 12.3 - - + -
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Residues in contact with ARG 45 (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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41B VAL* 2.9 27.0 + - - +
42B ALA* 3.8 3.6 - - - +
43B LEU 3.3 0.2 - - - -
44B ALA* 1.3 75.5 - - - +
46B LEU* 1.3 58.0 + - - +
47B GLY* 3.5 0.7 + - - -
68B ARG* 4.4 5.3 - - - +
72B GLU* 2.6 39.4 + - - +
288B HIS* 3.4 21.8 + - - -
289B GLU* 2.8 37.4 + - - -
291B ALA* 3.2 29.9 + - - -
292B PRO 3.0 16.6 - - - +
293B TYR* 3.0 48.5 + - + +
294B ARG* 2.8 21.7 + - - +
295B GLU* 4.4 1.6 - - - +
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Residues in contact with LEU 46 (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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42B ALA 3.2 13.6 + - - +
43B LEU* 2.9 12.1 + - - +
45B ARG* 1.3 79.3 - - - +
47B GLY* 1.3 58.1 + - - +
48B VAL* 3.4 4.5 - - + -
255B ALA 4.5 2.7 - - - +
256B GLY* 4.7 0.7 - - - -
259B ALA* 3.6 27.1 - - + -
263B TRP* 3.3 27.8 - - + -
273B LEU* 4.8 2.7 - - + -
277B LEU* 3.5 28.5 - - + -
292B PRO* 3.7 24.0 - - + +
294B ARG* 3.3 25.6 - - - +
297B LEU* 3.9 28.3 - - + -
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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
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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