Contacts of the helix formed by residues 3 - 19 (chain B) in PDB entry 5VXA
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 SER 3 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A GLU* 4.5 6.5 - - - -
49A ILE 5.2 0.9 + - - -
50A THR* 3.9 27.2 - - - +
2B GLY* 1.3 75.2 - - - +
4B GLU* 1.3 59.9 + - - +
5B ALA* 3.5 6.1 + - - +
6B ALA* 3.1 24.0 + - - +
7B GLN* 2.9 36.5 + - - +
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Residues in contact with GLU 4 (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* 3.3 20.0 - - - -
4A GLU* 3.5 15.8 + - + +
5A ALA* 3.1 40.3 + - + +
3B SER* 1.3 74.2 - - - +
5B ALA* 1.3 62.8 + - - +
7B GLN* 3.4 11.7 + - - +
8B LEU* 3.1 23.7 + - - +
50B THR* 4.4 12.8 - - - +
52B ILE* 4.0 16.1 - - + +
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Residues in contact with ALA 5 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A GLU* 3.4 23.7 + - + +
5A ALA 5.8 0.2 - - - +
8A LEU* 3.6 27.8 - - + +
44A THR* 4.3 2.5 - - + -
50A THR* 4.9 5.8 - - - +
52A ILE* 5.4 1.6 - - + -
55A LEU* 3.6 22.4 - - + -
3B SER* 3.2 5.5 - - - +
4B GLU* 1.3 78.5 - - - +
6B ALA* 1.3 64.1 + - - +
8B LEU 3.2 1.6 + - - -
9B LEU* 3.0 27.0 + - - +
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Residues in contact with ALA 6 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A THR* 3.7 33.7 - - - +
45A HIS* 5.9 0.4 - - - -
2B GLY 4.4 8.3 - - - +
3B SER* 3.1 24.7 + - - +
5B ALA* 1.3 78.7 - - - +
7B GLN* 1.3 58.7 + - - +
9B LEU* 3.4 1.4 + - - +
10B GLU* 2.9 37.4 + - + +
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Residues in contact with GLN 7 (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 GLY 4.4 16.7 - - - +
3B SER 2.9 28.1 + - - +
4B GLU* 3.8 8.9 + - - +
5B ALA 3.2 0.2 - - - -
6B ALA* 1.3 75.7 - - - +
8B LEU* 1.3 62.8 + - - +
10B GLU* 3.4 6.7 + - - +
11B ALA* 3.3 12.5 + - - +
52B ILE* 3.9 31.8 - - + +
56B GLN* 2.9 37.7 + - - +
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Residues in contact with LEU 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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5A ALA* 3.3 40.4 - - + +
8A LEU* 4.0 15.0 - - + -
9A LEU* 3.6 19.3 - - + -
4B GLU 3.1 16.8 + - - +
5B ALA 3.2 3.3 + - - +
7B GLN* 1.3 77.7 - - - +
9B LEU* 1.3 59.3 + - + +
11B ALA* 3.3 2.6 + - - -
12B ALA* 2.9 29.2 + - + +
52B ILE* 3.8 20.1 - - + +
55B LEU* 3.9 22.0 - - + -
56B GLN* 4.7 1.6 - - + +
59B LEU* 3.7 26.0 - - + +
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Residues in contact with LEU 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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8A LEU* 4.0 21.5 - - + -
12A ALA* 6.2 1.3 - - + -
37A ILE* 5.0 5.3 - - + +
40A ALA* 3.5 44.0 - - + +
41A ARG* 4.3 9.2 - - + +
44A THR* 3.6 30.5 - - + +
55A LEU* 4.4 7.6 - - + -
59A LEU* 4.4 18.2 - - + -
5B ALA 3.0 16.5 + - - +
6B ALA 4.0 0.2 - - - +
8B LEU* 1.3 74.7 - - + +
10B GLU* 1.3 66.9 + - - +
12B ALA* 4.0 10.9 - - + +
13B ASP* 2.9 27.4 + - - +
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Residues in contact with GLU 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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41A ARG* 2.7 45.8 + - - +
44A THR* 4.6 2.8 + - - -
45A HIS* 3.4 25.0 + - - +
6B ALA* 2.9 25.4 + - + +
7B GLN* 3.7 8.5 - - - +
8B LEU 3.3 0.4 - - - -
9B LEU* 1.3 77.2 - - - +
11B ALA* 1.3 58.2 + - - +
13B ASP* 4.1 0.9 - - - +
14B PHE* 3.0 30.8 + - - +
17B ARG* 5.2 0.7 + - - -
56B GLN* 5.0 0.9 - - - +
78B PHE* 3.9 13.9 - - + -
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Residues in contact with ALA 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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7B GLN 3.3 1.8 + - - +
8B LEU 3.3 7.7 + - - +
9B LEU 3.3 0.4 - - - -
10B GLU* 1.3 77.1 - - - +
12B ALA* 1.3 64.1 - - - +
14B PHE* 3.7 0.9 - - - +
15B ALA* 2.9 26.7 + - - +
56B GLN* 3.9 26.7 - - + +
59B LEU* 3.8 22.4 - - + -
60B LEU* 4.0 6.3 - - + +
78B PHE* 3.6 21.7 - - + -
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Residues in contact with ALA 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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9A LEU* 6.1 1.6 - - + -
12A ALA* 6.0 5.4 - - + -
37A ILE* 4.0 20.1 - - + +
8B LEU* 2.9 17.2 + - + +
9B LEU* 4.0 11.7 - - + +
11B ALA* 1.3 76.7 - - - +
13B ASP* 1.3 58.2 + - - +
15B ALA* 3.9 2.6 - - - +
16B ALA* 2.9 30.0 + - - +
33B ILE* 4.4 3.4 - - - +
37B ILE* 5.4 4.0 - - + -
59B LEU* 3.8 23.9 - - + +
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Residues in contact with ASP 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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34A ASN 5.0 1.6 - - - +
37A ILE* 3.7 13.7 - - + +
38A GLY* 3.7 23.9 + - - -
41A ARG* 3.3 32.1 + - + -
125A TYR* 5.7 0.7 - - - -
9B LEU 2.9 19.7 + - - +
10B GLU 4.1 0.7 - - - +
12B ALA* 1.3 75.5 - - - +
14B PHE* 1.3 65.4 + - - +
16B ALA* 3.3 3.9 + - - +
17B ARG* 2.5 64.7 + - - +
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Residues in contact with PHE 14 (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 GLU 3.0 18.9 + - - +
11B ALA 3.4 3.1 + - - +
13B ASP* 1.3 77.9 - - - +
15B ALA* 1.3 56.0 + - - +
17B ARG* 3.4 29.2 + - - +
18B LYS* 3.0 63.4 + - + +
60B LEU* 3.3 25.1 - - + -
63B THR* 4.4 4.0 - - + -
69B THR* 3.9 22.4 - - + -
73B GLU* 4.0 19.3 - - + -
74B VAL* 4.8 5.2 - - + -
77B HIS* 4.3 24.2 - + - -
78B PHE* 3.8 25.4 - + + -
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Residues in contact with ALA 15 (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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11B ALA 2.9 17.0 + - - +
12B ALA* 3.9 2.9 - - - +
14B PHE* 1.3 75.8 - - - +
16B ALA* 1.3 64.6 + - - +
18B LYS 3.3 0.2 + - - -
19B HIS* 2.9 36.0 + - + -
33B ILE* 3.7 15.7 - - + -
59B LEU* 3.3 29.2 - - + +
60B LEU* 4.4 1.1 - - + -
63B THR* 4.1 16.2 - - + -
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Residues in contact with ALA 16 (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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34A ASN* 3.1 38.4 + - - +
37A ILE* 4.1 14.8 - - + -
12B ALA 2.9 19.3 + - - +
13B ASP* 3.3 6.7 + - - +
15B ALA* 1.3 76.8 - - - +
17B ARG* 1.3 63.4 + - + +
19B HIS* 3.8 1.4 - - - +
20B ARG* 3.2 16.1 + - - -
33B ILE* 3.5 23.7 - - + +
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Residues in contact with ARG 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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34A ASN* 4.2 9.4 - - + +
41A ARG* 4.6 9.9 - - - +
10B GLU 5.2 0.4 + - - -
13B ASP* 2.5 57.1 + - - +
14B PHE* 3.6 37.7 + - - +
16B ALA* 1.3 77.2 - - + +
18B LYS* 1.3 71.8 + - + +
20B ARG* 3.1 40.5 + - - +
77B HIS* 6.1 1.0 + - - -
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Residues in contact with LYS 18 (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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14B PHE* 3.0 44.3 + - + +
15B ALA 3.3 3.3 + - - +
17B ARG* 1.3 85.4 - - + +
19B HIS* 1.3 58.5 + - - +
20B ARG* 3.3 5.7 + - - +
21B GLN 5.0 0.9 + - - -
22B GLN* 4.6 2.1 - - - +
63B THR* 4.1 11.9 - - + -
67B THR* 3.4 26.9 - - + +
68B ASP* 5.0 1.8 - - - +
69B THR* 3.2 33.4 + - - +
73B GLU* 2.9 32.9 + - - -
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Residues in contact with HIS 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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31A PRO* 5.3 1.4 - - - +
15B ALA* 2.9 32.5 + - + +
16B ALA 3.8 2.5 - - - +
18B LYS* 1.3 74.3 - - - +
20B ARG* 1.3 62.9 + - - +
21B GLN 3.2 2.9 - - - -
22B GLN* 2.7 50.1 + - - +
23B ARG* 4.4 0.2 + - - -
32B TYR* 3.6 16.3 + + + +
33B ILE* 4.3 22.2 + - + +
36B PRO* 4.1 19.2 - - + +
59B LEU 5.0 0.4 + - - -
62B ASP* 3.5 42.1 + - + +
63B THR* 3.8 19.8 - - + +
66B LYS* 4.5 1.3 - - + -
67B THR* 3.9 5.6 - - + +
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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