Contacts of the helix formed by residues 44 - 57 (chain B) in PDB entry 3V4R
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 44 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17B GLN* 2.9 23.7 + - - -
42B GLY 3.5 3.0 + - - -
43B THR* 1.3 76.5 + - - +
45B LYS* 1.3 63.4 + - - +
46B THR 3.5 2.2 - - - -
47B PHE* 3.7 5.9 + - - -
48B THR* 3.2 14.4 + - - -
410B GLN* 3.8 0.9 - - - -
701B ADP 3.5 21.3 + - - -
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Residues in contact with LYS 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B LEU* 4.7 3.6 - - + -
39B GLY* 5.4 7.9 - - - +
40B ALA 5.6 2.4 + - - +
43B THR* 3.8 3.4 + - - +
44B GLY* 1.3 71.5 - - - +
46B THR* 1.4 61.3 + - - +
48B THR* 3.2 6.6 + - - -
49B VAL* 2.9 33.1 + - - +
392B VAL* 4.3 23.8 - - + -
410B GLN* 3.8 13.6 - - - +
701B ADP 3.3 15.6 + - - +
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Residues in contact with THR 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B LYS* 1.4 75.8 - - - +
47B PHE* 1.3 51.4 + - - +
49B VAL* 3.2 8.5 + - - +
50B SER* 2.7 36.7 + - - -
73B LEU* 3.4 22.3 - - + +
76B GLU* 3.8 26.4 - - + +
77B PHE* 3.8 28.0 - - + -
80B PHE* 4.1 11.7 - - + -
701B ADP 3.3 24.0 + - - -
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Residues in contact with PHE 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B LEU* 6.0 5.8 - - + -
9B SER* 4.0 19.5 - - - -
11B TYR* 3.9 22.2 - - + -
12B GLN 4.3 3.1 - - - -
13B PRO* 3.8 31.0 - - + -
17B GLN* 4.0 20.9 - - + +
44B GLY* 3.7 11.2 + - - +
45B LYS 3.4 0.8 - - - -
46B THR* 1.3 76.5 - - - +
48B THR* 1.4 50.1 + - - +
50B SER* 3.0 7.5 + - - -
51B ASN* 2.8 69.2 + - - -
80B PHE* 3.6 36.6 - + + -
701B ADP 4.4 1.2 + - - -
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Residues in contact with THR 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B GLN* 3.8 9.2 - - - +
20B ALA* 4.1 13.2 - - + -
21B ILE* 3.7 29.8 - - + +
37B LEU* 4.3 14.6 - - + -
44B GLY 3.2 12.2 + - - -
45B LYS* 3.2 10.4 + - - -
47B PHE* 1.4 76.0 - - - +
49B VAL* 1.3 58.0 + - - +
51B ASN* 3.4 5.0 + - - +
52B LEU* 3.1 27.3 + - + +
410B GLN* 2.6 30.6 + - - +
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Residues in contact with VAL 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B LEU* 4.1 18.4 - - + -
45B LYS 2.9 19.2 + - - +
46B THR* 3.4 10.5 - - - +
48B THR* 1.3 74.6 - - + +
50B SER* 1.4 51.0 + - - +
52B LEU* 3.1 15.6 + - + +
53B ILE* 2.8 35.2 + - + +
60B THR* 6.6 0.2 - - + -
62B VAL* 5.7 0.7 - - + -
77B PHE* 3.8 22.9 - - + -
334B MET* 5.7 0.7 - - + -
336B VAL* 4.0 29.6 - - + -
390B VAL* 5.7 1.6 - - + -
392B VAL* 4.1 18.4 - - + -
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Residues in contact with SER 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B LEU* 5.0 4.7 - - - +
46B THR 2.7 22.4 + - - -
47B PHE* 3.0 16.4 + - - -
49B VAL* 1.4 68.9 - - - +
51B ASN* 1.3 65.9 + - - +
53B ILE* 4.3 2.5 - - - -
54B LYS* 3.1 20.3 + - - +
77B PHE* 3.3 17.3 - - - -
80B PHE* 3.2 26.1 - - - -
81B PHE* 3.4 29.3 - - - -
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Residues in contact with ASN 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B PRO* 4.2 6.3 - - - +
21B ILE* 3.6 35.7 - - + +
47B PHE* 2.8 69.7 + - - -
48B THR 3.5 7.4 - - - +
50B SER* 1.3 68.9 - - - +
52B LEU* 1.3 64.7 + - - +
54B LYS* 3.1 9.4 + - - +
55B GLU* 3.0 22.2 + - - +
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Residues in contact with LEU 52 (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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21B ILE* 4.0 3.5 - - + +
24B LEU* 3.8 27.1 - - + +
25B VAL* 3.9 24.5 - - + -
28B ILE* 3.7 23.1 - - + -
48B THR* 3.1 10.3 + - + +
49B VAL* 3.3 16.2 - - + +
51B ASN* 1.3 78.6 - - - +
53B ILE* 1.4 55.1 + - - +
55B GLU* 3.3 1.0 + - - -
56B VAL* 3.0 39.8 + - + +
334B MET* 3.9 28.9 - - + -
336B VAL* 4.9 3.8 - - + -
390B VAL* 4.3 22.2 - - + -
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Residues in contact with ILE 53 (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 PHE* 3.6 18.2 - - + -
49B VAL* 2.8 21.4 + - + +
50B SER* 3.7 7.9 - - - +
51B ASN 3.3 0.2 - - - -
52B LEU* 1.4 71.9 - - - +
54B LYS* 1.4 61.1 + - - +
56B VAL* 4.0 7.7 - - - +
57B ASN* 3.2 17.5 + - - -
58B LYS 4.4 1.9 + - - +
60B THR* 4.8 9.6 - - + -
77B PHE* 5.8 2.2 - - + -
81B PHE* 4.2 11.7 - - + -
137B ILE* 4.8 13.2 - - + -
334B MET* 4.4 13.0 - - + -
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Residues in contact with LYS 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B PHE* 4.1 25.2 - - - +
7B LEU* 4.4 12.6 - - + +
50B SER 3.1 11.8 + - - +
51B ASN* 3.1 11.5 + - - +
53B ILE* 1.4 73.1 - - - +
55B GLU* 1.4 64.5 + - - +
57B ASN* 3.4 20.4 + - - +
81B PHE* 4.3 8.7 - - + -
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Residues in contact with GLU 55 (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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21B ILE* 5.5 1.8 - - + -
25B VAL* 3.8 34.0 - - + +
29B GLN* 5.5 2.4 + - - -
51B ASN 3.0 15.0 + - - +
52B LEU 3.9 0.4 - - - +
54B LYS* 1.4 76.5 - - - +
56B VAL* 1.3 61.5 + - - +
57B ASN* 3.6 1.9 + - - +
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Residues in contact with VAL 56 (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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25B VAL* 3.8 22.7 - - + -
28B ILE* 3.8 31.9 - - + -
29B GLN* 5.9 1.3 - - + +
52B LEU* 3.0 36.6 + - + +
53B ILE* 4.0 4.5 - - - +
55B GLU* 1.3 75.1 - - - +
57B ASN* 1.4 70.1 + - - +
58B LYS* 4.3 22.7 + - + +
334B MET* 4.1 26.9 - - + -
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Residues in contact with ASN 57 (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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3B ASP 3.4 24.0 + - - -
4B ARG* 3.3 12.4 - - - +
5B PHE* 2.9 36.3 + - - +
53B ILE 3.2 13.9 + - - -
54B LYS 3.4 12.4 + - - +
55B GLU 3.4 2.6 - - - +
56B VAL* 1.4 79.9 - - - +
58B LYS* 1.3 59.7 + - - +
59B PRO* 5.0 0.2 - - - +
134B ARG* 5.8 2.4 + - - +
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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