Contacts of the helix formed by residues 44 - 57 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A GLN* 3.0 22.2 + - - -
42A GLY 3.5 4.2 + - - -
43A THR* 1.3 77.0 - - - +
45A LYS* 1.4 65.2 + - - +
46A THR 3.4 2.9 - - - -
47A PHE 3.4 3.0 + - - -
48A THR* 3.1 13.5 + - - -
410A GLN* 3.9 0.4 - - - -
701A ADP 3.5 39.1 + - - -
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Residues in contact with LYS 45 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A LEU* 4.7 4.0 - - + +
39A GLY* 3.3 29.0 + - - -
40A ALA 3.6 14.6 - - - +
41A THR* 3.5 30.1 - - - +
43A THR* 4.1 9.9 - - - +
44A GLY* 1.4 74.1 - - - +
46A THR* 1.4 57.8 + - - +
48A THR* 3.1 6.0 + - - -
49A VAL* 2.9 34.8 + - - +
338A ASP* 4.9 7.4 - - - +
339A GLU* 3.7 21.4 + - - -
392A VAL* 4.2 29.4 - - + -
394A ALA* 4.4 6.8 - - - +
410A GLN* 4.1 7.2 - - - +
701A ADP 3.0 19.4 + - - +
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Residues in contact with THR 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A LYS* 1.4 76.3 - - - +
47A PHE* 1.3 49.9 + - - +
49A VAL* 3.2 8.3 + - - +
50A SER* 2.7 42.8 + - - +
73A LEU* 3.4 20.1 - - + +
76A GLU* 3.8 28.1 + - + -
77A PHE* 3.9 27.7 - - + -
80A PHE* 4.1 9.2 - - + -
701A ADP 3.2 27.1 + - - -
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Residues in contact with PHE 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A LEU* 4.4 8.3 - - + -
9A SER* 3.9 22.0 - - - -
11A TYR* 3.9 24.7 - + - -
13A PRO* 3.8 25.6 - - + -
17A GLN* 3.6 17.5 - - + -
44A GLY 3.4 4.2 + - - +
45A LYS 3.3 0.6 - - - -
46A THR* 1.3 74.8 - - - +
48A THR* 1.3 65.1 + - - +
50A SER* 3.2 6.1 + - - -
51A ASN* 2.9 53.5 + - - -
80A PHE* 3.5 30.4 - + + -
701A ADP 3.5 45.6 + + + +
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Residues in contact with THR 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A GLN* 3.4 19.2 - - - +
20A ALA* 4.3 8.3 - - + -
21A ILE* 3.9 22.7 - - + +
24A LEU* 4.7 9.0 - - + -
37A LEU* 3.9 20.6 - - + -
44A GLY 3.1 8.2 + - - -
45A LYS 3.1 8.3 + - - -
47A PHE* 1.3 73.3 - - - +
49A VAL* 1.4 65.0 + - + +
51A ASN* 3.1 6.8 + - - +
52A LEU* 3.0 21.7 + - + +
410A GLN* 2.5 33.3 + - - +
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Residues in contact with VAL 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A LEU* 6.5 0.4 - - + -
37A LEU* 4.8 8.3 - - + -
45A LYS 2.9 19.1 + - - +
46A THR* 3.5 10.3 - - - +
48A THR* 1.4 76.2 - - + +
50A SER* 1.3 51.1 + - - +
52A LEU* 3.1 14.9 + - + +
53A ILE* 2.8 48.3 + - + +
77A PHE* 3.8 22.2 - - + -
336A VAL* 4.1 25.4 - - + -
390A VAL* 5.8 1.8 - - + -
392A VAL* 4.2 26.2 - - + -
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Residues in contact with SER 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A LEU* 3.9 9.6 - - - +
46A THR 2.7 25.6 + - - -
47A PHE* 3.5 7.0 - - - -
49A VAL* 1.3 71.3 - - - +
51A ASN* 1.3 62.8 + - - +
53A ILE* 3.4 5.0 + - - -
54A LYS* 3.1 20.8 + - - +
77A PHE* 3.3 17.3 - - - -
80A PHE* 3.4 24.7 - - - -
81A PHE* 3.3 30.5 - - - -
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Residues in contact with ASN 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A LEU* 3.9 9.8 - - - +
13A PRO* 4.0 10.3 - - - +
21A ILE* 3.6 29.5 - - + +
47A PHE* 2.9 60.2 + - - -
48A THR 3.1 8.3 + - - +
50A SER* 1.3 76.7 - - - +
52A LEU* 1.4 55.2 + - - +
54A LYS* 3.3 23.6 + - - +
55A GLU* 2.9 39.1 + - - +
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Residues in contact with LEU 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ILE* 4.0 4.4 - - + +
24A LEU* 3.9 29.8 - - + +
25A VAL* 3.9 24.5 - - + -
28A ILE* 3.7 24.0 - - + -
48A THR* 3.0 12.5 + - + +
49A VAL* 3.3 17.0 - - + +
51A ASN* 1.4 73.6 - - - +
53A ILE* 1.4 55.2 + - - +
55A GLU* 3.3 1.0 + - - -
56A VAL* 3.0 38.1 + - + +
334A MET* 3.9 27.8 - - + -
336A VAL* 4.9 4.5 - - + -
390A VAL* 4.3 22.2 - - + -
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Residues in contact with ILE 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A PHE* 3.6 29.9 - - + -
49A VAL* 2.8 29.7 + - + +
50A SER* 3.6 6.7 - - - +
52A LEU* 1.4 69.7 - - - +
54A LYS* 1.3 60.7 + - - +
56A VAL* 4.1 7.0 - - - +
57A ASN* 3.2 17.2 + - - -
58A LYS 4.4 1.8 + - - +
60A THR* 3.7 22.2 - - + -
62A VAL* 5.2 1.8 - - + -
77A PHE* 3.6 32.5 - - + -
81A PHE* 4.4 2.2 - - + -
137A ILE* 3.8 28.5 - - + -
334A MET* 3.9 20.9 - - + -
336A VAL* 5.6 0.7 - - + -
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Residues in contact with LYS 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A PHE* 3.6 29.6 - - - +
7A LEU* 3.7 32.5 - - + +
50A SER 3.1 12.8 + - - +
51A ASN* 3.3 29.8 + - - +
52A LEU 3.3 0.2 - - - -
53A ILE* 1.3 76.6 - - - +
55A GLU* 1.4 94.2 + - - +
57A ASN* 3.4 18.0 + - - +
81A PHE* 4.4 3.4 - - + -
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Residues in contact with GLU 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ILE* 4.2 11.2 - - + +
25A VAL* 3.8 34.8 - - + +
51A ASN* 2.9 25.4 + - - +
52A LEU 3.9 0.2 - - - +
54A LYS* 1.4 107.2 + - - +
56A VAL* 1.3 61.3 + - - +
57A ASN* 3.6 1.9 + - - +
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Residues in contact with VAL 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A VAL* 3.8 22.7 - - + -
28A ILE* 3.8 30.1 - - + -
52A LEU* 3.0 37.3 + - + +
53A ILE 4.1 4.5 - - - +
55A GLU* 1.3 76.2 - - - +
57A ASN* 1.4 70.3 + - - +
58A LYS* 3.7 22.9 + - + +
334A MET* 4.1 26.9 - - + -
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Residues in contact with ASN 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A ASP 2.9 27.7 + - - -
4A ARG* 3.3 11.1 - - - +
5A PHE* 2.8 37.4 + - - +
53A ILE 3.2 14.0 + - - -
54A LYS 3.4 12.1 + - - +
55A GLU 3.4 2.8 - - - +
56A VAL* 1.4 78.6 - - - +
58A LYS* 1.3 58.5 + - - +
59A PRO* 5.0 0.2 - - - +
134A ARG* 5.7 4.4 + - - +
135A ASP* 5.7 1.4 - - - +
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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