Contacts of the helix formed by residues 56 - 69 (chain A) in PDB entry 5VT2
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 ASN 56 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A ALA* 3.3 3.1 + - - +
55A ALA* 1.3 80.5 + - - +
57A MET* 1.3 64.2 + - - +
58A HIS* 3.4 5.0 + - - +
59A ALA* 3.1 33.4 + - - +
60A GLN* 3.5 16.1 + - - +
112A ILE* 4.1 5.5 - - - +
201A EDO 2.9 29.8 + - - +
83B TYR* 3.1 30.6 + - - -
103B ASP* 3.9 18.3 - - + +
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Residues in contact with MET 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A ASN* 1.3 74.7 - - - +
58A HIS* 1.3 64.1 - - - +
60A GLN* 3.0 38.4 + - - +
61A ILE* 3.0 15.1 + - + +
29B TRP* 4.4 19.5 - - + -
32B TRP* 5.1 11.2 - - + -
88B LEU* 6.1 0.2 - - - -
101B TYR* 3.5 34.1 - - + -
103B ASP 3.6 11.0 - - - +
104B LEU* 3.5 31.0 - - + -
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Residues in contact with HIS 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A ASN* 3.3 6.9 - - - +
57A MET* 1.3 74.5 - - - +
59A ALA* 1.3 57.3 + - - +
61A ILE* 3.2 8.9 + - + +
62A LYS* 2.9 45.1 + - + +
112A ILE 4.6 2.6 + - - -
41B VAL* 4.3 8.5 - - + +
42B THR 3.0 24.2 + - - -
43B MET* 3.9 28.6 - - + +
44B CYS 4.7 1.1 - - - -
80B PRO* 3.9 25.4 - - + +
83B TYR* 3.7 13.0 + + + -
103B ASP 3.0 18.9 + - - +
104B LEU* 2.8 29.3 - - - +
106B ALA* 4.0 5.3 + - + -
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Residues in contact with ALA 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A ALA* 4.1 8.3 - - + -
55A ALA 4.0 6.7 - - - +
56A ASN* 3.1 22.7 + - - +
57A MET 3.3 0.2 - - - -
58A HIS* 1.3 74.7 + - - +
60A GLN* 1.3 57.1 + - - +
62A LYS* 3.2 4.9 + - - +
63A THR* 3.0 24.5 + - - -
76A PRO* 3.4 16.6 - - + +
111A CYS 3.5 25.6 - - - +
112A ILE* 4.2 16.5 + - - -
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Residues in contact with GLN 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A GLN* 5.0 21.3 - - - +
54A ALA* 4.3 20.6 + - + +
56A ASN 3.5 15.6 + - - +
57A MET* 3.0 32.3 + - - +
59A ALA* 1.3 74.2 - - - +
61A ILE* 1.3 65.2 + - + +
63A THR* 3.3 10.2 + - - -
64A SER* 3.1 26.1 + - - -
29B TRP* 5.9 1.6 + - - +
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Residues in contact with ILE 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A MET 3.0 16.2 + - - +
58A HIS* 3.4 8.1 - - + +
60A GLN* 1.3 75.9 - - + +
62A LYS* 1.3 61.9 + - - +
64A SER* 3.2 7.9 + - - -
65A LEU* 3.0 44.9 + - + +
27B LEU* 4.1 13.5 - - + +
29B TRP* 3.8 27.4 - - + +
39B VAL* 6.0 0.4 - - + -
41B VAL* 3.9 24.2 - - + -
43B MET* 4.4 3.4 - - + -
104B LEU* 3.8 46.4 - - + +
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Residues in contact with LYS 62 (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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58A HIS* 2.9 37.9 + - + +
59A ALA* 3.2 7.6 + - - +
61A ILE* 1.3 75.0 - - - +
63A THR* 1.3 59.5 + - - +
65A LEU* 4.7 0.4 - - - -
66A HIS* 2.9 34.3 + - - +
73A VAL* 4.0 5.5 - - - +
74A PRO* 3.8 27.0 - - - +
75A ALA 3.4 25.4 + - - -
76A PRO* 3.7 6.5 - - + +
77A CYS* 3.9 5.9 - - - +
112A ILE 3.1 36.0 + - - +
43B MET* 4.3 18.2 - - + -
44B CYS 5.3 2.9 + - - -
78B CYS 4.4 14.5 + - - -
79B VAL* 4.7 2.2 - - - +
80B PRO* 5.4 2.8 - - + +
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Residues in contact with THR 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A CYS 4.8 1.7 + - - -
49A PRO 4.9 0.9 + - - -
50A SER* 3.7 31.3 - - - +
51A GLN* 5.0 4.0 + - - +
59A ALA 3.0 8.0 + - - -
60A GLN* 3.4 12.6 - - - +
62A LYS* 1.3 77.0 - - - +
64A SER* 1.3 63.2 + - - +
66A HIS* 3.7 4.2 - - - +
67A ARG* 3.3 45.0 + - - +
76A PRO* 3.3 27.5 - - - +
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Residues in contact with SER 64 (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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60A GLN 3.1 15.1 + - - -
61A ILE* 3.2 9.6 + - - -
63A THR* 1.3 77.5 - - - +
65A LEU* 1.3 62.4 + - - +
67A ARG* 3.4 33.5 + - - +
68A LEU* 3.6 13.2 + - - +
26B ASP 3.5 20.5 - - - +
27B LEU* 3.6 21.7 + - - -
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Residues in contact with LEU 65 (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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61A ILE* 3.0 34.3 + - + +
64A SER* 1.3 74.2 - - - +
66A HIS* 1.3 60.5 + - - +
68A LEU* 3.3 10.5 + - + +
69A LYS* 2.9 31.0 + - + +
73A VAL* 3.7 27.9 - - + +
20B VAL* 4.7 12.3 - - + -
22B ALA* 4.0 13.7 - - + -
26B ASP* 3.8 25.1 - - + +
27B LEU* 3.6 24.5 - - + -
41B VAL* 4.3 6.5 - - + -
43B MET* 3.8 17.0 - - + -
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Residues in contact with HIS 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A LYS 2.9 19.9 + - - +
63A THR* 3.7 6.3 - - - +
64A SER 3.3 0.2 - - - -
65A LEU* 1.3 77.0 - - - +
67A ARG* 1.3 60.7 + - + +
70A PRO* 3.1 57.2 - - + +
73A VAL* 2.7 31.9 + - - +
74A PRO* 3.9 5.6 - - + +
75A ALA* 3.5 33.7 + - + +
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Residues in contact with ARG 67 (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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50A SER* 3.5 27.9 + - - -
63A THR* 3.3 21.3 + - - +
64A SER* 3.4 30.8 + - - +
66A HIS* 1.3 82.1 - - + +
68A LEU* 1.3 64.5 + - + +
70A PRO* 4.2 6.3 - - - +
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Residues in contact with LEU 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A SER 3.6 11.8 + - - +
65A LEU* 3.3 12.9 + - + +
66A HIS 3.2 0.2 - - - -
67A ARG* 1.3 86.5 - - + +
69A LYS* 1.3 79.1 + - + +
70A PRO* 3.6 5.1 - - - +
71A ASP* 4.9 0.5 - - - +
26B ASP* 3.4 50.3 - - + +
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Residues in contact with LYS 69 (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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65A LEU* 2.9 17.3 + - + +
66A HIS 3.7 2.2 - - - -
68A LEU* 1.3 101.5 - - + +
70A PRO* 1.4 60.8 - - - +
71A ASP* 3.1 9.6 - - - +
72A THR* 2.9 24.6 + - + +
73A VAL* 2.8 35.9 + - + +
20B VAL* 5.1 11.4 - - + +
21B ARG 4.5 13.6 + - - -
26B ASP* 5.2 6.3 + - - -
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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