Contacts of the helix formed by residues 65 - 78 (chain A) in PDB entry 1VEP
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 PHE 65 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A MET* 3.7 35.4 - - + -
63A PHE* 3.5 35.7 - + + -
64A ASP* 1.3 72.5 + - - +
66A SER* 1.3 58.7 + - - +
67A TYR 3.3 2.7 - - - -
68A ALA* 3.1 10.9 + - + +
69A GLN* 2.8 39.4 + - + +
145A LEU* 4.5 5.6 - - + -
148A ALA* 3.6 34.5 - - + -
149A PHE* 3.6 29.4 - + + -
152A ALA* 3.3 28.3 - - + -
153A MET* 5.2 0.7 - - - -
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Residues in contact with SER 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ASP* 2.6 26.9 + - - -
65A PHE* 1.3 77.6 - - - +
67A TYR* 1.3 64.2 + - - +
69A GLN* 3.3 13.0 + - - +
70A ARG* 2.8 25.3 + - - +
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Residues in contact with TYR 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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21A LYS* 3.4 41.4 - - + -
22A ILE* 2.9 33.4 + - - +
23A PRO* 3.6 24.9 - - + -
28A TRP* 3.8 16.4 - + - -
48A VAL* 5.6 1.6 - - + -
49A ASP 5.3 3.4 - - - -
50A PHE* 4.1 25.6 - + - -
54A ASP* 5.8 3.4 - - + -
64A ASP* 5.1 2.1 + - - +
65A PHE 3.3 0.6 - - - -
66A SER* 1.3 81.8 + - - +
68A ALA* 1.3 56.2 + - - +
70A ARG* 3.2 5.3 + - + -
71A PHE* 2.8 47.7 + + + +
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Residues in contact with ALA 68 (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 PHE* 3.7 37.4 - - + -
55A MET* 5.1 3.8 - - + -
65A PHE* 3.1 19.1 + - + +
67A TYR* 1.3 81.3 - - - +
69A GLN* 1.3 60.7 + - - +
71A PHE* 3.4 2.6 + - - +
72A ALA* 3.1 23.9 + - - +
149A PHE* 4.4 8.7 - - + -
153A MET* 3.7 19.4 - - - +
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Residues in contact with GLN 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A PHE* 2.8 29.9 + - + +
66A SER* 3.7 12.8 - - - +
68A ALA* 1.3 70.1 - - - +
70A ARG* 1.3 65.2 + - - +
72A ALA* 3.2 3.5 + - - +
73A GLN* 3.0 22.7 + - - +
152A ALA* 2.8 36.0 + - - +
153A MET* 4.1 10.1 - - - -
155A PRO* 5.6 2.6 - - - +
156A TYR* 3.8 26.0 + - + +
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Residues in contact with ARG 70 (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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28A TRP* 3.3 64.7 - - + +
32A GLU* 4.7 3.6 + - - -
66A SER 2.8 17.2 + - - +
67A TYR* 3.7 6.3 - - + +
69A GLN* 1.3 75.4 - - - +
71A PHE* 1.3 64.3 + - - +
73A GLN* 3.2 24.4 + - - +
74A SER* 3.3 20.8 + - - -
77A ASN* 5.3 3.2 - - - +
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Residues in contact with PHE 71 (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 ALA* 4.9 1.6 - - + -
22A ILE* 3.8 18.4 - - + -
28A TRP* 3.9 13.4 - + + -
31A PHE* 3.7 24.1 - + - -
46A ILE* 4.2 16.4 - - + -
48A VAL* 3.6 40.8 - - + -
50A PHE* 4.0 18.8 - + + -
67A TYR* 2.8 40.5 + + + +
68A ALA 3.5 5.8 - - - +
69A GLN 3.2 0.2 - - - -
70A ARG* 1.3 78.0 - - - +
72A ALA* 1.3 63.5 + - - +
74A SER* 3.2 6.8 + - - -
75A VAL* 3.1 42.2 + - + +
82A MET* 4.2 6.5 - - + -
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Residues in contact with ALA 72 (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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68A ALA 3.1 13.8 + - - +
69A GLN 3.7 3.8 - - - +
71A PHE* 1.3 76.9 - - - +
73A GLN* 1.3 59.8 + - - +
75A VAL* 3.3 3.0 + - - +
76A LYS* 2.9 28.9 + - - +
82A MET* 3.8 28.3 - - - -
153A MET* 3.9 9.0 - - + -
156A TYR* 3.7 30.0 - - + -
159A VAL* 4.5 3.2 - - + +
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Residues in contact with GLN 73 (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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69A GLN 3.0 13.2 + - - +
70A ARG* 3.4 25.8 - - - +
71A PHE 3.1 0.2 - - - -
72A ALA* 1.3 77.0 - - - +
74A SER* 1.3 57.6 + - - +
76A LYS* 3.1 18.9 + - - +
77A ASN* 2.9 55.4 + - - +
156A TYR* 3.0 34.5 + - - +
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Residues in contact with SER 74 (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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28A TRP* 3.4 30.4 - - - +
31A PHE* 3.8 7.9 - - - -
32A GLU* 2.8 36.2 + - - +
35A LEU* 4.3 1.7 - - - +
70A ARG* 3.3 16.0 + - - -
71A PHE 3.2 8.7 + - - -
73A GLN* 1.3 75.7 - - - +
75A VAL* 1.3 67.5 + - - +
77A ASN* 3.3 2.7 + - - +
78A ALA* 3.0 24.3 + - - +
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Residues in contact with VAL 75 (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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31A PHE* 4.5 1.3 - - + -
35A LEU* 3.9 18.4 - - + -
46A ILE* 4.2 6.3 - - + -
71A PHE* 3.1 43.3 + - + +
72A ALA* 3.6 9.6 - - - +
74A SER* 1.3 74.7 - - - +
76A LYS* 1.3 64.2 + - - +
78A ALA* 3.3 5.2 + - - +
80A MET* 3.0 55.7 + - + +
81A LYS* 3.7 17.7 - - - +
82A MET* 4.0 10.1 - - + +
159A VAL* 4.6 4.0 - - + -
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Residues in contact with LYS 76 (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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72A ALA 2.9 13.2 + - - +
73A GLN* 3.3 22.4 + - - +
75A VAL* 1.3 78.8 - - - +
77A ASN* 1.3 57.8 + - - +
79A GLY* 2.9 20.4 + - - -
80A MET 4.8 0.9 - - - -
155A PRO 5.6 4.0 + - - -
156A TYR* 4.9 15.4 - - + -
158A ASP* 4.1 18.1 + - - +
159A VAL* 3.9 25.3 - - + +
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Residues in contact with ASN 77 (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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32A GLU* 2.8 35.6 + - - +
36A ARG* 3.2 15.1 + - - +
70A ARG* 5.3 3.2 - - - +
73A GLN* 2.9 42.6 + - - +
74A SER* 3.3 4.3 + - - +
76A LYS* 1.3 76.8 - - - +
78A ALA* 1.3 58.3 + - - +
79A GLY 3.2 0.9 + - - -
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Residues in contact with ALA 78 (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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32A GLU* 3.7 27.1 - - - +
35A LEU* 3.7 21.8 - - + -
36A ARG* 3.6 23.4 - - + +
39A LYS* 4.6 6.2 + - - +
74A SER 3.0 15.9 + - - +
75A VAL 3.8 4.3 - - - +
76A LYS 3.1 0.4 - - - -
77A ASN* 1.3 76.4 - - - +
79A GLY* 1.3 63.2 + - - +
80A MET* 3.3 5.9 + - - +
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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