Contacts of the helix formed by residues 69 - 83 (chain A) in PDB entry 1VE3
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 69 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67A ASP* 2.8 14.5 + - - -
68A ILE* 1.3 79.5 - - - +
70A GLU* 1.3 62.7 + - - +
71A ASP* 3.1 14.9 + - - +
72A MSE 3.0 32.2 + - - +
73A ILE* 3.1 27.5 + - - +
91A VAL* 4.8 0.7 - - - -
302A SAM 3.5 7.4 - - - -
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Residues in contact with GLU 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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68A ILE 3.7 3.6 + - - +
69A SER* 1.3 72.0 + - - +
71A ASP* 1.3 62.0 + - - +
73A ILE* 3.5 1.9 + - - +
74A ARG* 2.9 36.3 + - - +
77A ARG* 5.6 2.8 + - - -
91A VAL* 3.7 30.2 - - + +
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Residues in contact with ASP 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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4A LYS* 4.9 13.4 + - - +
69A SER* 3.1 8.4 + - - +
70A GLU* 1.3 78.9 + - - +
72A MSE 1.3 75.1 + - + +
74A ARG* 2.9 38.1 + - - +
75A LYS* 3.1 30.3 + - - +
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Residues in contact with MSE 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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7A TYR* 4.5 18.6 - - + -
13A TYR* 4.4 2.7 - - - +
14A THR* 3.5 33.9 - - + -
48A GLY* 3.5 23.7 - - - +
49A VAL* 4.0 17.3 - - + -
67A ASP* 3.9 7.2 - - - +
69A SER* 3.0 31.8 + - - +
71A ASP* 1.3 84.5 - - + +
73A ILE* 1.3 58.6 + - - +
75A LYS* 3.4 9.5 + - + +
76A ALA* 2.9 27.7 + - - +
302A SAM 3.5 24.2 - - - +
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Residues in contact with ILE 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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47A CYS* 4.1 12.8 - - - -
48A GLY 4.8 0.4 - - - +
67A ASP* 3.5 31.6 - - + +
69A SER 3.1 16.5 + - - +
70A GLU 3.8 2.0 - - - +
72A MSE 1.3 75.1 - - - +
74A ARG* 1.3 65.0 + - - +
76A ALA* 3.2 4.4 + - - +
77A ARG* 3.1 56.9 + - - +
89A PHE* 4.2 15.0 - - + +
90A ILE 3.6 15.9 - - - +
91A VAL* 3.5 29.2 - - + -
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Residues in contact with ARG 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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70A GLU* 2.9 26.2 + - - +
71A ASP* 2.9 44.7 + - - +
73A ILE* 1.3 78.6 - - - +
75A LYS* 1.3 66.8 + - - +
77A ARG* 3.4 11.8 + - - +
78A GLU* 3.3 35.1 + - + +
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Residues in contact with LYS 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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7A TYR 5.7 0.2 + - - -
8A ARG* 6.1 2.8 - - - +
14A THR* 3.8 31.7 + - - +
49A VAL* 4.0 22.4 - - + -
71A ASP* 3.1 19.2 + - - +
72A MSE 3.8 9.0 - - + +
74A ARG* 1.3 80.5 - - + +
76A ALA* 1.3 67.7 + - - +
78A GLU* 3.2 16.3 + - - +
79A TYR* 3.0 36.5 + - + +
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Residues in contact with ALA 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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48A GLY 4.2 2.2 - - - +
49A VAL* 3.4 28.0 + - - +
54A PHE* 3.6 0.5 - - - -
72A MSE 2.9 14.3 + - - +
73A ILE* 3.2 13.4 + - + +
75A LYS* 1.3 77.9 - - - +
77A ARG* 1.3 57.4 + - - +
79A TYR* 3.1 5.2 + - - +
80A ALA* 2.9 27.5 + - - +
89A PHE* 3.6 33.1 - - + -
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Residues in contact with ARG 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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70A GLU* 5.6 1.8 + - - -
73A ILE* 3.1 38.6 + - - +
74A ARG* 3.6 11.9 - - - +
75A LYS 3.2 0.2 - - - -
76A ALA* 1.3 75.3 - - - +
78A GLU* 1.3 57.2 + - + +
80A ALA* 3.1 8.8 + - - +
81A LYS* 2.8 29.2 + - - +
89A PHE* 2.8 39.0 + - + +
90A ILE* 4.3 4.8 - - - +
91A VAL* 4.8 7.7 - - - +
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Residues in contact with GLU 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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74A ARG* 3.3 33.8 + - + +
75A LYS* 3.2 15.7 + - - +
77A ARG* 1.3 77.4 - - + +
79A TYR* 1.3 58.7 + - + +
81A LYS* 3.3 11.7 + - + +
82A SER* 2.9 29.8 + - - -
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Residues in contact with TYR 79 (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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14A THR 3.5 24.9 + - - -
15A ASP* 3.7 10.6 + - - -
16A ILE* 3.5 45.5 + - + -
17A ASN* 4.2 17.7 - - - -
49A VAL* 3.8 11.7 - - + -
54A PHE* 3.6 17.9 - - + -
75A LYS* 3.0 34.8 + - + +
76A ALA 3.4 6.5 - - - +
78A GLU* 1.3 76.9 - - - +
80A ALA* 1.3 58.1 + - - +
82A SER* 2.9 10.6 + - - -
83A ARG* 2.9 39.4 + - + +
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Residues in contact with ALA 80 (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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54A PHE* 3.5 23.3 - - + -
76A ALA 2.9 13.2 + - - +
77A ARG* 3.4 10.5 - - - +
79A TYR* 1.3 73.8 - - - +
81A LYS* 1.3 56.2 + - - +
84A GLU* 2.8 12.8 + - - -
85A SER* 2.7 43.3 + - - +
87A VAL 4.7 4.5 - - - +
89A PHE* 3.9 12.1 - - + -
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Residues in contact with LYS 81 (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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77A ARG 2.8 14.5 + - - +
78A GLU* 3.4 14.1 - - + +
80A ALA* 1.3 76.9 - - - +
82A SER* 1.3 58.6 - - - +
84A GLU* 2.9 25.5 + - - +
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Residues in contact with SER 82 (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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78A GLU 2.9 14.5 + - - -
79A TYR* 2.9 25.3 + - - -
81A LYS* 1.3 76.2 - - - +
83A ARG* 1.3 63.1 + - - +
84A GLU* 3.3 4.9 + - - +
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Residues in contact with ARG 83 (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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16A ILE* 3.4 31.8 + - - +
17A ASN* 3.6 20.4 + - - +
22A ARG* 5.7 1.6 - - - +
25A ILE* 6.1 1.8 - - - +
51A GLY 5.3 1.4 + - - -
54A PHE* 3.8 37.6 - - + +
55A LEU 5.5 0.4 - - - +
58A ASP* 5.1 5.3 + - - -
79A TYR* 2.9 24.8 + - + +
80A ALA* 4.2 3.1 - - - +
82A SER* 1.3 82.2 - - - +
84A GLU* 1.3 72.7 + - - +
85A SER* 4.3 7.2 - - - +
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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