Contacts of the helix formed by residues 79 - 89 (chain A) in PDB entry 7V3X
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 THR 79 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77A GLU 3.3 5.0 + - - +
78A GLU* 1.3 72.1 - - - +
80A PRO* 1.4 63.0 - - - +
81A GLN* 3.0 24.3 + - + +
82A ASP* 2.7 48.4 + - - +
83A ILE* 3.1 9.5 + - - -
107A ASP* 5.2 2.7 - - - -
109A SER* 5.9 1.1 - - - -
172B LYS* 6.2 4.0 - - + -
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Residues in contact with PRO 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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75A THR* 4.1 7.2 - - + -
78A GLU 3.7 5.1 - - - +
79A THR* 1.4 85.4 - - - +
81A GLN* 1.3 62.5 + - - +
83A ILE* 3.5 12.8 + - + +
84A ILE* 3.3 32.0 + - + +
105A ILE* 4.4 22.7 - - + +
107A ASP* 3.7 43.5 - - + +
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Residues in contact with GLN 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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79A THR* 3.0 13.1 + - - +
80A PRO* 1.3 78.7 - - - +
82A ASP* 1.3 61.5 + - - +
84A ILE* 3.6 9.6 - - - +
85A LYS* 3.3 23.1 + - - +
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Residues in contact with ASP 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* 4.6 10.6 - - + +
79A THR* 2.7 40.0 + - - +
81A GLN* 1.3 73.8 - - - +
83A ILE* 1.3 56.0 + - - +
84A ILE 3.1 1.3 - - - -
85A LYS* 3.0 13.8 + - - +
86A ASN* 2.7 43.7 + - - +
40B ARG* 4.0 24.3 + - - +
172B LYS* 5.7 4.7 - - - +
202B ASP* 4.9 7.3 - - - +
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Residues in contact with ILE 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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53A THR* 5.7 0.7 - - + -
57A ILE* 3.4 29.3 - - + +
73A PHE* 3.5 23.3 - - + -
75A THR* 3.5 42.4 - - + +
78A GLU* 3.7 29.6 - - + +
79A THR 3.1 5.0 + - - +
80A PRO* 3.9 11.4 - - + +
82A ASP* 1.3 74.9 - - - +
84A ILE* 1.3 62.0 + - + +
86A ASN* 3.7 9.6 + - - +
87A ALA* 3.2 22.9 + - - +
94A LEU* 4.5 7.9 - - + -
105A ILE* 5.7 6.1 - - + -
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Residues in contact with ILE 84 (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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80A PRO* 3.3 18.7 + - + +
81A GLN* 3.6 10.3 - - - +
82A ASP 3.1 0.4 - - - -
83A ILE* 1.3 76.1 - - + +
85A LYS* 1.3 67.0 + - - +
87A ALA* 3.2 4.2 + - - +
88A ARG* 3.2 21.5 + - + +
92A TRP 5.3 0.2 - - - +
93A ASP* 5.6 1.6 - - - +
94A LEU* 4.2 24.5 + - + +
95A ALA* 4.2 35.7 - - + +
98A VAL* 4.8 12.1 - - + -
103A LEU* 6.3 0.2 - - + -
105A ILE* 5.9 2.9 - - + -
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Residues in contact with LYS 85 (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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81A GLN 3.3 11.7 + - - +
82A ASP* 3.0 18.7 + - - +
84A ILE* 1.3 79.0 - - - +
86A ASN* 1.3 61.6 + - - +
88A ARG* 3.3 21.2 + - + +
89A SER 3.9 2.6 + - - -
17B ALA 5.4 5.4 - - - +
18B ILE* 3.6 41.1 - - + +
19B ALA* 5.3 5.6 - - - +
38B ILE 5.9 2.6 + - - -
40B ARG* 4.4 8.5 - - - +
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Residues in contact with ASN 86 (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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57A ILE* 6.2 2.0 - - + -
78A GLU* 2.6 31.7 + - - +
82A ASP* 2.7 24.9 + - - +
83A ILE* 3.8 5.8 - - - +
85A LYS* 1.3 73.0 - - - +
87A ALA* 1.3 56.0 + - - +
89A SER* 3.0 26.5 - - - -
90A PHE* 4.6 6.4 - - - -
18B ILE* 4.4 0.2 - - - -
40B ARG* 2.5 33.4 + - - +
202B ASP* 5.4 0.8 + - - -
226B ARG* 3.7 12.1 - - - +
227B GLY* 3.4 28.8 - - - +
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Residues in contact with ALA 87 (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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57A ILE* 4.7 7.4 - - + +
83A ILE 3.2 14.6 + - - +
84A ILE 3.2 5.2 + - - +
86A ASN* 1.3 73.4 - - - +
88A ARG* 1.3 65.1 + - - +
89A SER 3.1 2.5 - - - -
90A PHE* 3.0 26.0 + - - +
92A TRP* 3.4 28.3 + - + +
94A LEU* 3.6 30.7 - - + -
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Residues in contact with ARG 88 (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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84A ILE* 3.2 11.9 + - + +
85A LYS* 3.3 15.9 - - + +
87A ALA* 1.3 71.5 - - - +
89A SER* 1.3 66.7 + - - +
91A GLY* 3.0 15.8 + - - -
92A TRP 3.5 12.9 + - - +
93A ASP* 6.2 0.2 - - - -
17B ALA 4.6 15.0 + - - +
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Residues in contact with SER 89 (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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85A LYS 3.9 2.4 + - - -
86A ASN 3.0 20.5 + - - -
88A ARG* 1.3 74.9 - - - +
90A PHE* 1.3 79.9 + - - -
91A GLY* 3.1 5.9 + - - -
241A ASP* 4.9 10.9 + - - +
17B ALA* 4.5 16.1 + - - +
227B GLY 3.2 24.7 + - - -
228B THR* 4.7 4.7 + - - -
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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