Contacts of the helix formed by residues 80 - 94 (chain A) in PDB entry 2VDY
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 GLU 80 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56A SER* 3.5 18.5 + - - +
57A LEU* 3.9 3.8 + - - +
64A ARG* 4.3 12.0 + - - +
68A LEU* 4.5 21.3 - - + +
75A LEU* 6.2 3.7 - - + +
79A SER* 1.3 72.1 - - - +
81A THR* 1.3 66.1 + - + +
82A GLU 3.2 0.9 - - - -
83A ILE* 3.1 25.7 + - + +
84A HIS* 3.0 47.5 + - + +
311A ARG* 3.3 37.5 + - - -
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Residues in contact with THR 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 SER* 3.1 19.0 + - - -
80A GLU* 1.3 78.8 - - + +
82A GLU* 1.3 55.2 + - - +
84A HIS* 3.5 6.8 + - + +
85A GLN* 3.0 47.2 + - - +
128A TYR* 4.4 17.4 - - + +
120B SER* 4.2 23.2 - - - -
123B ALA* 5.9 4.7 - - + -
124B ASP* 6.1 1.1 - - - +
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Residues in contact with GLU 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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17A LEU* 4.7 3.4 - - - +
79A SER* 3.4 34.0 + - - +
80A GLU 3.2 0.6 - - - -
81A THR* 1.3 79.4 + - - +
83A ILE* 1.3 61.6 + - + +
85A GLN* 4.0 8.2 - - - +
86A GLY* 3.2 17.3 + - - -
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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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17A LEU* 3.7 11.0 - - + +
53A ALA* 4.3 8.5 - - + -
68A LEU* 4.0 19.1 - - + -
73A PHE* 3.7 51.6 - - + -
75A LEU* 6.3 1.1 - - + -
79A SER 4.3 15.0 - - - +
80A GLU* 3.1 15.1 + - + +
82A GLU* 1.3 78.5 - - + +
84A HIS* 1.3 67.1 + - + +
86A GLY* 3.1 14.9 + - - -
87A PHE* 3.1 38.0 + - + -
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Residues in contact with HIS 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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53A ALA 3.1 26.0 - - - -
56A SER* 3.6 7.4 - - - -
57A LEU* 3.5 28.1 - - + +
80A GLU* 3.0 53.4 + - + +
81A THR* 4.2 4.9 - - + +
83A ILE* 1.3 80.0 - - + +
85A GLN* 1.3 60.4 + - - +
86A GLY 3.2 1.6 - - - -
87A PHE* 3.5 1.8 + - - +
88A GLN* 3.0 27.5 + - - +
128A TYR* 3.5 35.1 - + + +
129A TYR* 2.8 28.2 + + - -
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Residues in contact with GLN 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 THR* 3.0 34.9 + - - +
82A GLU* 4.0 8.1 + - - +
84A HIS* 1.3 75.4 - - - +
86A GLY* 1.3 58.1 + - - +
88A GLN* 3.6 11.0 + - - +
89A HIS* 3.1 26.3 + - - +
128A TYR* 3.9 6.1 + - + -
119B GLU* 3.3 37.1 + - - +
120B SER* 4.1 12.6 + - - -
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Residues in contact with GLY 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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17A LEU* 3.7 19.9 - - - +
82A GLU 3.2 9.3 + - - -
83A ILE 3.1 9.7 + - - -
85A GLN* 1.3 80.3 - - - +
87A PHE* 1.3 55.9 + - - +
89A HIS* 3.3 10.4 - - - +
90A LEU* 3.2 28.9 + - - +
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Residues in contact with PHE 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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17A LEU* 4.0 5.8 - - + -
21A ASN* 3.6 34.5 - - - -
46A VAL* 4.6 3.4 - - + -
49A SER* 3.6 17.7 - - - -
50A MET* 3.5 39.2 - - + +
53A ALA* 3.6 16.2 - - + -
73A PHE* 4.0 8.7 - + - -
83A ILE* 3.1 35.9 + - + +
84A HIS 4.2 0.7 - - - +
85A GLN 3.4 0.2 - - - -
86A GLY* 1.3 73.9 - - - +
88A GLN* 1.3 60.4 + - - +
89A HIS 3.2 0.4 - - - -
90A LEU* 3.7 16.4 - - + +
91A HIS* 2.9 30.5 + - - +
128A TYR 4.3 2.2 - - - +
129A TYR* 3.6 37.6 - + + +
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Residues in contact with GLN 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 HIS 3.0 14.4 + - - +
85A GLN* 3.6 8.0 - - - +
87A PHE* 1.3 76.1 - - - +
89A HIS* 1.3 62.2 + - - +
91A HIS* 3.6 3.8 + - - +
92A GLN* 3.2 24.4 + - + +
127A HIS* 3.8 33.2 + - - +
128A TYR* 3.2 32.7 + - - +
119B GLU* 2.9 27.0 + - - +
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Residues in contact with HIS 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 GLN 3.1 14.6 + - - +
86A GLY* 3.3 14.4 - - - +
87A PHE 3.2 0.2 - - - -
88A GLN* 1.3 76.7 - - - +
90A LEU* 1.3 65.1 + - + +
92A GLN* 3.6 11.8 + - - +
93A LEU* 3.3 56.5 + - + +
369A PHE* 5.0 5.7 - + - -
370A THR* 4.8 9.8 - - + +
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Residues in contact with LEU 90 (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 LEU* 4.4 6.1 - - + -
21A ASN* 4.2 11.4 - - - +
46A VAL* 4.2 12.1 - - + -
50A MET* 4.3 4.9 - - + -
86A GLY 3.2 16.5 + - - +
87A PHE* 3.8 33.9 - - + +
88A GLN 3.4 0.2 - - - -
89A HIS* 1.3 79.5 - - + +
91A HIS* 1.3 59.3 + - - +
92A GLN 3.2 0.2 + - - -
93A LEU* 3.3 4.0 + - - -
94A PHE* 2.9 51.1 + - + -
370A THR* 3.8 27.6 - - + +
372A SER* 3.5 26.2 - - - +
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Residues in contact with HIS 91 (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 MET* 3.9 13.9 - - + +
87A PHE 2.9 18.6 + - - +
88A GLN* 3.9 7.2 + - - +
90A LEU* 1.3 76.5 - - - +
92A GLN* 1.3 62.4 + - - +
94A PHE* 3.7 11.6 + - - +
95A ALA* 4.0 10.2 + - - +
105A MET* 3.0 39.0 + - - +
106A GLY* 3.7 8.3 - - - -
107A ASN* 3.9 20.2 - - - +
128A TYR 4.9 2.7 - - - +
129A TYR* 3.9 10.6 + - - -
130A GLU* 3.6 40.5 + - + +
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Residues in contact with GLN 92 (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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88A GLN* 3.2 15.6 + - + +
89A HIS* 3.8 12.2 + - - +
90A LEU 3.2 0.4 - - - -
91A HIS* 1.3 79.8 + - - +
93A LEU* 1.3 87.1 + - - +
94A PHE 3.2 0.9 + - - -
95A ALA* 3.4 19.8 + - - +
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Residues in contact with LEU 93 (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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89A HIS* 3.3 46.4 + - + +
90A LEU* 3.3 5.4 + - - +
92A GLN* 1.3 98.6 - - - +
94A PHE* 1.3 67.6 + - + +
95A ALA 3.2 4.9 + - - +
96A LYS* 3.9 17.5 - - - +
103A MET* 4.1 2.4 - - - +
369A PHE* 3.9 23.3 - - + -
370A THR* 3.7 23.6 - - + -
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Residues in contact with PHE 94 (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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46A VAL* 4.2 13.9 - - + -
90A LEU* 2.9 41.8 + - + +
91A HIS 3.7 5.4 + - - +
92A GLN 3.2 0.8 - - - -
93A LEU* 1.3 82.1 - - + +
95A ALA* 1.3 55.8 + - - +
96A LYS 3.9 0.7 - - - -
103A MET* 3.0 49.6 - - + +
104A THR* 3.3 14.9 - - - -
105A MET* 3.6 35.2 + - + -
179A ILE* 5.5 0.9 - - + -
367A ASP* 3.7 23.3 - - + -
370A THR* 3.8 21.3 - - + -
372A SER* 4.1 2.0 - - - -
374A LEU* 3.8 28.9 - - + -
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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