Contacts of the helix formed by residues 85 - 99 (chain A) in PDB entry 2V1T
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 ASP 85 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80A LEU* 2.8 29.8 + - + +
83A GLN* 3.6 4.3 - - + -
84A GLY* 1.3 73.1 - - - +
86A TYR* 1.3 57.0 + - - +
87A GLU* 3.6 10.0 + - - +
88A LYS* 3.1 40.8 + - - +
89A GLY* 3.0 25.3 + - - -
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Residues in contact with TYR 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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81A LEU* 3.5 40.6 - - + +
84A GLY* 3.2 18.7 + - - -
85A ASP* 1.3 71.3 + - - +
87A GLU* 1.3 59.9 + - - +
90A VAL* 3.0 36.7 + - - +
115A PRO* 4.9 12.7 - - + +
118A VAL* 3.8 34.8 - - + -
121A MSE 4.6 10.8 - - + -
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Residues in contact with GLU 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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85A ASP* 3.6 8.7 - - - +
86A TYR* 1.3 79.0 - - - +
88A LYS* 1.3 75.1 + - + +
90A VAL 3.4 0.3 + - - -
91A ASP* 3.3 13.9 + - - +
121A MSE 4.3 16.1 - - - +
125A LYS* 2.9 44.5 + - - +
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Residues in contact with LYS 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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80A LEU* 3.9 14.8 - - + -
85A ASP* 3.1 29.0 + - - +
87A GLU* 1.3 85.7 - - + +
89A GLY* 1.3 66.3 + - - +
91A ASP* 2.6 34.2 + - - +
92A HIS* 3.0 45.0 + - - -
88B LYS* 6.3 0.6 - - - +
91B ASP* 5.1 9.1 + - - -
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Residues in contact with GLY 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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77A GLY* 3.6 23.8 - - - -
80A LEU* 3.7 6.8 - - - +
81A LEU* 4.3 6.1 - - - -
85A ASP 3.0 19.0 + - - -
86A TYR 3.9 0.9 - - - -
88A LYS* 1.3 77.9 - - - +
90A VAL* 1.3 56.1 + - - +
92A HIS 3.2 2.9 + - - -
93A LEU* 2.9 36.4 + - - +
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Residues in contact with VAL 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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81A LEU* 4.7 4.7 - - + -
86A TYR 3.0 22.6 + - - +
87A GLU 4.0 3.1 - - - +
89A GLY* 1.3 71.5 - - - +
91A ASP* 1.3 60.2 + - - +
93A LEU* 3.7 8.2 - - + -
94A THR* 2.8 35.3 + - + -
114A LEU* 5.0 5.6 - - + -
118A VAL* 3.6 32.5 - - + +
121A MSE 4.2 7.2 - - + -
122A LEU* 3.3 39.9 - - + +
125A LYS* 3.7 17.9 - - + +
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Residues in contact with ASP 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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87A GLU* 3.3 15.4 + - - +
88A LYS* 2.6 48.0 + - - +
89A GLY 3.3 0.2 - - - -
90A VAL* 1.3 74.0 - - - +
92A HIS* 1.3 60.9 + - + +
94A THR* 2.9 18.8 + - - -
95A ASN* 3.1 25.0 + - - +
125A LYS* 2.7 33.6 + - - +
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Residues in contact with HIS 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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73A GLU* 2.6 57.7 + - - +
76A LEU* 3.4 24.8 - - + +
77A GLY 3.9 4.9 - - - +
80A LEU* 3.5 22.8 - - + +
88A LYS* 3.0 38.9 + - - -
89A GLY 3.2 7.2 + - - +
91A ASP* 1.3 76.3 - - + +
93A LEU* 1.3 63.7 + - - +
95A ASN* 3.2 8.8 + - - +
96A ALA* 3.1 18.2 + - - +
95B ASN* 5.7 2.9 - - - -
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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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73A GLU 4.6 2.5 - - - +
74A ILE* 4.8 7.4 - - + +
77A GLY* 3.2 34.1 - - - +
78A GLU* 4.0 6.1 - - - +
81A LEU* 3.7 21.3 - - + -
89A GLY 2.9 31.5 + - - +
90A VAL* 3.7 10.1 - - + +
92A HIS* 1.3 74.8 - - - +
94A THR* 1.3 58.5 + - - +
96A ALA* 3.3 8.8 + - - +
97A ILE* 3.1 30.9 + - - +
110A LEU* 3.9 32.8 - - + -
114A LEU* 4.3 12.8 - - + -
122A LEU* 4.4 10.1 - - + -
19C LEU* 4.7 7.6 - - + -
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Residues in contact with THR 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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90A VAL* 2.8 24.1 + - + +
91A ASP* 2.9 14.6 + - - -
93A LEU* 1.3 73.0 - - - +
95A ASN* 1.3 60.4 + - - +
97A ILE* 3.5 9.6 + - + +
98A ALA* 2.9 29.7 + - - +
122A LEU* 3.7 42.8 - - + +
125A LYS* 3.6 30.1 + - + +
126A LEU* 4.1 10.3 - - + +
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Residues in contact with ASN 95 (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 PHE* 4.0 14.2 - - + -
73A GLU* 3.0 24.4 + - - +
91A ASP* 3.1 22.6 + - - +
92A HIS* 3.2 15.4 + - - +
94A THR* 1.3 77.6 + - - +
96A ALA* 1.3 62.3 + - - +
98A ALA* 3.1 19.0 + - - +
99A VAL* 3.5 14.4 + - - +
69B PHE* 4.0 13.8 - - + -
73B GLU* 4.8 2.6 - - - +
92B HIS* 5.3 4.7 - - - -
95B ASN* 3.6 27.7 + - - +
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Residues in contact with ALA 96 (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 PHE* 3.2 32.8 - - + +
73A GLU* 3.9 12.7 - - + +
74A ILE* 3.4 36.6 - - + -
92A HIS 3.1 11.0 + - - +
93A LEU 3.4 9.4 - - - +
95A ASN* 1.3 76.1 - - - +
97A ILE* 1.3 61.9 + - - +
98A ALA 3.3 0.3 + - - -
99A VAL* 3.4 15.0 + - - +
100A CYS 3.6 2.3 + - - -
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Residues in contact with ILE 97 (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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93A LEU 3.1 17.8 + - - +
94A THR* 3.8 7.9 - - - +
96A ALA* 1.3 75.7 - - - +
98A ALA* 1.3 62.4 + - - +
100A CYS* 3.2 21.7 + - - +
103A PRO* 3.9 22.6 - - + +
106A LEU* 3.7 25.8 - - + -
107A LEU* 3.8 21.8 - - + -
110A LEU* 3.5 25.6 - - + -
122A LEU* 4.2 16.8 - - + -
126A LEU* 4.0 20.6 - - + +
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Residues in contact with ALA 98 (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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94A THR 2.9 18.7 + - - +
95A ASN* 3.1 7.5 + - - +
97A ILE* 1.3 77.6 - - - +
99A VAL* 1.3 58.3 + - - +
100A CYS 3.4 0.7 - - - -
126A LEU 5.3 7.6 - - - +
65B ALA* 3.5 21.8 - - - +
69B PHE* 3.6 26.3 - - + +
72B GLU* 5.3 4.3 - - - +
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Residues in contact with VAL 99 (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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66A VAL* 3.7 29.4 - - + +
69A PHE* 4.0 17.7 - - + -
70A PHE* 4.3 16.8 - - + -
95A ASN 3.5 9.6 + - - +
96A ALA* 3.4 13.0 - - - +
98A ALA* 1.3 75.3 - - - +
100A CYS* 1.3 60.6 + - - +
101A GLY 3.7 2.4 + - - -
65B ALA* 3.9 9.6 - - - +
66B VAL* 4.3 16.2 + - + +
69B PHE* 3.4 41.5 - - + -
99B VAL* 4.4 0.2 - - + -
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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