Contacts of the helix formed by residues 64 - 83 (chain B) 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 GLU 64 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A GLY* 3.9 20.6 - - - +
63B ALA* 1.3 81.4 - - + +
65B ALA* 1.3 65.9 + - - +
66B VAL* 3.5 24.5 - - + +
67B GLN* 2.9 44.0 + - + +
68B LYS* 3.2 15.1 + - - +
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Residues in contact with ALA 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A ALA 3.5 18.1 - - - +
99A VAL* 3.9 7.9 - - - +
100A CYS 3.7 26.0 - - - +
101A GLY* 4.1 10.0 - - - +
63B ALA 3.8 2.2 + - - -
64B GLU* 1.3 71.4 - - - +
66B VAL* 1.3 57.0 + - - +
68B LYS* 3.3 15.6 + - - +
69B PHE* 2.9 27.4 + - - +
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Residues in contact with VAL 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A LEU* 3.9 13.2 - - + -
62A ASP 5.9 0.4 - - - +
66A VAL* 3.5 41.5 - - + -
99A VAL* 4.3 11.4 + - + +
64B GLU* 3.5 25.1 - - + +
65B ALA* 1.3 76.7 - - - +
67B GLN* 1.3 61.1 + - - +
69B PHE* 3.5 5.5 - - + +
70B PHE* 2.9 27.5 + - - +
99B VAL* 3.6 30.1 - - + +
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Residues in contact with GLN 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A LEU* 2.9 42.3 + - + +
57A GLY* 4.1 3.0 - - - -
61B LYS* 3.1 30.7 + - - +
62B ASP* 3.4 4.2 + - - -
63B ALA* 2.9 14.6 + - - +
64B GLU* 2.9 55.4 + - + +
66B VAL* 1.3 74.0 - - - +
68B LYS* 1.3 65.2 + - - +
70B PHE* 3.3 3.3 + - - +
71B LEU* 3.2 31.5 + - + +
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Residues in contact with LYS 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B ASP* 2.7 36.8 + - + +
63B ALA* 3.0 21.6 + - - +
64B GLU 3.2 8.2 + - - +
65B ALA* 3.5 13.2 - - + +
67B GLN* 1.3 77.0 - - - +
69B PHE* 1.3 62.5 + - - +
71B LEU* 3.4 8.4 + - - +
72B GLU* 3.0 43.4 + - - +
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Residues in contact with PHE 69 (chain B).
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* 3.7 35.4 - + - -
95A ASN* 4.0 17.3 - - - -
98A ALA* 3.6 30.5 - - + +
99A VAL* 3.4 20.4 - - + -
65B ALA 2.9 17.4 + - - +
66B VAL 3.5 4.0 - - - +
68B LYS* 1.3 76.5 - - - +
70B PHE* 1.3 58.3 + - - +
72B GLU* 3.3 13.6 + - - +
73B GLU* 2.9 71.3 + - + +
95B ASN* 3.9 16.8 - - + -
99B VAL* 4.3 13.0 - - + -
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Residues in contact with PHE 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A LEU* 3.7 24.2 - - + -
66B VAL 2.9 16.1 + - - +
67B GLN* 3.3 5.1 + - - +
69B PHE* 1.3 80.9 - - - +
71B LEU* 1.3 72.7 + - + +
73B GLU* 3.3 1.9 + - - +
74B ILE* 3.1 51.8 + - + +
96B ALA* 3.4 39.5 - - + -
99B VAL* 4.1 6.1 - - + -
106B LEU* 3.8 31.6 - - + -
19D LEU 4.7 3.4 - - - -
20D SER* 4.2 15.3 - - - -
23D GLY* 5.5 2.9 - - - -
24D CY3 4.1 17.5 - - - -
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Residues in contact with LEU 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B LEU* 5.5 12.1 - - + -
61B LYS 5.3 4.0 - - - +
62B ASP* 4.5 20.4 - - + -
67B GLN 3.2 16.9 + - - +
68B LYS* 3.8 5.8 - - - +
70B PHE* 1.3 83.0 - - + +
72B GLU* 1.3 63.9 + - + +
74B ILE* 3.1 25.8 - - + +
75B GLN* 3.2 13.9 + - - +
16D SER* 5.1 0.3 - - - -
20D SER* 4.0 27.8 - - - +
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Residues in contact with GLU 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A ALA* 5.3 3.8 - - - +
68B LYS* 3.0 37.6 + - - +
69B PHE* 3.4 23.4 - - - +
71B LEU* 1.3 77.9 - - - +
73B GLU* 1.3 62.8 + - - +
75B GLN* 3.9 4.1 - - - +
76B LEU* 2.9 32.6 + - - +
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Residues in contact with GLU 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A ASN* 4.9 2.1 - - - +
69B PHE* 2.9 59.3 + - + +
70B PHE 3.8 3.6 - - - +
72B GLU* 1.3 80.8 - - - +
74B ILE* 1.3 55.1 + - - +
76B LEU* 4.6 6.5 - - - +
77B GLY* 2.8 32.6 + - - -
92B HIS* 2.6 58.4 + - - +
93B LEU* 4.2 0.2 - - - +
95B ASN* 2.9 18.4 + - + -
96B ALA* 4.0 7.9 - - + -
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Residues in contact with ILE 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B PHE* 3.1 43.8 + - + +
71B LEU* 3.1 29.6 - - + +
73B GLU* 1.3 76.2 - - - +
75B GLN* 1.3 55.4 + - - +
78B GLU* 3.1 31.0 + - - +
93B LEU* 3.8 14.3 - - + +
96B ALA* 3.7 19.1 - - + -
106B LEU* 5.2 3.1 - - + -
16D SER* 3.7 34.3 - - - +
19D LEU* 4.1 22.8 - - + +
20D SER* 4.0 12.1 - - - +
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Residues in contact with GLN 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B LEU 3.2 14.1 + - - +
72B GLU* 4.0 4.1 - - - +
74B ILE* 1.3 78.4 - - - +
76B LEU* 1.3 59.5 + - - +
78B GLU* 3.3 5.4 + - - +
79B GLU* 3.0 55.5 + - - +
13D PRO* 4.2 25.0 - - + +
16D SER* 4.3 17.0 + - - -
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Residues in contact with LEU 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B GLU 2.9 21.0 + - - +
73B GLU* 4.0 8.5 - - - +
75B GLN* 1.3 72.7 - - - +
77B GLY* 1.3 64.8 + - - +
79B GLU* 3.3 16.4 + - + +
80B LEU* 2.9 52.0 + - + +
92B HIS* 3.6 33.9 - - + +
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Residues in contact with GLY 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B GLU 2.8 18.7 + - - -
76B LEU* 1.3 77.0 - - - +
78B GLU* 1.3 61.1 + - - +
80B LEU 3.5 0.2 + - - -
81B LEU* 3.1 28.9 + - - +
89B GLY* 3.5 27.8 - - - -
92B HIS* 3.8 7.1 - - - +
93B LEU* 3.9 9.4 - - - -
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Residues in contact with GLU 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B ILE 3.1 16.1 + - - +
75B GLN* 3.7 5.6 - - - +
77B GLY* 1.3 75.2 - - - +
79B GLU* 1.3 64.0 + - - +
81B LEU* 3.3 24.4 + - - +
82B ALA* 3.2 22.2 + - - +
93B LEU* 4.2 7.1 - - - +
110B LEU* 4.9 2.6 - - - +
113B THR* 5.4 2.3 + - - -
114B LEU* 4.6 6.5 - - - +
12D GLY 4.5 4.9 - - - +
13D PRO* 5.0 9.6 - - + +
15D LEU* 3.5 44.9 - - + +
16D SER 4.9 3.6 - - - +
19D LEU* 3.5 27.4 - - - +
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Residues in contact with GLU 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B GLN* 3.0 51.3 + - + +
76B LEU* 3.6 22.6 + - + +
78B GLU* 1.3 75.5 - - - +
80B LEU* 1.3 62.3 + - + +
82B ALA* 3.3 16.0 + - - +
83B GLN* 3.4 23.2 + - - +
13D PRO* 4.1 25.0 - - + +
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Residues in contact with LEU 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B LEU* 2.9 43.5 + - + +
79B GLU* 1.3 75.0 - - + +
81B LEU* 1.3 65.3 + - - +
83B GLN* 3.2 24.8 + - - +
85B ASP* 2.8 48.6 + - + +
88B LYS* 3.9 16.6 - - + -
89B GLY* 3.8 14.4 - - - +
92B HIS* 3.5 27.6 - - + +
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Residues in contact with LEU 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B GLY 3.1 17.9 + - - +
78B GLU* 3.3 26.7 + - - +
80B LEU* 1.3 75.6 - - - +
82B ALA* 1.3 58.8 + - - +
84B GLY* 2.9 20.1 + - - +
85B ASP 4.4 2.5 - - - +
86B TYR* 3.8 54.2 + - + +
89B GLY* 4.3 7.0 - - - -
90B VAL* 4.3 3.1 - - + +
93B LEU* 3.7 15.9 - - + -
114B LEU* 3.6 25.6 - - + -
118B VAL* 4.2 12.3 - - + -
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Residues in contact with ALA 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B GLU 3.2 12.6 + - - +
79B GLU* 3.5 12.6 - - - +
80B LEU 3.2 0.2 - - - -
81B LEU* 1.3 76.4 - - - +
83B GLN* 1.3 60.3 + - + +
84B GLY 3.3 0.8 + - - -
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Residues in contact with GLN 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B GLU* 3.4 15.7 - - - +
80B LEU* 3.2 33.7 + - - +
81B LEU 3.1 0.4 - - - -
82B ALA* 1.3 79.2 - - + +
84B GLY* 1.3 60.6 + - - +
85B ASP* 3.5 6.8 + - + +
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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
------------------------------------------------------------
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