Contacts of the helix formed by residues 56 - 70 (chain B) in PDB entry 2VF8
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 56 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B VAL* 5.7 1.6 - - + -
21B ALA* 4.3 10.8 - - + -
23B GLN* 3.3 21.2 - - + +
26B LEU* 3.8 2.8 - - - +
51B SER 2.6 25.9 + - - -
52B LEU* 3.1 16.9 + - - -
54B PHE 2.7 6.6 + - - -
55B GLY* 1.3 71.3 - - - +
57B LEU* 1.3 69.8 + - - +
60B GLU* 3.0 25.8 + - - +
83B PRO* 4.6 7.4 - - + +
84B ASP 4.9 1.6 - - - +
85B VAL* 3.8 35.7 - - + -
88B ILE* 4.9 4.0 - - + -
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Residues in contact with LEU 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B VAL* 4.1 16.4 - - + -
18B VAL* 3.8 28.3 - - + -
33B VAL* 4.8 7.2 - - + -
41B PHE* 3.9 18.8 - - + -
52B LEU* 2.6 51.0 + - + +
53B ALA* 3.5 16.4 - - - +
56B THR* 1.3 72.8 - - - +
58B TYR* 1.4 70.1 + - - +
60B GLU 3.3 0.2 + - - -
61B ALA* 3.1 14.8 + - - -
88B ILE* 4.6 12.8 - - + -
91B LEU* 3.4 16.8 - - + +
435B PHE* 3.9 25.8 - - + -
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Residues in contact with TYR 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A VAL* 5.6 1.4 - - + +
53B ALA 3.1 18.0 + - - +
54B PHE* 3.7 20.6 - + + +
57B LEU* 1.4 77.5 - - - +
59B ALA* 1.4 69.5 + - + +
61B ALA* 2.6 25.5 + - - +
62B GLN* 2.9 56.7 + - + +
94B ALA* 3.5 33.9 - - + -
95B VAL* 4.3 0.2 - - - -
96B ALA* 3.5 42.7 + - + +
404B VAL* 3.9 15.3 - - + +
435B PHE* 5.5 0.6 - - - -
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Residues in contact with ALA 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B PHE 3.2 8.8 + - - +
55B GLY* 3.2 31.0 - - - +
56B THR 3.8 0.4 - - - +
58B TYR* 1.4 87.2 - - + +
60B GLU* 1.3 58.4 + - - +
62B GLN* 3.8 5.2 + - - +
63B ARG* 3.1 23.7 + - - +
74B ARG* 5.7 0.7 + - - -
83B PRO* 4.0 12.3 - - + +
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Residues in contact with GLU 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B THR 3.0 19.5 + - - +
57B LEU 3.7 2.7 - - - +
59B ALA* 1.3 73.7 - - - +
61B ALA* 1.3 66.5 + - - +
63B ARG* 2.8 34.6 + - - -
64B ARG* 3.0 54.8 + - - +
83B PRO* 3.6 27.1 - - + +
85B VAL* 4.4 10.6 - - - +
88B ILE* 3.7 23.8 - - + -
91B LEU* 4.3 1.6 - - + -
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Residues in contact with ALA 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A TYR* 5.8 0.2 - - - -
398A LEU* 5.1 0.3 - - - +
57B LEU 3.1 6.3 + - - +
58B TYR 2.6 17.3 + - - +
60B GLU* 1.3 72.0 - - - +
62B GLN* 1.3 55.7 + - - +
64B ARG* 3.7 5.9 + - - +
65B TYR* 2.9 29.7 + - - +
91B LEU* 3.6 24.8 - - + +
92B PRO 3.6 17.9 - - - +
93B PRO* 4.2 2.9 - - + +
94B ALA* 3.6 25.8 - - + +
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Residues in contact with GLN 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A TYR* 4.7 5.9 + - - +
69A VAL* 4.1 27.0 - - - +
58B TYR* 2.9 52.8 + - + +
59B ALA* 3.9 7.1 + - - +
61B ALA* 1.3 72.6 - - + +
63B ARG* 1.3 69.3 + - - +
64B ARG 3.0 1.8 - - - -
65B TYR* 2.7 16.5 + - - +
66B LEU* 2.9 30.2 + - + +
74B ARG* 5.6 1.1 - - - +
94B ALA 5.0 4.3 - - - +
657B LEU* 3.9 22.7 - - - +
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Residues in contact with ARG 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A SER 5.6 2.2 + - - -
59B ALA 3.1 16.7 + - - +
60B GLU* 2.8 41.6 + - - +
62B GLN* 1.3 79.1 - - - +
64B ARG* 1.3 73.0 + - - +
67B GLU* 2.9 59.0 + - - +
74B ARG* 3.6 33.1 - - - +
75B ARG* 4.3 7.5 - - - +
78B ASN* 5.4 4.3 - - - +
81B GLY 3.3 24.2 - - - +
83B PRO* 4.2 10.5 - - + -
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Residues in contact with ARG 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A SER 3.6 21.5 - - - +
397A ASN* 3.5 38.7 + - + +
398A LEU* 3.6 17.9 - - + +
60B GLU* 3.0 55.8 + - - +
61B ALA* 3.9 4.5 - - - +
62B GLN 3.0 0.8 - - - -
63B ARG* 1.3 86.3 - - - +
65B TYR* 1.3 64.3 + - - +
67B GLU* 3.9 4.1 - - - +
68B SER* 3.0 27.5 + - - -
88B ILE* 2.9 36.8 + - - +
91B LEU* 4.1 29.4 + - - +
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Residues in contact with TYR 65 (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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62A GLN* 4.0 11.4 + - - -
65A TYR* 3.4 48.0 - + - +
66A LEU* 6.4 0.7 - - + -
93A PRO* 4.0 19.6 - - + +
94A ALA 3.0 25.1 + - - -
95A VAL* 3.7 23.8 - - + -
398A LEU* 3.6 10.8 - - + -
401A VAL* 4.4 10.5 - - + -
61B ALA 2.9 19.4 + - - +
62B GLN* 2.7 11.9 + - - +
64B ARG* 1.3 75.4 - - - +
66B LEU* 1.3 70.3 + - + +
68B SER* 3.5 2.4 + - - -
69B VAL* 3.2 32.0 + - + +
93B PRO* 4.2 16.2 - - + -
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Residues in contact with LEU 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A TYR* 5.4 5.4 - - + -
66A LEU* 5.6 9.2 - - + -
69A VAL* 5.6 5.4 - - + -
62B GLN* 2.9 31.2 + - + +
65B TYR* 1.3 90.0 - - + +
67B GLU* 1.3 65.7 + - - +
68B SER 3.0 1.3 - - - -
69B VAL* 2.9 9.0 + - + +
70B SER* 2.8 29.4 + - - +
74B ARG* 3.6 28.5 - - + +
655B LEU* 5.8 2.0 - - + -
657B LEU* 3.8 42.4 - - + -
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Residues in contact with GLU 67 (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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63B ARG* 2.9 63.1 + - - +
64B ARG* 3.9 2.8 - - - +
65B TYR 3.4 0.2 - - - -
66B LEU* 1.3 79.7 - - - +
68B SER* 1.3 59.0 + - - +
71B PRO* 3.0 31.9 - - - +
74B ARG* 3.7 29.9 + - - -
75B ARG* 3.0 54.6 + - + +
78B ASN* 4.3 6.2 + - - +
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Residues in contact with SER 68 (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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95A VAL* 3.4 8.6 - - - +
389A ARG* 3.1 27.5 + - - -
393A GLN* 2.9 37.5 + - - +
396A SER* 3.9 7.6 + - - -
398A LEU* 3.7 19.0 - - - +
64B ARG 3.0 18.6 + - - -
65B TYR 3.8 4.7 - - - -
66B LEU 3.0 0.6 - - - -
67B GLU* 1.3 78.9 - - - +
69B VAL* 1.3 59.0 + - - +
71B PRO* 4.0 3.5 - - - +
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Residues in contact with VAL 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A TYR* 4.3 14.8 + - - +
62A GLN* 4.6 12.8 - - - +
66A LEU* 6.2 4.5 - - + -
94A ALA 3.9 10.8 - - - +
95A VAL* 3.7 35.2 - - + -
96A ALA 5.0 0.9 - - - +
389A ARG* 5.1 1.5 + - - +
65B TYR* 3.2 28.2 + - + +
66B LEU* 2.9 12.6 + - + +
68B SER* 1.3 77.5 - - - +
70B SER* 1.3 60.6 + - - +
71B PRO* 3.7 4.0 - - - +
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Residues in contact with SER 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
658A PRO* 6.0 6.7 - - - -
66B LEU* 2.8 17.9 + - - +
67B GLU 3.8 1.8 - - - -
69B VAL* 1.3 77.3 - - - +
71B PRO* 1.4 53.9 - - - +
72B TYR* 2.5 22.0 + - - -
73B ALA* 2.5 39.1 + - - +
74B ARG* 3.4 13.5 + - - +
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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