Contacts of the helix formed by residues 59 - 72 (chain B) in PDB entry 1V1A
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 59 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100A ARG* 4.6 5.4 - - - +
102A PHE* 3.7 28.8 - - + +
104A TYR* 4.0 6.2 + - - -
57B GLY 3.1 2.4 + - - -
58B GLU* 1.3 78.4 - - - +
60B GLU* 1.3 63.4 + - - +
61B LEU* 4.0 6.1 - - - +
62B GLY 2.8 31.0 + - - -
63B ALA 3.4 5.5 + - - -
81B ARG* 2.6 25.6 + - - +
84B GLY 4.8 1.1 - - - +
85B PHE* 3.3 11.4 - - + +
86B THR* 2.7 36.7 + - - -
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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
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21A HIS* 3.6 7.4 - - - +
22A LEU* 3.2 29.0 + - + -
23A ARG* 2.6 78.0 + - - +
92A GLU* 2.8 29.2 - - - +
100A ARG* 4.0 10.1 + - - +
102A PHE* 3.5 24.1 - - + -
59B ASP* 1.3 75.8 - - - +
61B LEU* 1.3 64.0 + - + +
63B ALA* 3.4 3.2 + - - +
64B MET* 3.2 15.6 + - - +
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Residues in contact with LEU 61 (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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22A LEU* 4.6 12.3 - - + -
28A LEU* 6.3 1.1 - - + -
90A LEU* 4.3 21.3 - - + -
104A TYR* 3.9 19.5 - - + +
12B VAL* 3.6 36.9 - - + +
30B VAL* 5.1 1.6 - - + -
59B ASP* 3.3 4.7 + - - +
60B GLU* 1.3 76.3 - - + +
62B GLY* 1.3 65.3 + - - +
63B ALA 3.1 2.0 - - - -
64B MET* 2.9 38.8 + - + +
65B VAL* 3.0 17.0 + - - +
86B THR* 3.9 15.0 - - + +
88B LEU* 4.0 19.7 - - + -
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Residues in contact with GLY 62 (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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56B VAL* 3.5 25.8 - - - +
57B GLY 3.8 3.6 - - - -
59B ASP* 2.8 17.3 + - - -
61B LEU* 1.3 72.5 - - - +
63B ALA* 1.3 57.8 + - - +
65B VAL* 3.5 1.6 + - - +
66B GLU* 3.1 27.2 + - - +
81B ARG* 3.8 6.5 - - - -
86B THR* 3.0 20.0 + - - -
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Residues in contact with ALA 63 (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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23A ARG* 3.6 38.8 - - - +
59B ASP 3.4 12.3 + - - +
60B GLU 3.4 10.3 - - - +
61B LEU 3.1 0.6 - - - -
62B GLY* 1.3 76.9 - - - +
64B MET* 1.3 60.9 + - - +
66B GLU* 3.7 7.2 + - - +
67B GLU* 3.0 32.9 + - - +
70B ARG* 5.2 0.2 + - - -
81B ARG* 3.8 14.3 - - - +
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Residues in contact with MET 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LEU* 3.8 11.2 - - + +
23A ARG* 3.5 29.8 - - - +
25A LYS 3.7 19.1 - - - +
26A ARG* 3.6 17.0 - - - +
12B VAL* 4.3 12.3 - - + -
30B VAL* 3.8 28.9 - - + +
31B TYR 5.1 2.2 - - - +
32B VAL* 4.2 15.3 - - + -
60B GLU 3.2 8.0 + - - +
61B LEU* 2.9 27.7 + - + +
63B ALA* 1.3 74.5 - - - +
65B VAL* 1.3 65.2 + - - +
67B GLU* 3.3 9.1 + - - +
68B ARG* 3.1 21.3 + - - +
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Residues in contact with VAL 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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10B PRO* 3.6 29.4 - - + -
11B LEU 4.7 2.9 - - - +
12B VAL* 4.0 17.9 - - + -
32B VAL* 4.1 26.0 - - + +
37B VAL* 5.0 0.9 - - + -
56B VAL* 3.7 18.8 - - + -
61B LEU 3.0 15.2 + - - +
62B GLY 3.6 6.7 - - - +
64B MET* 1.3 76.0 - - - +
66B GLU* 1.3 63.2 + - - +
68B ARG* 3.1 5.0 + - - +
69B LEU* 3.0 35.9 + - + +
79B PHE* 4.3 0.4 - - + -
86B THR* 4.3 6.1 - - + -
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Residues in contact with GLU 66 (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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62B GLY 3.1 16.7 + - - +
63B ALA* 4.0 6.7 - - - +
64B MET 3.3 0.2 - - - -
65B VAL* 1.3 74.9 - - - +
67B GLU* 1.3 57.8 + - - +
69B LEU* 3.8 1.5 - - - +
70B ARG* 2.8 60.4 + - - +
76B LEU* 3.7 21.8 - - + +
79B PHE* 3.7 24.1 - - + +
80B ARG* 5.4 2.1 - - - -
81B ARG* 4.1 21.6 + - + +
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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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23A ARG* 3.1 41.6 + - - +
24A GLY* 5.9 0.9 - - - -
26A ARG* 5.8 0.5 + - - -
63B ALA 3.0 21.2 + - - +
64B MET* 3.3 7.1 + - - +
66B GLU* 1.3 76.5 - - - +
68B ARG* 1.3 55.6 + - - +
70B ARG* 3.7 26.0 + - - +
71B ALA* 2.7 38.2 + - + +
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Residues in contact with ARG 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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26A ARG* 4.9 12.1 - - - +
32B VAL* 4.0 27.6 - - + +
41B VAL* 4.4 5.8 - - + -
45B ARG* 4.4 3.0 - - - +
64B MET 3.1 11.5 + - - +
65B VAL 3.1 9.9 + - - +
67B GLU* 1.3 78.2 - - - +
69B LEU* 1.3 58.3 - - + +
71B ALA* 4.1 3.8 - - - +
72B GLU* 2.8 62.5 + - + +
288B HIS* 2.6 48.7 + - + +
289B GLU* 3.3 32.8 + - - -
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Residues in contact with LEU 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B VAL* 3.8 32.5 - - + -
40B ALA* 4.7 1.8 - - + -
41B VAL* 4.0 12.6 - - + -
52B PHE* 3.6 34.8 - - + -
65B VAL* 3.0 25.3 + - + +
66B GLU 3.9 3.1 - - - +
68B ARG* 1.3 77.1 - - + +
70B ARG* 1.3 59.9 + - - +
72B GLU* 3.5 3.2 + - - -
73B GLY 3.2 4.3 + - - -
74B VAL* 2.9 42.8 + - + +
76B LEU* 3.7 23.6 - - + -
79B PHE* 3.9 19.5 - - + -
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Residues in contact with ARG 70 (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 ALA 5.2 0.2 + - - -
66B GLU* 2.8 45.0 + - - +
67B GLU* 3.7 31.2 + - - +
69B LEU* 1.3 76.5 - - - +
71B ALA* 1.3 64.6 + - - +
73B GLY* 3.0 13.9 + - - +
74B VAL 4.8 3.4 - - - +
76B LEU* 4.2 12.5 - - + +
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Residues in contact with ALA 71 (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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67B GLU* 2.7 23.7 + - + +
68B ARG* 4.1 4.9 - - - +
70B ARG* 1.3 75.5 - - - +
72B GLU* 1.3 60.5 + - + +
73B GLY* 3.0 4.7 + - - -
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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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41B VAL* 3.5 27.8 - - + -
44B ALA* 3.4 18.7 - - + +
45B ARG* 2.6 50.2 + - - +
68B ARG* 2.8 47.2 + - - +
69B LEU 3.8 4.9 - - - +
70B ARG 3.2 0.2 - - - -
71B ALA* 1.3 76.5 - - + +
73B GLY* 1.3 64.9 + - - +
74B VAL* 4.2 4.5 - - + -
293B TYR* 4.3 7.6 + - - -
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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