Contacts of the helix formed by residues 8 - 18 (chain G) in PDB entry 1V8O
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 8 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6G LEU 4.0 0.8 + - - -
7G VAL* 1.3 74.4 - - - +
9G ALA* 1.3 54.9 + - - +
10G SER* 2.7 26.2 + - - -
11G ALA* 2.9 7.1 + - - +
12G LEU* 2.8 34.8 + - - +
35G THR* 3.8 4.0 - - - -
92G ASP* 5.5 0.2 - - - +
95G TYR* 3.4 40.9 - - + -
106G LEU* 4.7 2.6 - - + +
107G VAL 3.3 7.4 + - - +
108G THR* 2.5 33.2 + - - -
110G ASP* 5.0 0.9 - - - +
113G LEU* 3.7 11.3 - - - +
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Residues in contact with ALA 9 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8G ASP* 1.3 74.5 + - - +
10G SER* 1.3 60.4 + - - +
11G ALA 3.0 1.8 - - - -
12G LEU* 3.5 7.4 - - - +
13G TYR* 2.8 35.1 + - - +
35G THR* 3.8 8.1 - - + +
38G GLU* 3.4 38.6 + - + +
39G ALA* 4.2 12.5 - - - +
95G TYR* 3.8 2.4 + - - -
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Residues in contact with SER 10 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49E LEU* 4.0 23.1 - - - -
8G ASP* 2.7 28.1 + - - -
9G ALA* 1.3 75.5 - - - +
11G ALA* 1.3 61.2 + - - +
13G TYR* 3.7 6.6 + - - +
14G ALA* 3.4 16.8 + - - +
108G THR* 3.3 1.2 + - - -
109G GLN* 2.9 41.9 + - - +
110G ASP* 3.7 2.8 + - - +
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Residues in contact with ALA 11 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7G VAL* 3.4 15.7 - - + -
8G ASP* 2.9 7.5 + - - +
10G SER* 1.3 75.9 + - - +
12G LEU* 1.3 68.7 + - - +
14G ALA* 2.7 16.3 + - - +
15G LEU* 2.8 15.2 + - + +
107G VAL* 3.3 34.5 - - + +
108G THR* 4.0 1.3 - - - -
109G GLN 4.7 0.4 - - - +
123G VAL* 3.5 23.6 - - + -
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Residues in contact with LEU 12 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7G VAL* 3.4 7.1 - - + +
8G ASP 2.8 22.9 + - - +
9G ALA* 3.5 9.0 - - - +
11G ALA* 1.3 71.4 - - - +
13G TYR* 1.3 66.4 + - + +
15G LEU* 3.3 3.2 + - - +
16G ALA* 3.0 21.4 + - + +
31G ILE* 4.6 4.3 - - + -
35G THR* 4.4 4.5 - - + -
39G ALA* 4.2 8.7 - - + -
61G LEU* 3.8 23.8 - - + -
64G VAL* 4.3 6.7 - - + -
65G MSE 3.1 31.2 - - + -
68G PHE* 3.3 43.1 - - + -
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Residues in contact with TYR 13 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9G ALA 2.8 21.2 + - - +
10G SER* 3.8 7.4 - - - +
12G LEU* 1.3 85.2 - - + +
14G ALA* 1.3 62.2 + - - +
16G ALA* 3.4 17.6 + - + +
17G ALA* 3.9 4.0 + - - +
39G ALA* 4.3 15.3 - - + -
42G ALA* 4.2 23.8 - - + -
43G LEU* 3.5 19.6 + - + +
46G GLU* 3.4 39.2 + - - +
51G ARG* 4.7 3.9 + - - -
61G LEU* 4.8 11.7 - - + -
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Residues in contact with ALA 14 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10G SER 3.4 5.0 + - - +
11G ALA 2.7 12.8 + - - +
13G TYR* 1.3 75.8 - - - +
15G LEU* 1.3 61.6 + - - +
17G ALA* 3.2 21.6 + - - +
18G HIS* 3.7 11.2 + - + +
109G GLN* 3.6 26.7 - - - +
123G VAL* 3.9 14.1 - - + -
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Residues in contact with LEU 15 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7G VAL* 4.0 31.2 - - + -
11G ALA* 2.8 13.4 + - + +
12G LEU* 3.7 8.1 - - - +
14G ALA* 1.3 70.3 - - - +
16G ALA* 1.3 63.1 + - - +
17G ALA 2.9 5.2 - - - -
18G HIS* 2.9 14.1 + - - +
22G TRP* 2.6 49.8 + - + +
29G LEU* 5.0 2.9 - - + -
68G PHE* 4.5 13.0 - - + -
107G VAL* 5.2 0.2 - - + -
123G VAL* 3.5 23.8 - - + -
126G LEU* 3.9 26.0 - - + -
127G LEU* 4.0 15.7 - - + -
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Residues in contact with ALA 16 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12G LEU* 3.0 15.9 + - + +
13G TYR* 3.4 16.6 - - + +
15G LEU* 1.3 76.7 - - - +
17G ALA* 1.3 59.9 + - - +
19G TYR* 3.8 9.8 + - - +
22G TRP* 4.5 1.5 - - - -
60G HIS* 3.7 24.8 + - + +
61G LEU* 5.4 6.1 - - + -
64G VAL* 4.2 30.0 - - + +
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Residues in contact with ALA 17 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13G TYR 3.9 3.5 + - - +
14G ALA* 3.2 14.7 + - - +
15G LEU 2.9 0.6 - - - -
16G ALA* 1.3 80.1 - - - +
18G HIS* 1.3 70.4 + - + +
19G TYR* 3.2 6.1 + - - +
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Residues in contact with HIS 18 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14G ALA* 3.7 18.6 + - - +
15G LEU* 2.9 10.0 + - - +
17G ALA* 1.3 83.0 + - + +
19G TYR* 1.3 68.1 + - - +
20G ASP* 3.5 1.6 - - - -
21G LYS* 3.3 47.6 + - + +
22G TRP* 2.9 13.4 - - + -
123G VAL* 5.0 3.8 - - + -
127G LEU* 3.3 31.8 - - + +
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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
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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