Contacts of the helix formed by residues 35 - 43 (chain C) in PDB entry 1V14
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 PRO 35 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C LYS 3.5 7.6 - - - +
18C VAL* 3.9 22.9 - - + -
22C TRP* 3.6 31.6 - - + -
33C PRO 3.6 7.4 - - - +
34C ILE* 1.3 94.4 - - + +
36C ASP* 1.3 59.7 + - - +
37C ARG* 4.4 2.5 - - + +
38C ILE* 3.2 27.2 + - + +
39C ALA* 2.8 26.2 + - - +
57C VAL* 6.4 0.4 - - + -
67C LEU* 3.9 13.9 - - + -
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Residues in contact with ASP 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C LYS 4.0 12.3 - - - +
15C GLY 4.1 0.7 - - - -
16C LYS* 3.1 32.6 + - - +
17C PRO* 3.8 25.7 - - + +
35C PRO* 1.3 73.0 - - - +
37C ARG* 1.3 74.3 + - - +
39C ALA* 3.5 0.7 + - - +
40C ASP* 2.8 44.6 + - - +
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Residues in contact with ARG 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C VAL 5.4 5.1 + - - -
35C PRO* 3.3 3.7 - - + +
36C ASP* 1.3 90.1 + - - +
38C ILE* 1.3 61.6 + - - +
40C ASP* 3.3 23.6 + - + +
41C LYS* 3.3 13.5 + - - +
64C ASP* 2.6 49.7 + - - +
66C GLU* 3.9 18.5 - - - +
67C LEU* 4.1 9.6 - - + +
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Residues in contact with ILE 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C ILE* 3.8 17.5 - - + -
35C PRO* 3.2 23.0 + - + +
37C ARG* 1.3 75.5 - - - +
39C ALA* 1.3 60.4 + - - +
41C LYS* 3.0 22.7 + - + +
42C LEU* 3.4 23.7 + - + +
57C VAL* 4.0 20.0 - - + +
60C GLU* 3.5 42.8 - - + +
61C VAL* 3.6 13.5 - - + +
64C ASP* 5.3 0.7 - - - +
67C LEU* 3.6 26.2 - - + -
116C MET* 5.5 1.3 - - - -
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Residues in contact with ALA 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C LYS* 3.2 36.3 - - - +
15C GLY* 3.6 4.9 - - - +
34C ILE* 4.4 3.4 - - + -
35C PRO 2.8 16.6 + - - +
36C ASP 3.8 0.9 - - - +
37C ARG 3.4 0.2 - - - -
38C ILE* 1.3 77.3 - - - +
40C ASP* 1.3 60.7 + - - +
42C LEU 4.2 0.2 - - - -
43C ARG* 3.4 30.7 + - - +
116C MET* 3.8 26.0 - - + +
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Residues in contact with ASP 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C LYS 4.2 4.3 - - - +
36C ASP* 2.8 35.6 + - - +
37C ARG* 3.3 17.4 - - + +
38C ILE 3.1 0.2 - - - -
39C ALA* 1.3 77.2 - - - +
41C LYS* 1.3 66.3 + - + +
43C ARG* 2.9 33.5 + - - +
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Residues in contact with LYS 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C ARG 3.3 10.5 + - - +
38C ILE* 3.0 11.5 + - - +
40C ASP* 1.3 83.2 - - + +
42C LEU* 1.3 63.8 + - - +
43C ARG 3.6 3.8 + - - +
45C LYS* 4.0 19.1 + - - +
60C GLU* 2.7 57.9 + - + +
63C LYS* 5.0 5.9 - - - +
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Residues in contact with LEU 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C ALA* 3.5 8.0 - - + +
38C ILE* 3.4 19.7 + - + +
41C LYS* 1.3 80.2 - - + +
43C ARG* 1.3 67.8 + - - +
45C LYS* 2.9 41.4 + - + +
47C PHE* 4.1 22.2 - - + -
53C PHE* 4.7 4.0 - - + -
56C ALA* 3.8 31.4 - - + +
57C VAL* 3.9 26.0 - - + -
60C GLU* 4.0 19.1 - - + +
116C MET* 3.9 16.2 - - + -
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Residues in contact with ARG 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C ALA 3.4 13.7 - - - +
12C THR* 4.8 3.4 - - - -
13C GLY 3.0 29.0 + - - +
14C LYS* 3.0 31.8 + - - +
39C ALA 3.4 20.5 + - - +
40C ASP* 2.9 39.5 + - - +
41C LYS 3.4 5.5 - - - +
42C LEU* 1.3 77.5 - - - +
44C ASP* 1.3 81.2 + - - +
45C LYS* 3.0 8.5 + - - +
116C MET* 3.6 4.2 - - + +
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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