Contacts of the strand formed by residues 12 - 17 (chain V) in PDB entry 5M32
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 ILE 12 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6V VAL 3.3 7.4 - - - +
7V VAL* 3.8 17.7 - - + -
8V TYR* 3.4 3.3 - - - -
11V GLY* 1.3 78.5 - - - +
13V VAL* 1.3 69.1 + - - +
14V LEU* 3.9 21.3 - - + +
101V GLY* 3.6 32.5 - - - -
102V GLY* 4.4 3.8 - - - +
103V VAL* 4.9 1.6 - - + -
108V PRO* 4.6 1.1 - - + -
109V HIS 4.4 18.2 - - - +
110V LEU* 3.9 19.3 - - + -
177V VAL* 3.6 0.2 - - - -
178V ILE* 2.9 62.9 + - + +
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Residues in contact with VAL 13 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5V GLY* 3.1 3.5 - - - -
6V VAL* 2.9 37.5 + - + +
8V TYR* 3.6 20.0 - - + -
12V ILE* 1.3 79.4 - - - +
14V LEU* 1.3 73.2 + - - +
148V GLU* 4.9 2.2 - - - +
151V ALA* 4.6 4.0 - - + -
152V LYS* 4.4 18.8 - - - +
155V VAL* 3.8 24.7 - - + +
175V LEU* 3.9 19.1 - - + -
176V CYS 3.3 8.7 - - - +
177V VAL* 3.9 15.9 - - + -
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Residues in contact with LEU 14 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4V ALA 3.4 5.4 - - - +
5V GLY* 4.1 14.8 - - - -
12V ILE* 3.9 24.2 - - + -
13V VAL* 1.3 78.4 - - - +
15V GLY* 1.3 61.2 + - - +
34V ILE* 4.4 7.9 - - + -
42V TYR* 3.3 42.4 - - + +
43V CYS 3.8 2.0 - - - +
44V CYS* 3.7 29.2 - - - -
99V VAL* 4.5 9.0 - - + -
100V LEU 5.0 0.7 - - - -
101V GLY 4.6 7.0 - - - +
110V LEU* 4.7 6.7 - - + -
155V VAL* 3.3 9.3 - - - +
175V LEU* 3.3 18.0 - - - +
176V CYS* 2.9 18.3 + - + +
178V ILE* 4.5 2.5 - - + -
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Residues in contact with GLY 15 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3V ILE* 3.6 3.6 - - - +
4V ALA 3.0 31.2 + - - +
14V LEU* 1.3 80.5 - - - +
16V ALA* 1.3 62.4 + - - +
34V ILE* 4.0 5.9 - - - +
44V CYS* 4.7 0.2 - - - -
155V VAL* 4.2 7.2 - - - -
159V ILE* 3.6 9.2 - - - +
174V ASP 3.5 11.9 - - - -
175V LEU* 3.8 7.4 - - - -
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Residues in contact with ALA 16 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2V THR 3.9 10.3 - - - +
3V ILE* 4.8 5.6 - - + -
15V GLY* 1.3 75.9 - - - +
17V ASP* 1.3 64.2 + - - +
33V LYS* 3.8 33.0 - - + -
34V ILE* 3.8 14.1 - - + +
159V ILE* 3.7 10.7 - - - +
173V ILE* 3.8 3.1 - - - -
174V ASP* 2.9 35.6 + - - +
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Residues in contact with ASP 17 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1V THR* 3.4 8.7 - - - -
2V THR* 3.0 31.9 + - - +
16V ALA* 1.3 75.6 - - - +
18V THR* 1.3 56.1 - - - +
19V ARG 5.0 0.4 - - - -
33V LYS* 2.6 34.6 + - - +
159V ILE* 3.6 11.2 - - + +
162V GLY 4.9 1.2 - - - +
163V ILE* 3.7 16.9 - - + +
168V GLY 3.0 24.6 - - - +
169V SER* 3.2 2.2 - - - -
170V GLY* 3.2 24.2 + - - -
172V ASN 3.9 5.2 - - - +
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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