Contacts of the strand formed by residues 3 - 8 (chain V) in PDB entry 3SDI
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 3 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1V THR* 3.8 15.5 - - + -
2V THR* 1.3 78.5 - - - +
4V VAL* 1.3 65.9 + - - +
15V ALA 3.4 6.7 - - - +
16V ALA* 3.6 18.6 - - + -
33V LYS* 4.9 2.0 - - + -
44V ALA* 3.4 42.4 - - + +
45V GLY* 3.9 15.9 - - - +
46V ALA* 4.1 4.9 - - + +
100V ILE* 3.8 8.7 - - + +
126V SER* 3.0 6.6 - - - -
127V LEU* 2.9 63.7 + - + +
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Residues in contact with VAL 4 (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* 1.3 80.9 - - - +
5V GLY* 1.3 60.1 + - - +
6V VAL* 4.7 1.3 - - + -
14V ILE* 3.3 7.1 - - - +
15V ALA* 3.0 35.2 + - + +
44V ALA* 5.9 0.3 - - - +
100V ILE* 4.0 7.2 - - - +
125V LEU 3.2 13.2 - - - +
126V SER* 3.9 2.0 - - - -
134V ALA* 3.8 27.6 - - + -
138V LEU* 4.1 7.4 - - + -
155V ALA* 3.5 41.5 - - + +
158V ALA* 3.9 10.3 - - + -
159V ILE* 3.7 15.4 - - + +
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Residues in contact with GLY 5 (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 VAL* 1.3 74.7 - - - +
6V VAL* 1.3 65.5 + - - +
13V VAL 3.3 9.4 - - - -
14V ILE* 4.0 4.9 - - - -
100V ILE* 4.0 5.2 - - - +
110V LEU* 3.6 24.6 - - - +
124V TYR* 3.2 4.2 - - - -
125V LEU 2.9 31.7 + - - +
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Residues in contact with VAL 6 (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 VAL* 4.7 2.9 - - + -
5V GLY* 1.3 80.4 - - - +
7V LYS* 1.3 69.2 + - - +
12V VAL* 4.0 3.4 - - - -
13V VAL* 2.7 52.9 + - + +
110V LEU* 4.0 0.8 - - - +
123V TYR 3.7 2.2 - - - -
124V TYR* 4.5 3.8 - - + -
138V LEU* 3.8 28.5 - - + -
142V TRP* 4.2 6.5 - - + -
146V LEU* 4.2 9.6 - - + -
151V ALA* 4.2 13.9 - - + -
154V LEU* 4.0 19.5 - - + -
155V ALA* 4.1 20.0 - - + +
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Residues in contact with LYS 7 (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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6V VAL* 1.3 76.3 - - - +
8V PHE* 1.3 62.7 + - - +
11V GLY 3.7 14.1 - - - +
12V VAL* 4.2 4.9 - - + -
108V SER* 3.3 37.7 + - - +
109V HIS* 3.9 7.1 + - - +
110V LEU* 3.8 28.5 + - + +
121V VAL* 5.6 6.3 - - - +
122V GLY 4.1 9.6 + - - +
123V TYR* 2.8 53.7 + - + +
142V TRP* 3.9 19.2 + - - -
146V LEU* 4.4 3.8 + - - +
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Residues in contact with PHE 8 (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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7V LYS* 1.3 78.0 - - - +
9V ASN* 1.3 86.0 + - - +
10V ASN 3.0 8.1 + - - -
11V GLY* 3.0 37.9 + - - +
12V VAL* 3.3 28.9 - - - -
13V VAL* 4.1 5.4 - - + -
108V SER* 4.9 1.4 + - - -
145V ASP* 5.6 0.2 - - - -
146V LEU* 3.5 17.9 - - + +
147V THR 3.9 0.9 - - - +
148V LYS* 3.7 30.1 - - + -
151V ALA* 3.7 32.3 - - + -
177V VAL* 4.0 24.5 - - + -
178V MET 4.2 3.1 - - - -
179V GLU* 4.2 15.3 - - + -
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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