Contacts of the strand formed by residues 93 - 98 (chain V) in PDB entry 3J7Y
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 THR 93 (chain V).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68V LYS* 4.5 13.5 + - - +
69V ASP* 4.2 11.4 + - - +
90V GLY* 3.2 37.1 + - - +
91V LEU 3.9 1.3 - - - +
92V ASN* 1.3 77.7 - - - +
94V HIS* 1.3 60.7 + - - +
95V TYR* 5.1 12.5 + - - -
110V PRO* 4.1 26.9 - - + +
111V SER 3.3 9.2 - - - +
112V GLU* 4.3 8.3 - - + -
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Residues in contact with HIS 94 (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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1801A A 4.8 2.0 - - - -
1802A A 3.3 35.0 + + + +
1805A A 3.1 46.1 + - - -
68V LYS* 4.6 14.4 - - + +
92V ASN 4.1 1.3 - - - -
93V THR* 1.3 75.1 - - - +
95V TYR* 1.3 67.9 + - - +
110V PRO* 4.6 0.2 - - - -
111V SER* 2.6 57.0 + - - -
112V GLU 4.6 0.2 - - - -
113V ALA* 3.5 33.0 + - + +
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Residues in contact with TYR 95 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1805A A 4.1 11.7 + - - -
1806A U 4.5 0.3 + - - -
93V THR* 5.1 11.2 + - - -
94V HIS* 1.3 84.7 + - - +
96V ARG* 1.3 60.4 + - - +
97V TYR* 4.2 5.8 + - - -
108V MET* 3.4 24.9 - - + +
109V ILE 3.3 16.4 - - - +
110V PRO* 3.9 14.6 - - + -
111V SER* 4.5 0.4 - - - -
161d HIS* 3.0 65.6 + + + +
166d GLU* 3.6 24.8 + - + -
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Residues in contact with ARG 96 (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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1804A A 2.9 54.7 + - - -
1805A A 3.6 20.9 - - - +
1806A U 3.5 26.7 - - - +
94V HIS 3.9 0.4 + - - -
95V TYR* 1.3 72.8 - - - +
97V TYR* 1.3 68.9 + - - +
98V ILE* 3.2 35.2 + - - +
108V MET* 4.7 1.1 - - - -
109V ILE* 2.8 64.7 + - + +
111V SER* 3.8 18.6 - - - +
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Residues in contact with TYR 97 (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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1806A U 3.9 18.6 + - - +
95V TYR 5.0 5.6 - - - -
96V ARG* 1.3 85.8 - - - +
98V ILE* 1.3 59.7 + - - +
100V LYS* 4.9 20.5 - - + +
105V ARG* 3.4 31.4 - - + +
106V GLY 5.3 0.2 - - - -
107V THR 3.5 6.1 - - - -
108V MET* 3.3 45.1 - - + +
169d PHE* 4.1 7.6 - - - -
170d PRO* 3.7 26.8 - - + +
173d THR* 4.5 2.9 + - - -
174d TRP* 5.8 7.2 - + - +
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Residues in contact with ILE 98 (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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96V ARG* 3.2 39.3 - - - +
97V TYR* 1.3 76.0 - - - +
99V GLY* 1.3 70.5 + - - +
100V LYS* 3.4 3.8 + - - -
106V GLY* 3.6 1.0 - - - -
107V THR* 2.8 62.8 + - + +
109V ILE* 3.7 23.8 - - + -
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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