Contacts of the strand formed by residues 92 - 97 (chain I) in PDB entry 6A3V
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 PHE 92 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90I GLY 3.5 23.1 - - - -
91I MET* 1.3 79.6 - - - +
93I ALA* 1.3 67.1 + - - +
119I SER* 3.1 28.5 - - - -
121I THR* 2.8 46.3 + - + -
124I LEU* 3.8 9.2 - - - +
237I LEU* 3.2 16.8 - - - +
238I PHE* 3.5 15.7 - - + +
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Residues in contact with ALA 93 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92I PHE* 1.3 77.1 - - - +
94I GLN* 1.3 61.5 + - - +
95I LEU* 5.3 1.3 - - + -
119I SER* 3.2 8.7 - - - -
120I LEU* 3.7 23.8 - - + -
124I LEU* 3.8 16.8 - - + -
133I LEU* 4.5 12.3 - - + -
144I PHE* 5.3 0.2 - - - -
236I GLY* 3.4 0.9 - - - -
237I LEU* 2.6 49.1 + - + +
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Residues in contact with GLN 94 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93I ALA* 1.3 74.7 - - - +
95I LEU* 1.3 72.0 + - - +
117I GLY* 3.2 25.3 + - - +
118I VAL* 3.4 4.5 - - - +
119I SER* 2.6 48.0 + - - +
144I PHE* 3.5 28.1 - - - -
234I VAL* 3.6 26.3 - - + +
235I LEU 3.6 4.3 - - - -
236I GLY* 4.2 0.2 - - - -
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Residues in contact with LEU 95 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93I ALA* 5.3 0.2 - - + -
94I GLN* 1.3 86.7 - - - +
96I VAL* 1.3 64.0 + - - +
109I TRP* 3.7 37.2 - - + -
110I TYR 3.7 15.5 - - - +
111I SER* 4.0 15.7 - - - -
118I VAL* 4.7 0.4 - - - -
119I SER 4.8 0.2 - - - +
120I LEU* 4.2 19.1 - - + -
126I TYR* 4.4 9.6 - - + -
133I LEU* 4.0 40.4 - - + -
234I VAL* 3.3 8.2 - - - +
235I LEU* 2.8 40.5 + - + +
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Residues in contact with VAL 96 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95I LEU* 1.3 75.4 - - - +
97I ALA* 1.3 72.9 + - - +
98I GLN 3.3 0.5 + - - -
109I TRP* 3.3 5.0 - - - -
110I TYR* 3.1 42.4 + - + -
117I GLY* 4.0 21.3 - - - +
118I VAL* 3.7 23.5 - - + +
231I GLY* 3.6 32.8 - - - +
233I THR 3.7 6.5 - - - +
234I VAL* 4.0 14.1 - - + -
64J ILE* 4.2 10.3 - - + -
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Residues in contact with ALA 97 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96I VAL* 1.3 77.0 - - - +
98I GLN* 1.3 62.8 + - - +
99I ASN 3.4 13.3 - - - +
107I LEU* 4.5 9.9 - - + -
108I SER 3.6 2.2 - - - +
109I TRP* 3.4 19.6 - - + -
110I TYR* 3.8 7.0 - - - -
228I LEU* 5.2 1.8 - - + -
230I GLN* 5.8 0.9 - - - -
231I GLY 4.9 5.5 + - - -
233I THR* 2.8 45.3 + - + +
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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