Contacts of the strand formed by residues 93 - 98 (chain A) in PDB entry 3Q72
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 LYS 93 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91A VAL* 3.1 41.4 - - + +
92A TYR* 1.3 72.5 - - - +
94A VAL* 1.3 61.6 + - - +
95A LEU* 4.5 2.7 - - + -
141A MET* 3.6 10.8 - - + -
143A TYR* 3.2 39.7 - - + +
162A GLY* 3.8 7.4 - - - -
163A ASP* 2.8 43.9 + - - +
164A ALA 3.4 4.5 + - - -
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Residues in contact with VAL 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A TYR 3.8 11.7 - - - +
93A LYS* 1.3 79.4 - - - +
95A LEU* 1.3 69.7 + - - +
96A LEU* 3.8 7.4 + - + -
140A LEU* 4.1 17.0 - - + -
141A MET 3.0 10.4 + - - +
142A VAL* 4.4 6.5 - - + +
143A TYR* 2.8 29.8 + - - -
164A ALA* 3.5 10.1 - - + +
166A VAL* 3.7 30.7 - - + -
244A PHE* 4.6 7.6 - - + -
247A VAL* 3.8 26.9 - - + -
251A ILE* 4.8 2.0 - - + -
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Residues in contact with LEU 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A LYS* 4.5 1.1 - - + -
94A VAL* 1.3 84.2 - - - +
96A LEU* 1.3 62.9 + - - +
97A LEU* 3.6 12.7 + - + +
143A TYR* 3.6 29.4 - - + -
145A ILE* 4.4 11.2 - - + -
162A GLY* 4.1 25.8 - - - +
164A ALA 3.0 8.2 + - - +
165A TYR* 3.6 36.5 - - + +
166A VAL* 2.8 28.8 + - - +
191A ARG* 5.6 1.1 - - - +
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Residues in contact with LEU 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A VAL* 3.8 3.1 + - + -
95A LEU* 1.3 71.8 - - - +
97A LEU* 1.3 66.9 + - - +
104A LYS* 3.4 39.4 - - + +
107A LEU* 5.3 3.1 - - + -
108A ALA* 3.4 25.1 - - + +
142A VAL* 3.6 23.3 - - + -
143A TYR 2.8 17.7 + - - +
144A ASP* 4.0 13.1 - - - +
145A ILE* 3.5 17.0 + - - +
146A TRP* 4.6 0.2 - - - -
166A VAL* 3.7 33.7 - - + +
168A VAL* 4.9 6.5 - - + -
243A LEU* 6.1 0.2 - - + -
244A PHE* 4.5 8.7 - - + -
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Residues in contact with LEU 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A LEU* 4.0 19.1 - - + +
96A LEU* 1.3 79.6 - - - +
98A GLY* 1.3 59.9 + - - +
104A LYS* 3.6 11.3 - - - +
145A ILE* 3.2 34.3 - - + -
146A TRP* 4.8 4.3 - - - +
165A TYR* 3.3 33.9 - - + -
166A VAL 3.0 9.6 + - - +
167A ILE* 4.4 4.7 - - + -
168A VAL* 2.9 26.1 + - - +
183A LEU* 3.6 31.0 - - + -
187A LEU* 4.2 9.9 - - + -
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Residues in contact with GLY 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A LEU* 1.3 77.1 - - - +
99A ALA* 1.3 69.7 + - - +
100A PRO* 4.6 0.5 - - - +
104A LYS* 3.2 15.6 + - - +
146A TRP* 3.8 17.6 + - - +
167A ILE* 5.1 2.5 - - - -
168A VAL 3.6 13.5 - - - -
179A LYS* 5.4 2.7 - - - -
180A ALA* 6.4 0.9 - - - -
183A LEU* 4.5 9.6 - - - +
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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