Contacts of the strand formed by residues 93 - 98 (chain A) in PDB entry 2P2B
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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A ASP 3.6 2.4 + - - -
92A ARG* 1.3 79.4 - - - +
94A ALA* 1.3 59.1 + - - +
95A ILE 3.4 31.2 - - - +
96A ILE* 3.7 17.5 - - + -
107A HIS* 3.7 22.8 - - + +
108A ILE 3.7 14.6 - - - +
109A SER* 3.9 3.4 + - - +
110A TYR* 4.1 0.2 - - - -
325A ALA 3.9 0.9 - - - +
326A THR* 2.6 38.5 + - + -
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Residues in contact with ALA 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 ARG 3.5 2.6 + - - -
93A THR* 1.3 72.8 - - - +
95A ILE* 1.3 59.3 + - - +
108A ILE 2.7 14.3 + - - +
109A SER 4.0 0.4 - - - -
110A TYR* 3.5 42.0 - - + +
113A LEU* 3.9 26.2 - - + -
321A LEU* 3.9 3.3 - - + +
325A ALA 3.6 3.0 - - - +
326A THR* 3.5 2.0 - - - -
327A THR* 2.9 32.7 + - - +
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Residues in contact with ILE 95 (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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93A THR* 3.4 4.7 - - - +
94A ALA* 1.3 85.1 - - + +
96A ILE* 1.3 75.8 + - - +
97A TRP* 3.8 8.5 + - + +
106A LYS 3.7 1.9 - - - +
108A ILE* 2.9 45.9 + - + +
113A LEU* 3.9 29.6 - - + -
143A PRO* 5.0 10.1 - - + +
146A ALA* 3.8 28.5 - - + -
317A LEU* 4.4 9.2 - - + -
321A LEU* 4.8 2.7 - - + -
327A THR* 3.2 18.4 - - + +
329A MET* 4.3 17.9 - - + -
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Residues in contact with ILE 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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93A THR* 3.7 19.1 - - + -
94A ALA 4.3 0.2 - - - -
95A ILE* 1.3 75.2 - - - +
97A TRP* 1.3 64.3 + - - +
106A LYS 3.5 7.0 - - - +
107A HIS* 3.8 21.3 - - + +
300A ILE* 4.0 23.6 - - + -
326A THR* 3.8 18.8 - - + +
327A THR 2.9 8.4 + - - +
328A LEU* 3.3 13.5 - - + +
329A MET 2.7 28.4 + - - +
349A HIS* 3.5 50.9 - - + +
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Residues in contact with TRP 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 ILE* 3.8 6.6 + - + -
96A ILE* 1.3 74.9 - - - +
98A GLU* 1.3 61.4 + - - +
99A GLY* 3.7 13.9 - - - -
104A GLN* 4.1 24.5 - - + -
105A SER* 3.0 17.1 - - - -
106A LYS* 2.8 64.9 + - + +
108A ILE* 5.0 0.7 - - + -
141A MET 2.9 25.2 + - - -
142A VAL* 3.6 8.6 - - + +
143A PRO* 3.5 36.8 - - + -
222A ARG* 4.2 12.6 - - - -
329A MET* 3.4 22.4 - - - -
331A GLU* 3.4 34.0 - - - +
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Residues in contact with GLU 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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96A ILE 3.9 1.0 + - - -
97A TRP* 1.3 75.2 + - - +
99A GLY* 1.3 64.4 + - - +
102A THR* 3.3 8.0 + - - -
104A GLN 4.0 1.8 - - - -
105A SER* 3.6 2.4 - - - -
328A LEU* 4.2 13.9 - - + -
329A MET 3.0 7.1 + - - +
330A PHE* 3.4 23.1 - - + -
331A GLU* 2.9 29.3 + - - +
341A ARG* 3.0 21.2 + - - +
345A VAL* 4.1 12.6 - - + +
348A LYS* 2.8 31.7 + - - +
349A HIS* 2.7 35.8 + - - +
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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