Contacts of the strand formed by residues 93 - 98 (chain B) in PDB entry 2P2J
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B ASP 3.6 3.0 + - - -
92B ARG* 1.3 78.9 - - - +
94B ALA* 1.3 59.3 + - - +
95B ILE 3.4 29.6 - - - +
96B ILE* 3.7 7.6 - - + -
107B HIS* 3.5 42.2 - - + +
108B ILE 3.7 6.7 - - - +
109B SER* 4.0 3.4 - - - +
110B TYR* 3.8 1.4 - - - -
300B ILE* 6.2 0.2 - - - -
326B THR* 2.6 37.8 + - + -
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Residues in contact with ALA 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B ARG 3.4 2.8 + - - -
93B THR* 1.3 72.3 - - - +
95B ILE* 1.3 59.3 + - - +
108B ILE 2.7 14.1 + - - +
109B SER 3.9 0.4 - - - -
110B TYR* 3.5 42.2 - - + +
113B LEU* 3.8 25.6 - - + -
321B LEU* 3.9 2.3 - - + +
325B ALA 3.5 3.5 - - - +
327B THR* 3.0 34.0 + - - +
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Residues in contact with ILE 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B THR* 3.4 5.4 - - - +
94B ALA* 1.3 84.8 - - + +
96B ILE* 1.3 75.1 + - - +
97B TRP* 4.2 4.3 - - + +
107B HIS* 3.7 0.7 - - - -
108B ILE* 2.9 49.6 + - + +
113B LEU* 3.9 27.1 - - + -
143B PRO* 4.9 11.2 - - + +
146B ALA* 3.7 31.0 - - + -
316B LEU* 5.9 0.4 - - + -
317B LEU* 4.6 8.3 - - + -
321B LEU* 4.9 2.2 - - + -
327B THR* 3.2 17.9 - - + +
329B MET* 4.0 21.8 - - + +
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Residues in contact with ILE 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B THR* 3.7 11.7 - - + -
94B ALA 4.4 0.2 - - - -
95B ILE* 1.3 74.0 - - - +
97B TRP* 1.3 59.1 + - - +
105B SER* 5.8 0.2 - - - -
106B LYS 3.5 8.1 - - - +
107B HIS* 3.7 20.6 - - + +
300B ILE* 4.2 17.7 - - + -
326B THR* 3.7 26.9 - - + -
327B THR 2.9 7.6 + - - +
328B LEU* 3.3 12.2 - - + +
329B MET 2.7 33.6 + - - +
349B HIS* 3.5 55.0 - - + +
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Residues in contact with TRP 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B ILE* 3.9 3.5 + - + -
96B ILE* 1.3 72.9 - - - +
98B GLU* 1.3 59.5 + - - +
99B GLY* 4.0 4.9 - - - -
104B GLN* 3.9 26.9 - - + -
105B SER* 3.1 18.9 - - - -
106B LYS* 2.8 56.7 + - + +
108B ILE* 4.5 2.9 - - + -
141B MET 2.9 25.5 + - - -
142B VAL* 3.6 12.7 - - + +
143B PRO* 3.6 36.3 - - + -
222B ARG* 3.9 15.7 - - - -
329B MET* 3.3 21.1 - - + +
331B GLU* 3.4 41.0 - - + +
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Residues in contact with GLU 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B ILE 3.9 0.6 + - - -
97B TRP* 1.3 74.3 + - - +
99B GLY* 1.3 61.2 + - - +
102B THR* 2.8 19.3 + - - -
105B SER* 3.9 3.3 - - - -
328B LEU* 4.0 17.0 - - + -
329B MET 3.0 6.7 + - - +
330B PHE* 3.4 23.7 - - + -
331B GLU* 2.8 30.1 + - - +
341B ARG* 2.7 27.6 + - - +
345B VAL* 4.1 15.5 - - + +
348B LYS* 3.1 19.5 + - - +
349B HIS* 2.9 27.3 + - + +
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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
------------------------------------------------------------
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