Contacts of the strand formed by residues 331 - 338 (chain B) in PDB entry 2P80
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 MET 331 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102A ALA* 3.5 31.6 - - + -
103A THR 4.0 6.3 - - - +
104A GLY 2.8 31.9 - - - +
105A ALA* 3.5 15.7 - - - -
107A GLY 4.0 0.2 - - - -
108A GLY* 3.7 14.4 - - - +
111A LEU* 3.9 1.6 - - + -
122A LEU* 3.5 26.7 - - + -
123A ARG 3.3 8.5 - - - +
124A PHE* 4.2 4.7 - - + -
297B GLN* 4.0 4.5 - - - +
326B TRP* 2.8 39.9 + - + -
327B ASN 3.2 2.2 + - - -
328B ASP* 2.8 16.2 + - - +
330B LEU* 1.3 80.2 - - - +
332B THR* 1.3 61.8 + - - +
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Residues in contact with THR 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A LEU* 5.8 0.2 - - - -
122A LEU* 4.3 4.5 - - - -
123A ARG* 2.9 65.1 + - - +
326B TRP* 4.7 2.2 - - - +
328B ASP* 2.5 34.1 + - - +
331B MET* 1.3 78.8 - - - +
333B SER* 1.3 60.9 + - - +
334B VAL* 3.1 15.3 + - + +
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Residues in contact with SER 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A LEU* 4.1 37.7 + - - +
120A THR* 4.1 0.7 + - - -
121A ILE 3.8 4.8 + - - -
122A LEU* 4.5 6.6 - - - +
332B THR* 1.3 73.1 + - - +
334B VAL* 1.3 66.2 + - - +
335B LEU* 3.6 4.0 + - - -
336B ALA* 3.5 29.2 + - - +
337B PRO* 4.8 0.5 - - - +
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Residues in contact with VAL 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A GLU* 3.4 29.6 - - - +
121A ILE* 2.9 28.9 + - + +
123A ARG* 4.1 11.2 - - + +
332B THR* 3.1 22.9 + - + +
333B SER* 1.3 74.2 - - - +
335B LEU* 1.3 63.0 + - + +
336B ALA 4.2 0.2 + - - -
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Residues in contact with LEU 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A LYS* 3.7 34.3 - - - +
120A THR* 1.9 37.4 + - - -
121A ILE* 3.0 38.2 + - + +
333B SER* 3.6 2.5 - - - -
334B VAL* 1.3 83.5 - - + +
336B ALA* 1.3 60.2 + - - +
338B SER* 4.0 14.8 - - - +
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Residues in contact with ALA 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A LYS 4.1 0.2 - - - +
333B SER* 3.5 12.8 + - - +
334B VAL 4.1 1.0 + - - -
335B LEU* 1.3 81.4 - - - +
337B PRO* 1.3 81.5 - - + +
338B SER* 3.0 15.1 + - - -
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Residues in contact with PRO 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A LEU* 4.3 11.4 - - - +
112A THR* 4.3 3.1 - - - +
113A GLU* 3.0 41.1 - - + +
114A ILE* 3.6 22.4 - - + -
118A GLU* 3.8 12.3 - - - +
120A THR* 3.9 10.1 - - - +
333B SER* 4.8 0.4 - - - +
335B LEU 3.6 0.2 - - - -
336B ALA* 1.3 88.8 - - + +
338B SER* 1.3 60.1 + - - +
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Residues in contact with SER 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A GLU* 2.7 46.6 - - - +
119A LYS 3.0 15.1 + - - -
335B LEU* 4.0 16.7 - - - +
336B ALA 3.0 11.6 + - - -
337B PRO* 1.3 76.0 - - - +
339B GLY* 1.3 60.8 + - - +
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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