Contacts of the strand formed by residues 327 - 331 (chain A) in PDB entry 2H3W
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 LEU 327 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A ILE* 3.3 36.3 + - + +
177A LEU* 3.5 26.7 - - + -
283A ILE 5.1 0.2 - - - +
284A PHE* 3.7 14.1 - - + +
285A THR 3.0 24.6 + - - +
325A LYS* 3.8 7.7 - - - +
326A THR* 1.3 82.6 - - + +
328A GLN* 1.3 62.5 + - - +
329A PHE* 4.2 15.3 - - + -
339A MET* 4.0 18.8 - - + -
340A VAL 4.4 0.4 - - - -
341A TYR* 4.1 0.4 - - + -
351A ILE* 3.7 30.1 - - + -
354A LEU* 4.2 13.7 - - + -
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Residues in contact with GLN 328 (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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285A THR* 3.4 18.9 - - - +
287A CYS* 3.6 17.1 - - - -
321A ARG* 3.2 16.9 - - - +
322A TRP* 2.9 50.0 - - - +
323A PHE* 3.7 14.6 - - - -
325A LYS* 4.2 8.5 - - + +
327A LEU* 1.3 78.2 - - - +
329A PHE* 1.3 61.4 + - - +
330A ILE* 4.4 0.6 - - + +
339A MET* 3.0 23.7 - - - +
340A VAL* 3.1 43.1 + - + +
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Residues in contact with PHE 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A LEU* 5.3 5.8 - - + -
142A LEU* 3.8 36.8 - - + -
146A VAL* 4.1 18.4 - - + -
284A PHE* 3.8 26.7 - + + -
285A THR 2.9 9.8 + - - +
286A VAL* 3.4 8.7 - - + +
287A CYS* 2.8 32.2 + - - +
327A LEU* 4.3 24.0 - - + -
328A GLN* 1.3 75.7 - - - +
330A ILE* 1.3 55.4 + - - +
331A VAL* 5.1 0.7 - - + -
338A GLY 3.7 4.3 - - - -
339A MET* 3.7 28.7 - - + -
354A LEU* 3.4 31.6 - - + -
355A VAL* 4.9 4.3 - - + -
358A VAL* 5.1 5.6 - - + -
359A MET* 6.0 0.7 - - + -
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Residues in contact with ILE 330 (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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142A LEU* 5.5 1.2 - - - +
287A CYS* 3.6 9.9 - - + +
289A ASP* 3.3 34.5 - - + +
307A GLN* 4.7 0.2 - - - +
308A MET* 3.6 52.5 - - + +
321A ARG* 3.6 31.9 - - - +
328A GLN 4.4 2.7 - - - +
329A PHE* 1.3 76.2 - - - +
331A VAL* 1.3 70.4 + - - +
332A ALA 4.5 0.4 - - - +
337A CYS* 3.2 6.6 - - - +
338A GLY 2.8 33.8 + - - +
339A MET* 4.1 11.9 - - - -
340A VAL* 4.2 7.2 - - + -
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Residues in contact with VAL 331 (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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129A PHE* 3.9 14.1 - - + -
135A GLN* 3.2 40.7 - - + +
138A PHE* 4.1 21.3 - - + -
139A ALA* 4.2 20.2 - - + -
142A LEU* 4.6 9.9 - - + -
286A VAL* 4.6 10.3 - - + -
287A CYS 2.9 12.9 + - - +
288A LEU* 3.8 6.9 - - + -
289A ASP 3.2 20.8 + - - -
329A PHE 5.1 0.2 - - - -
330A ILE* 1.3 81.6 - - - +
332A ALA* 1.3 63.2 + - - +
336A SER 4.0 2.7 - - - +
337A CYS* 4.3 0.9 - - + -
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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