Contacts of the strand formed by residues 335 - 342 (chain A) in PDB entry 2P02
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 ARG 335 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A TYR* 3.0 36.4 + - + +
164A ALA 3.3 11.2 - - - +
165A THR* 3.9 15.0 - - - -
166A ASP* 5.6 0.2 - - - +
215A GLY* 2.9 29.0 + - - +
216A ALA* 4.5 5.4 - - - +
217A VAL* 4.0 26.4 - - - +
296A TRP* 3.8 17.4 - - - -
297A GLY 5.7 0.4 - - - +
328A VAL* 4.2 0.6 - - - +
333A CYS* 3.6 2.1 - - - -
334A ARG* 1.3 78.4 - - + +
336A VAL* 1.3 67.1 + - - +
356A HIS* 3.1 14.7 - - - +
357A TYR* 3.3 41.6 + - + +
359A THR* 3.0 24.9 + - + -
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Residues in contact with VAL 336 (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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163A TYR* 3.3 7.8 - - - -
164A ALA 3.0 31.8 + - - +
324A ALA* 3.6 37.7 - - + +
327A LEU* 4.1 11.7 - - + -
328A VAL* 4.0 5.2 - - + -
333A CYS* 3.6 20.2 - - - -
335A ARG* 1.3 77.9 - - - +
337A LEU* 1.3 65.3 + - - +
338A VAL* 4.3 1.3 - - + -
354A ILE* 3.6 26.9 - - + -
355A PHE 3.4 14.8 - - - +
356A HIS* 4.3 2.9 - - + -
357A TYR* 4.0 5.6 - - - -
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Residues in contact with LEU 337 (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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161A PHE* 3.7 26.5 - - + -
162A GLY 3.4 16.4 - - - +
163A TYR* 4.4 2.9 - - + -
297A GLY* 3.8 11.4 - - - +
298A ALA* 3.7 37.2 - - + +
336A VAL* 1.3 75.0 - - - +
338A VAL* 1.3 61.4 + - - +
354A ILE* 3.5 3.6 - - - -
355A PHE* 2.8 59.0 + - + +
357A TYR* 3.7 22.6 - - + +
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Residues in contact with VAL 338 (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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160A MET 3.7 0.2 - - - +
161A PHE* 3.0 11.6 - - - +
162A GLY 2.8 32.6 + - - +
320A ALA* 4.2 19.2 - - + +
323A VAL* 4.0 22.7 - - + -
324A ALA* 4.0 25.4 - - + +
327A LEU* 4.6 0.9 - - + -
336A VAL* 4.5 6.7 - - + -
337A LEU* 1.3 77.7 - - - +
339A GLN* 1.3 70.0 + - - +
340A VAL* 4.6 7.2 - - + -
352A ILE* 4.8 4.0 - - + -
353A SER 3.3 8.5 - - - +
354A ILE* 3.9 21.3 - - + -
371A VAL* 5.7 0.2 - - + -
377A LEU* 5.9 0.9 - - + -
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Residues in contact with GLN 339 (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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159A LEU* 3.5 26.6 - - + +
160A MET 3.4 8.7 - - - +
161A PHE* 3.3 38.5 - - + -
337A LEU 4.3 0.4 - - - -
338A VAL* 1.3 72.8 - - - +
340A VAL* 1.3 74.8 + - - +
341A SER* 5.5 0.9 - - - -
351A SER* 4.2 12.9 + - - -
352A ILE* 3.2 5.9 - - - +
353A SER* 2.9 50.2 + - - +
355A PHE* 4.6 7.1 - - + -
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Residues in contact with VAL 340 (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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159A LEU* 3.3 4.7 - - - +
160A MET* 2.9 51.3 + - + +
316A ALA* 4.1 14.8 - - + +
320A ALA* 4.6 5.8 - - + -
338A VAL* 4.6 7.6 - - + -
339A GLN* 1.3 82.3 - - - +
341A SER* 1.3 61.9 + - - +
342A TYR* 4.0 22.9 - - + +
349A PRO* 4.8 2.2 - - + -
351A SER* 3.3 8.5 - - - +
352A ILE* 4.0 15.0 - - + -
377A LEU* 3.6 30.5 - - + -
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Residues in contact with SER 341 (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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158A GLY 3.1 14.6 - - - -
159A LEU* 4.1 9.0 - - - -
339A GLN* 5.5 2.0 - - - -
340A VAL* 1.3 78.3 - - - +
342A TYR* 1.3 65.1 + - - +
349A PRO* 3.2 8.5 - - - +
350A LEU* 2.8 36.1 + - - +
351A SER* 2.8 32.7 + - - -
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Residues in contact with TYR 342 (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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154A ALA* 3.7 28.9 - - + -
156A ASP 4.0 7.0 - - - +
157A GLN* 3.2 5.2 - - - +
158A GLY 2.9 24.5 + - - +
160A MET* 3.7 17.5 - - - -
312A VAL* 4.0 15.7 - - + -
316A ALA* 3.3 34.1 - - + +
340A VAL* 4.0 13.4 - - + +
341A SER* 1.3 78.3 - - - +
343A ALA* 1.3 59.5 + - - +
346A VAL 4.5 0.9 - - - -
347A SER 3.8 14.4 - - - -
348A HIS 4.4 1.8 - - - -
349A PRO* 3.8 21.3 - - + +
350A LEU* 3.8 15.7 - - - +
377A LEU* 2.7 40.5 + - - +
379A PRO* 4.2 1.8 - - + -
382A ILE* 4.1 1.4 - - - +
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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