Contacts of the strand formed by residues 335 - 342 (chain A) in PDB entry 2C11
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 TRP 335 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330A VAL 4.7 0.2 - - - -
331A ALA* 3.2 4.0 - - - -
332A SER* 2.7 47.9 + - - +
334A LEU* 1.3 87.0 - - + +
336A THR* 1.3 63.9 + - - +
337A PHE* 4.5 12.3 - - + -
352A VAL* 3.6 14.1 - - + -
353A ARG 3.5 8.1 - - - -
354A PHE* 3.4 27.7 - + - -
359A LEU* 3.8 12.3 - - + -
460A LEU* 4.5 13.7 - - + -
479A PHE* 3.2 43.2 + + + +
480A HIS 3.2 32.4 + - - -
481A PRO 4.6 0.4 - - - -
483A GLY* 3.7 15.9 - - - -
484A ALA 3.9 1.1 - - - -
485A ILE* 3.3 40.6 - - + -
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Residues in contact with THR 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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329A ARG* 2.8 27.6 - - - +
330A VAL 3.5 6.1 - - - +
331A ALA* 3.9 12.8 - - - +
332A SER 5.3 0.2 + - - -
335A TRP* 1.3 76.7 + - - +
337A PHE* 1.3 65.7 + - - +
351A ASP 3.0 0.3 - - - +
352A VAL* 3.2 0.7 - - - +
353A ARG* 2.7 69.1 + - - +
356A GLY* 5.6 2.2 - - - -
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Residues in contact with PHE 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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329A ARG* 3.1 11.3 - - - +
330A VAL* 2.9 69.6 + - + +
335A TRP* 4.5 4.3 - - + -
336A THR* 1.3 86.7 - - - +
338A SER* 1.3 67.2 + - - +
339A PHE* 4.1 8.5 - + - -
349A ILE* 3.6 24.9 - - + -
350A PHE 3.5 8.3 - - - +
351A ASP 3.1 10.3 - - - +
352A VAL* 3.9 12.6 - - + -
460A LEU* 4.3 10.8 - - + -
462A VAL* 3.3 28.0 - - + -
479A PHE* 3.7 32.1 - + - -
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Residues in contact with SER 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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58A GLN* 5.5 1.0 - - - +
60A PHE* 3.4 30.7 + - - +
61A ALA 4.2 1.0 + - - -
328A SER* 3.0 16.4 + - - -
329A ARG* 3.4 27.4 - - - +
337A PHE* 1.3 76.2 - - - +
339A PHE* 1.3 65.4 + - - +
349A ILE* 3.2 4.0 - - - +
350A PHE* 2.6 43.3 + - - +
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Residues in contact with PHE 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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60A PHE 4.6 6.5 - - - +
61A ALA* 4.8 0.2 - - - -
325A VAL* 4.3 6.1 - - + -
327A GLY 3.6 18.2 - - - -
328A SER* 2.6 60.5 + - - -
330A VAL* 3.6 30.1 - - + -
337A PHE* 4.1 7.9 - + + -
338A SER* 1.3 78.3 + - - +
340A GLY* 1.3 64.1 + - - +
348A ARG* 3.4 8.3 - - - +
349A ILE* 3.8 15.9 - - + -
350A PHE* 5.5 2.2 - - - -
411A VAL* 4.2 23.3 - - + -
429A PHE* 3.9 38.6 - + + -
431A VAL* 4.4 6.7 - - + -
462A VAL* 4.3 14.8 - - + -
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Residues in contact with GLY 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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60A PHE 5.5 0.7 - - - -
62A ASP* 3.2 18.8 - - - -
328A SER* 5.1 0.2 - - - -
339A PHE* 1.3 86.5 - - - +
341A LEU* 1.3 64.4 + - - +
347A PRO* 3.8 0.7 - - - +
348A ARG* 3.0 31.6 + - - +
429A PHE* 3.4 13.5 - - - -
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Residues in contact with LEU 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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62A ASP* 3.0 14.9 + - - +
100A GLU* 4.0 2.1 - - - +
340A GLY* 1.3 75.2 - - - +
342A GLY* 1.3 64.4 + - - +
343A ALA 3.8 0.5 + - - -
346A GLY* 3.4 3.1 - - - -
347A PRO* 3.3 39.9 - - + -
348A ARG* 3.8 8.8 + - - +
391A MET 5.3 0.9 - - - +
392A GLY* 3.4 30.3 - - - -
395A THR* 3.6 28.7 - - + +
413A TRP* 3.2 32.4 + - + +
428A ALA* 5.4 0.9 - - + -
429A PHE* 3.4 20.2 - - + -
464A SER* 3.8 11.7 - - - +
466A SER* 5.7 0.4 - - - +
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Residues in contact with GLY 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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100A GLU* 3.3 12.6 - - - -
341A LEU* 1.3 73.2 - - - +
343A ALA* 1.3 63.1 + - - -
344A PHE 3.3 2.7 - - - -
345A SER* 4.0 8.1 - - - -
346A GLY 2.6 29.5 + - - -
348A ARG* 3.4 13.9 - - - +
392A GLY* 2.9 22.1 - - - -
413A TRP* 4.5 0.2 - - - -
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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