Contacts of the strand formed by residues 335 - 342 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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330D VAL 4.6 0.4 - - - -
331D ALA* 3.6 0.7 - - - -
332D SER* 2.8 44.7 + - - +
334D LEU* 1.3 89.4 - - + +
336D THR* 1.3 61.3 + - - +
337D PHE* 4.2 17.7 - - + -
352D VAL* 3.6 15.0 - - + -
353D ARG 3.4 5.6 - - - -
354D PHE* 3.7 31.6 - + + -
359D LEU* 3.7 13.9 - - + -
460D LEU* 4.3 8.2 - - + +
479D PHE* 3.4 37.4 + + + +
480D HIS 3.0 30.7 + - - -
481D PRO 4.6 0.2 - - - -
483D GLY* 3.2 37.2 - - - -
484D ALA 3.7 6.7 - - - -
485D ILE* 3.6 18.8 - - + -
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Residues in contact with THR 336 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329D ARG* 3.0 18.3 + - - +
330D VAL 3.2 6.5 - - - -
331D ALA* 3.5 24.0 - - + -
332D SER 4.5 4.9 - - - +
335D TRP* 1.3 79.9 - - - +
337D PHE* 1.3 68.3 + - - +
351D ASP 3.3 1.2 - - - +
352D VAL* 3.4 0.5 - - - +
353D ARG* 3.0 52.4 + - - +
356D GLY* 5.2 2.8 + - - -
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Residues in contact with PHE 337 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329D ARG* 3.0 18.2 - - - +
330D VAL* 2.6 75.2 + - + -
335D TRP* 4.2 5.2 - - + -
336D THR* 1.3 83.3 - - - +
338D SER* 1.3 68.0 + - - +
339D PHE* 4.1 5.8 - + - -
349D ILE* 3.9 18.8 - - + -
350D PHE 3.8 9.9 - - - +
351D ASP 3.5 5.6 - - - +
352D VAL* 4.0 5.2 - - + -
460D LEU* 3.9 15.0 - - + -
462D VAL* 3.5 29.4 - - + -
479D PHE* 3.3 38.4 - + - -
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Residues in contact with SER 338 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58D GLN* 4.4 3.0 + - - +
60D PHE* 3.6 33.1 + - - +
328D SER* 3.0 26.1 - - - -
329D ARG* 3.6 19.0 - - - +
337D PHE* 1.3 75.3 - - - +
339D PHE* 1.3 63.1 + - - +
349D ILE* 3.4 9.0 - - - +
350D PHE* 3.1 34.3 + - - -
351D ASP* 5.8 1.1 - - - -
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Residues in contact with PHE 339 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60D PHE 4.2 4.3 - - - +
62D ASP* 3.8 4.5 - - - +
325D VAL* 3.7 21.5 - - + -
327D GLY 3.8 11.0 - - - -
328D SER* 2.8 42.8 + - - -
330D VAL* 3.3 33.9 - - + -
337D PHE* 4.1 7.6 - + + -
338D SER* 1.3 75.8 + - - +
340D GLY* 1.3 60.2 + - - +
348D ARG* 3.4 11.2 - - - +
349D ILE* 3.9 14.1 - - + -
350D PHE* 5.5 2.9 - - - -
411D VAL* 3.9 16.2 - - + -
429D PHE* 4.0 39.9 - + + -
431D VAL* 4.3 7.6 - - + -
462D VAL* 4.6 12.8 - - + -
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Residues in contact with GLY 340 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60D PHE 5.4 0.4 - - - -
62D ASP* 3.0 15.9 - - - -
339D PHE* 1.3 78.7 - - - +
341D LEU* 1.3 62.1 + - - -
347D PRO* 3.7 2.1 - - - +
348D ARG* 2.9 40.0 + - - +
350D PHE* 5.8 0.4 - - - -
429D PHE* 3.5 19.8 - - - -
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Residues in contact with LEU 341 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62D ASP* 2.7 25.0 + - - +
100D GLU* 4.0 1.2 - - - +
340D GLY* 1.3 74.3 - - - -
342D GLY* 1.3 64.0 + - - +
343D ALA 3.4 0.9 + - - -
346D GLY 4.1 1.3 - - - -
347D PRO* 3.6 28.7 - - + -
348D ARG* 3.4 5.3 + - - +
392D GLY* 3.5 17.3 - - - -
395D THR* 3.2 28.3 - - + +
413D TRP* 3.2 50.5 - - + +
428D ALA* 4.9 0.7 - - + -
429D PHE* 3.7 14.3 - - + -
464D SER* 3.5 23.1 - - - +
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Residues in contact with GLY 342 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D GLU* 3.8 3.1 - - - -
341D LEU* 1.3 72.0 - - - +
343D ALA* 1.3 67.7 + - - -
344D PHE 3.0 3.7 + - - -
345D SER* 3.3 22.4 - - - -
346D GLY 3.1 22.1 + - - -
348D ARG* 3.7 17.9 - - - +
392D GLY* 3.1 16.2 - - - -
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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