Contacts of the strand formed by residues 312 - 322 (chain A) in PDB entry 6GE4
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 SER 312 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233A LEU* 3.7 20.6 - - - +
234A GLU 3.3 12.3 - - - -
235A GLN* 3.9 15.7 - - - -
310A GLY 5.3 0.4 - - - -
311A SER* 1.3 80.7 + - - +
313A PHE* 1.3 63.0 + - - +
314A TYR* 4.0 13.2 + - - -
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Residues in contact with PHE 313 (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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232A PHE* 3.8 7.1 - + - +
233A LEU* 3.6 1.7 - - - -
234A GLU* 2.8 45.3 + - + +
312A SER* 1.3 76.6 - - - +
314A TYR* 1.3 65.7 + - - +
315A GLY* 3.7 19.8 + - - -
363A ARG* 3.5 64.6 - - + +
365A PRO* 4.0 27.1 - - + -
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Residues in contact with TYR 314 (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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232A PHE 3.5 4.9 - - - +
233A LEU* 3.6 31.2 - - + +
247A PHE* 4.0 32.5 - + - -
312A SER* 4.0 12.9 + - - -
313A PHE* 1.3 80.3 - - - +
315A GLY* 1.3 58.4 + - - +
365A PRO* 3.7 5.4 - - - +
366A LEU* 2.9 48.6 + - + +
371A ILE* 3.8 39.6 - - + +
374A ILE* 4.5 13.8 - - + +
375A HIS* 2.9 30.5 + + - -
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Residues in contact with GLY 315 (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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231A ALA* 3.4 3.3 - - - +
232A PHE* 2.9 46.2 + - - +
313A PHE* 3.7 18.4 + - - -
314A TYR* 1.3 75.1 - - - +
316A VAL* 1.3 66.7 + - - +
363A ARG 5.0 0.2 - - - -
364A SER 3.3 8.5 - - - -
366A LEU* 4.2 2.7 - - - +
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Residues in contact with VAL 316 (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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229A PHE* 4.0 30.3 - - + -
230A SER 3.2 11.0 - - - +
231A ALA* 4.5 2.2 - - + -
232A PHE* 4.1 0.6 - - - -
315A GLY* 1.3 79.2 - - - +
317A SER* 1.3 67.9 + - - +
318A SER* 5.6 1.6 - - - +
361A ILE* 4.0 2.5 - - - +
363A ARG 3.6 0.7 + - - -
364A SER* 2.8 45.6 + - - +
365A PRO 5.5 0.2 - - - -
366A LEU* 3.6 29.8 - - + -
501A MYR 3.8 23.3 - - + -
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Residues in contact with SER 317 (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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228A GLU* 3.0 15.1 - - - +
229A PHE* 3.4 0.3 - - - -
230A SER* 2.8 41.3 + - - +
232A PHE* 3.7 11.6 - - - -
316A VAL* 1.3 74.7 + - - +
318A SER* 1.3 61.9 + - - +
361A ILE 3.3 7.2 - - - -
362A HIS* 3.7 14.9 - - - -
363A ARG* 2.8 28.4 + - - +
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Residues in contact with SER 318 (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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226A MET* 4.6 0.2 - - - -
228A GLU* 3.1 20.3 + - - -
229A PHE* 4.1 15.7 - - - -
316A VAL* 5.6 1.8 - - - +
317A SER* 1.3 76.9 - - - +
319A GLN* 1.3 65.4 + - - +
320A TYR* 3.0 33.7 + - - -
360A ARG* 3.7 0.7 - - - +
361A ILE* 2.9 45.3 + - - +
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Residues in contact with GLN 319 (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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226A MET* 3.4 6.8 - - - +
227A LEU* 2.9 34.9 + - + +
228A GLU* 2.9 44.6 + - + +
318A SER* 1.3 76.7 - - - +
320A TYR* 1.3 66.2 + - - +
359A TYR 3.5 4.7 - - - +
360A ARG* 3.1 55.3 + - + +
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Residues in contact with TYR 320 (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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224A LEU* 3.8 32.3 - - + -
225A TRP 3.1 7.4 - - - +
226A MET* 3.6 36.0 - - + -
227A LEU* 3.8 0.9 - - - -
318A SER* 3.0 36.7 + - - -
319A GLN* 1.3 74.8 - - - +
321A GLU* 1.3 69.2 + - - +
328A ILE* 4.7 6.7 - - + -
330A CYS* 4.1 1.8 - - + -
358A SER* 3.4 2.8 - - - -
359A TYR* 2.8 52.8 + - + +
361A ILE* 3.8 22.5 - - + +
397A GLN* 2.7 29.0 + - - -
399A VAL* 4.3 13.9 - - + -
409A LEU* 4.2 3.1 - - + -
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Residues in contact with GLU 321 (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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217A ARG* 4.8 10.2 + - - +
224A LEU* 3.5 6.7 - - - +
225A TRP* 2.9 54.1 + - + +
227A LEU* 3.4 30.9 - - + +
320A TYR* 1.3 79.9 - - - +
322A SER* 1.3 60.0 + - - +
323A PRO* 4.7 0.5 - - - +
353A GLU* 3.1 16.8 - - - +
356A HIS* 3.4 35.1 + - + +
357A TYR 3.3 5.2 - - - +
358A SER* 4.3 6.2 - - - -
359A TYR* 4.8 0.2 - - - -
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Residues in contact with SER 322 (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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217A ARG* 6.3 0.2 - - - -
223A LYS 2.7 22.2 + - - -
224A LEU* 3.8 1.6 - - - -
321A GLU* 1.3 76.1 - - - +
323A PRO* 1.3 65.6 - - - +
324A GLU* 3.0 26.9 + - - +
326A MET* 3.3 15.6 - - - +
356A HIS* 3.5 5.6 - - - +
357A TYR* 2.8 33.0 + - - -
359A TYR* 3.7 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