Contacts of the strand formed by residues 387 - 393 (chain G) in PDB entry 4ZZ7
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 VAL 387 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272G ALA* 4.5 6.2 + - - +
273G PHE* 3.9 3.0 - - - -
284G SER* 3.8 22.3 - - - +
332G VAL* 4.5 3.4 - - + -
336G ILE* 4.3 18.6 - - + -
367G THR* 3.7 20.4 - - + +
369G ILE* 4.0 18.6 - - + -
383G ILE* 3.8 46.9 - - + -
385G GLY 2.8 15.0 + - - +
386G PRO* 1.3 78.8 - - + +
388G LEU* 1.3 68.6 + - - +
389G GLN* 4.3 4.5 - - + -
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Residues in contact with LEU 388 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268G LEU* 4.7 16.2 - - + -
272G ALA* 3.9 11.9 - - + -
273G PHE* 3.7 18.3 - - + -
283G LEU 3.5 23.3 - - - +
284G SER 3.9 5.4 - - - -
285G VAL 4.2 1.6 - - - +
286G ALA* 4.1 19.1 - - + -
297G LEU* 6.0 2.0 - - + -
301G MET* 3.7 37.7 - - + -
367G THR 3.3 8.4 + - - +
368G LEU* 3.5 11.7 - - + +
369G ILE 3.2 20.4 + - - -
387G VAL* 1.3 75.3 - - - +
389G GLN* 1.3 73.9 + - - +
390G VAL* 4.9 3.6 - - + -
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Residues in contact with GLN 389 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250G LYS* 3.6 28.6 + - - -
284G SER 2.8 14.8 + - - +
285G VAL* 3.3 7.8 - - + +
286G ALA* 2.7 33.5 + - - +
339G ALA* 4.9 0.2 - - - +
369G ILE* 3.4 19.9 - - + +
372G VAL* 3.9 31.4 - - + +
378G SER* 3.3 40.6 + - - +
379G TYR* 3.7 7.7 - - - +
383G ILE* 3.9 11.9 - - - +
387G VAL* 4.0 6.3 - - + -
388G LEU* 1.3 72.4 - - - +
390G VAL* 1.3 63.5 + - - +
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Residues in contact with VAL 390 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286G ALA* 3.3 17.9 - - + +
288G ALA* 4.6 5.6 - - + -
294G GLY 5.2 2.0 - - - +
297G LEU* 3.8 25.4 - - + -
298G VAL* 4.4 13.2 - - + -
368G LEU* 3.5 30.7 - - + -
369G ILE 3.0 7.3 + - - +
370G ASP* 4.0 15.5 - - - +
371G HIS 3.4 7.0 + - - -
372G VAL* 3.0 26.7 + - - +
388G LEU* 4.2 4.9 - - + +
389G GLN* 1.3 81.5 - - - +
391G VAL* 1.3 67.9 + - - +
392G ARG* 5.2 2.9 - - - +
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Residues in contact with VAL 391 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285G VAL* 4.1 16.8 - - + -
286G ALA 3.2 4.7 + - - +
287G VAL* 4.4 11.2 - - + -
288G ALA* 2.9 30.4 + - - +
372G VAL* 3.3 38.4 - - + +
373G THR* 5.3 2.2 - - - -
374G PRO* 5.6 4.9 - - + -
379G TYR* 4.2 12.8 - - + -
390G VAL* 1.3 75.0 - - - +
392G ARG* 1.3 72.3 + - - +
393G VAL* 3.9 9.6 - - + -
402G LEU* 3.7 24.9 - - + -
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Residues in contact with ARG 392 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288G ALA* 3.4 7.0 - - + +
290G GLY 4.8 2.9 - - - +
291G ASP* 3.0 47.3 + - - +
294G GLY* 2.7 40.2 + - - -
295G ASP* 3.4 15.9 + - - +
298G VAL* 3.9 1.8 - - - +
370G ASP* 3.1 35.3 + - - +
371G HIS* 3.4 34.1 + - - +
372G VAL 4.8 1.6 + - - -
390G VAL* 5.2 1.9 - - + +
391G VAL* 1.3 78.8 - - - +
393G VAL* 1.3 68.8 + - - +
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Residues in contact with VAL 393 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287G VAL* 3.6 24.9 - - + -
288G ALA 2.9 13.0 + - - +
289G VAL* 3.9 6.7 - - - -
290G GLY* 2.9 28.4 + - - +
391G VAL* 3.9 16.8 - - + -
392G ARG* 1.3 79.5 - - - +
394G ALA* 1.3 60.9 + - - +
395G THR 3.7 17.9 - - - +
398G ASP* 4.1 17.0 - - + +
399G ALA* 4.0 8.1 - - + +
402G LEU* 4.6 8.3 - - + -
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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