Contacts of the strand formed by residues 387 - 393 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272E ALA* 4.7 6.6 + - - +
273E PHE* 4.2 2.8 - - - -
284E SER* 4.0 18.7 - - - +
332E VAL* 4.2 12.1 - - + -
336E ILE* 4.2 10.1 - - + -
367E THR* 3.5 14.6 - - + +
369E ILE* 3.4 33.2 - - + -
383E ILE* 3.7 45.4 - - + +
385E GLY 2.6 16.5 + - - +
386E PRO* 1.3 80.6 - - - +
388E LEU* 1.3 62.7 + - - +
389E GLN* 4.4 5.1 - - + +
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Residues in contact with LEU 388 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268E LEU* 4.9 11.7 - - + -
272E ALA* 3.9 9.4 - - + -
273E PHE* 3.8 21.5 - - + -
283E LEU 3.4 25.1 - - - +
284E SER 3.7 7.9 - - - +
285E VAL 4.6 0.2 - - - -
286E ALA* 4.3 23.8 - - + +
297E LEU* 6.3 1.3 - - + -
301E MET* 3.8 36.6 - - + -
367E THR 3.0 8.1 + - - +
368E LEU* 3.6 12.5 - - + +
369E ILE* 2.9 28.8 + - - +
387E VAL* 1.3 74.0 - - - +
389E GLN* 1.3 68.7 + - - +
390E VAL* 5.1 2.9 - - + -
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Residues in contact with GLN 389 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250E LYS* 3.3 23.0 + - - -
284E SER 2.8 15.5 + - - +
285E VAL* 3.3 11.5 - - + +
286E ALA* 2.9 25.3 + - - +
339E ALA* 4.8 1.4 - - - +
369E ILE* 3.4 22.6 - - + +
372E VAL* 4.2 26.1 - - + +
376E MET* 5.7 0.2 - - - -
378E SER* 3.3 49.7 + - - +
379E TYR* 3.7 9.2 - - - +
383E ILE* 3.8 7.0 - - - +
387E VAL* 4.4 4.9 - - + -
388E LEU* 1.3 77.2 - - - +
390E VAL* 1.3 62.8 + - - +
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Residues in contact with VAL 390 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286E ALA* 3.5 15.7 - - + +
288E ALA* 4.7 3.8 - - + -
294E GLY 5.1 0.7 - - - +
297E LEU* 4.6 17.7 - - + -
298E VAL* 4.2 17.9 - - + -
368E LEU* 3.8 26.7 - - + -
369E ILE 2.9 11.0 + - - +
370E ASP* 3.6 20.0 - - - +
371E HIS 3.5 5.7 + - - -
372E VAL* 3.1 25.7 + - - +
388E LEU* 5.1 4.7 - - + -
389E GLN* 1.3 75.0 - - - +
391E VAL* 1.3 75.9 + - - +
392E ARG* 4.4 9.0 - - + +
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Residues in contact with VAL 391 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285E VAL* 3.5 29.4 - - + -
286E ALA 3.4 4.2 + - - +
287E VAL* 4.6 6.7 - - + -
288E ALA 3.2 23.4 + - - -
372E VAL* 3.5 31.6 - - + +
373E THR* 5.0 0.7 - - - -
374E PRO* 5.0 11.0 - - + -
379E TYR* 4.0 11.4 - - + -
390E VAL* 1.3 83.0 - - - +
392E ARG* 1.3 70.4 + - - +
393E VAL* 4.2 4.3 - - + -
402E LEU* 3.7 26.9 - - + -
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Residues in contact with ARG 392 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288E ALA* 3.6 10.8 - - + +
291E ASP* 3.4 29.9 + - - +
294E GLY* 3.1 31.3 + - - -
295E ASP* 2.9 26.9 + - - +
298E VAL* 3.8 3.6 - - - +
370E ASP* 2.5 42.6 + - - +
371E HIS* 3.4 32.7 + - - +
372E VAL 4.7 1.4 + - - -
390E VAL* 4.4 7.6 - - + +
391E VAL* 1.3 83.0 - - - +
393E VAL* 1.3 65.7 + - - +
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Residues in contact with VAL 393 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287E VAL* 3.3 33.4 - - + -
288E ALA 3.1 7.1 + - - +
289E VAL* 3.3 6.2 - - - -
290E GLY* 3.0 26.9 + - - -
291E ASP* 5.5 0.3 - - - +
391E VAL* 4.5 4.0 - - + -
392E ARG* 1.3 78.5 - - - +
394E ALA* 1.3 60.8 + - - +
395E THR 3.6 16.4 - - - +
398E ASP* 4.1 13.5 - - + -
399E ALA* 3.9 11.0 - - + +
402E LEU* 4.2 18.2 - - + -
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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