Contacts of the strand formed by residues 387 - 393 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272B ALA* 4.7 3.7 + - - +
273B PHE* 4.0 2.6 - - - -
283B LEU 4.8 0.9 - - - +
284B SER* 3.8 22.5 - - - +
332B VAL* 4.4 4.3 - - + -
336B ILE* 4.0 21.8 - - + -
367B THR* 3.2 25.6 - - + +
369B ILE* 3.4 29.6 - - + -
383B ILE* 4.2 34.4 - - + +
385B GLY 2.9 8.7 + - - +
386B PRO* 1.3 84.3 - - + +
388B LEU* 1.3 64.8 + - - +
389B GLN* 4.2 1.8 - - + -
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Residues in contact with LEU 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B LEU* 4.5 17.0 - - + -
272B ALA* 4.1 13.7 - - + -
273B PHE* 3.8 17.7 - - + -
283B LEU* 3.6 25.6 - - + +
284B SER 3.7 9.4 - - - -
285B VAL 4.0 3.8 - - - +
286B ALA* 4.0 14.6 - - + +
297B LEU* 6.1 1.6 - - + -
301B MET* 4.0 33.2 - - + -
367B THR 3.1 7.8 + - - +
368B LEU* 3.3 11.9 - - + +
369B ILE 2.8 25.1 + - - +
387B VAL* 1.3 74.2 - - - +
389B GLN* 1.3 72.9 + - - +
390B VAL* 5.2 2.0 - - + -
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Residues in contact with GLN 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250B LYS* 3.6 19.8 + - - -
284B SER 2.8 14.6 + - - +
285B VAL* 3.4 8.2 - - + +
286B ALA* 2.7 32.9 + - - +
339B ALA* 4.9 1.4 - - - +
369B ILE* 3.4 28.9 - - + +
372B VAL* 4.1 28.0 - - + +
378B SER* 3.2 47.6 + - - +
379B TYR* 3.8 6.2 - - - +
383B ILE* 4.2 8.1 - - + +
387B VAL* 4.6 4.0 - - + -
388B LEU* 1.3 77.3 - - - +
390B VAL* 1.3 57.8 + - - +
391B VAL 4.1 0.2 - - - -
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Residues in contact with VAL 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B ALA* 3.2 12.3 - - + +
288B ALA* 4.5 9.4 - - + -
294B GLY* 5.1 1.1 - - - -
297B LEU* 4.3 22.2 - - + -
298B VAL* 3.9 19.7 - - + -
301B MET* 6.5 0.2 - - + -
368B LEU* 3.8 25.1 - - + -
369B ILE 2.9 9.5 + - - +
370B ASP* 3.6 17.6 - - - +
371B HIS* 3.3 21.8 + - - -
372B VAL* 3.3 7.2 + - - +
388B LEU* 5.2 3.8 - - + -
389B GLN* 1.3 77.4 - - - +
391B VAL* 1.3 71.3 + - - +
392B ARG* 4.2 6.0 + - - +
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Residues in contact with VAL 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B VAL* 4.0 20.2 - - + -
286B ALA 2.9 5.1 + - - -
287B VAL* 3.2 13.2 - - + +
288B ALA* 2.7 32.6 + - - +
372B VAL* 3.1 43.7 - - + +
373B THR 5.0 0.2 - - - +
374B PRO* 4.9 10.8 - - + -
379B TYR* 4.2 11.0 - - + -
390B VAL* 1.3 73.8 - - - +
392B ARG* 1.3 66.2 + - - +
393B VAL* 4.5 5.6 - - + -
402B LEU* 3.9 20.4 - - + -
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Residues in contact with ARG 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288B ALA* 3.4 18.4 - - + +
290B GLY 4.8 0.7 - - - +
291B ASP* 3.0 46.7 + - + +
294B GLY* 3.3 25.2 + - - -
295B ASP* 2.9 29.6 + - - +
298B VAL* 3.8 2.2 - - - +
370B ASP* 2.9 37.9 + - - -
371B HIS* 3.8 30.8 + - - +
372B VAL 4.7 2.2 + - - -
390B VAL* 4.2 2.3 + - + +
391B VAL* 1.3 80.8 - - - +
393B VAL* 1.3 66.6 + - - +
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Residues in contact with VAL 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B VAL* 3.8 26.7 - - + -
288B ALA 2.9 15.1 + - - +
289B VAL* 4.0 7.0 - - - -
290B GLY* 2.8 32.2 + - - -
291B ASP* 5.5 0.5 - - - +
391B VAL* 4.5 10.3 - - + -
392B ARG* 1.3 79.4 - - - +
394B ALA* 1.3 54.2 + - - +
395B THR 3.6 18.6 - - - +
398B ASP* 4.0 16.8 - - + +
399B ALA* 3.9 9.9 - - + +
402B LEU* 4.6 8.1 - - + -
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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