Contacts of the strand formed by residues 387 - 393 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272H ALA* 4.4 7.6 + - - +
273H PHE* 4.0 3.8 - - - -
284H SER* 4.0 18.4 - - - +
332H VAL* 4.4 4.3 - - + -
336H ILE* 4.1 20.9 - - + -
367H THR* 3.5 23.1 - - + +
369H ILE* 3.8 17.5 - - + -
383H ILE* 3.9 43.5 - - + -
385H GLY 2.9 8.6 + - - +
386H PRO* 1.3 82.4 - - + +
388H LEU* 1.3 74.1 + - - +
389H GLN* 4.6 2.7 - - + +
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Residues in contact with LEU 388 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268H LEU* 4.8 11.9 - - + -
272H ALA* 3.7 21.1 - - + -
273H PHE* 4.0 14.1 - - + -
283H LEU* 3.9 8.1 - - + +
284H SER 3.5 12.6 - - - +
285H VAL 4.0 0.4 - - - -
286H ALA* 3.8 25.4 - - + +
297H LEU* 6.3 1.3 - - + -
301H MET* 4.1 33.2 - - + -
367H THR 3.0 7.7 + - - +
368H LEU* 4.9 9.4 - - + -
369H ILE* 3.1 25.5 + - - +
387H VAL* 1.3 78.7 - - - +
389H GLN* 1.3 82.6 + - - +
390H VAL* 5.0 4.7 - - + -
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Residues in contact with GLN 389 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250H LYS* 3.5 18.4 + - - -
284H SER* 2.7 15.7 + - - +
285H VAL* 4.2 9.0 - - + +
286H ALA 2.8 25.4 + - - -
339H ALA* 5.4 0.2 - - - +
369H ILE* 3.4 16.3 - - + +
372H VAL* 4.0 26.5 - - + +
378H SER* 3.0 52.4 + - - +
379H TYR* 3.3 10.2 - - - +
383H ILE* 3.6 13.7 - - - +
387H VAL* 4.6 1.3 - - + +
388H LEU* 1.3 83.0 - - - +
390H VAL* 1.3 62.8 + - - +
391H VAL 4.2 0.2 - - - -
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Residues in contact with VAL 390 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286H ALA* 3.3 11.9 - - + +
288H ALA* 4.7 5.4 - - + -
294H GLY 4.9 0.9 - - - +
297H LEU* 4.1 27.6 - - + -
298H VAL* 4.2 12.6 - - + -
301H MET* 6.3 0.9 - - + -
368H LEU* 3.8 24.5 - - + -
369H ILE 2.8 12.7 + - - +
370H ASP* 3.8 17.7 - - - +
371H HIS* 3.3 22.0 + - - -
372H VAL* 3.3 9.2 + - - +
388H LEU* 5.0 6.1 - - + -
389H GLN* 1.3 81.1 - - - +
391H VAL* 1.3 71.7 + - - +
392H ARG* 4.7 4.7 - - + +
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Residues in contact with VAL 391 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285H VAL* 3.9 20.9 - - + -
286H ALA 2.9 8.2 + - - +
287H VAL* 3.5 6.9 - - + -
288H ALA* 2.8 33.8 + - - +
372H VAL* 3.4 38.8 - - + +
373H THR* 5.7 2.5 - - - -
374H PRO* 5.8 3.6 - - + -
379H TYR* 4.2 11.7 - - + -
390H VAL* 1.3 73.7 - - - +
392H ARG* 1.3 63.9 + - - +
393H VAL* 3.9 13.9 - - + -
402H LEU* 3.6 26.2 - - + -
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Residues in contact with ARG 392 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288H ALA 3.6 6.7 - - - +
291H ASP* 3.2 49.4 + - - +
294H GLY* 2.9 32.2 + - - -
295H ASP* 3.2 19.7 + - - +
298H VAL* 3.7 1.8 - - - +
370H ASP* 2.9 40.0 + - - +
371H HIS* 3.4 36.1 + - - +
372H VAL 4.9 1.4 + - - +
390H VAL* 4.7 3.3 - - + +
391H VAL* 1.3 80.8 - - - +
393H VAL* 1.3 64.1 + - - +
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Residues in contact with VAL 393 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287H VAL* 3.5 26.5 - - + -
288H ALA 3.3 2.8 + - - +
289H VAL* 3.3 12.6 - - - -
290H GLY* 2.7 34.3 + - - -
291H ASP* 5.7 0.2 - - - +
391H VAL* 3.9 18.8 - - + -
392H ARG* 1.3 79.2 - - - +
394H ALA* 1.3 56.0 + - - +
395H THR 3.9 15.5 - - - +
398H ASP* 4.1 15.9 - - + +
399H ALA* 3.9 10.3 - - + +
402H LEU* 4.5 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