Contacts of the strand formed by residues 387 - 393 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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272A ALA* 4.5 6.0 + - - +
273A PHE* 4.0 3.2 - - - -
283A LEU 4.9 0.7 - - - +
284A SER* 4.0 19.6 - - - +
332A VAL* 4.3 4.5 - - + -
336A ILE* 4.0 22.2 - - + -
367A THR* 3.4 22.9 - - + +
369A ILE* 3.8 26.2 - - + -
383A ILE* 4.0 34.2 - - + +
385A GLY 2.7 19.7 + - - +
386A PRO* 1.3 80.6 - - + +
388A LEU* 1.3 63.9 + - - +
389A GLN* 4.6 2.6 - - + +
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Residues in contact with LEU 388 (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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268A LEU* 4.7 13.0 - - + -
272A ALA* 3.7 21.5 - - + -
273A PHE* 3.6 17.9 - - + -
283A LEU* 4.2 5.4 - - + +
284A SER 3.7 11.4 - - - +
285A VAL 4.2 0.9 - - - +
286A ALA* 3.9 21.5 - - + +
297A LEU* 6.0 2.7 - - + -
301A MET* 4.2 32.5 - - + -
367A THR 3.0 9.0 + - - +
368A LEU* 3.5 14.7 - - + +
369A ILE 2.9 25.1 + - - -
387A VAL* 1.3 74.1 - - - +
389A GLN* 1.3 76.8 + - - +
390A VAL* 5.5 1.3 - - + -
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Residues in contact with GLN 389 (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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250A LYS* 3.5 30.0 + - - -
284A SER* 2.9 16.0 + - - +
285A VAL* 3.3 9.6 - - + +
286A ALA 2.8 25.1 + - - -
339A ALA* 5.0 0.6 - - - +
369A ILE* 3.6 22.8 - - + +
372A VAL* 3.9 27.2 - - + +
376A MET* 6.0 0.4 - - - -
378A SER* 3.2 40.0 + - - +
379A TYR* 3.6 10.4 - - - +
383A ILE* 3.9 10.2 - - - +
387A VAL* 4.1 3.5 - - + +
388A LEU* 1.3 77.1 - - - +
390A VAL* 1.3 60.3 + - - +
391A VAL 4.2 0.2 - - - -
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Residues in contact with VAL 390 (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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286A ALA* 3.2 17.7 - - + +
288A ALA* 4.4 7.9 - - + -
294A GLY 5.1 1.6 - - - +
297A LEU* 4.2 17.9 - - + -
298A VAL* 4.0 13.9 - - + -
368A LEU* 3.6 18.8 - - + -
369A ILE 3.1 20.0 + - - +
370A ASP* 3.6 19.2 - - - +
371A HIS* 3.4 21.0 + - - -
372A VAL* 3.6 6.9 + - - +
388A LEU* 5.5 1.8 - - + -
389A GLN* 1.3 73.6 - - - +
391A VAL* 1.3 70.9 + - - +
392A ARG* 4.7 4.4 - - + +
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Residues in contact with VAL 391 (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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285A VAL* 4.0 17.7 - - + -
286A ALA 2.9 7.5 + - - +
287A VAL* 3.5 5.9 - - + -
288A ALA* 2.7 34.1 + - - +
372A VAL* 3.2 40.8 - - + +
373A THR* 5.3 1.8 - - - -
374A PRO* 5.5 7.9 - - + -
379A TYR* 4.3 11.7 - - + -
390A VAL* 1.3 73.7 - - - +
392A ARG* 1.3 73.0 + - - +
393A VAL* 4.1 5.6 - - + -
402A LEU* 4.0 24.2 - - + -
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Residues in contact with ARG 392 (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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288A ALA* 3.4 7.6 - - + +
290A GLY 5.1 1.1 - - - +
291A ASP* 3.0 43.1 + - + +
294A GLY* 3.4 30.0 + - - -
295A ASP* 2.9 30.0 + - - +
298A VAL* 3.7 5.8 - - - +
370A ASP* 3.0 37.7 + - - +
371A HIS* 3.6 33.7 + - - +
372A VAL 4.9 1.4 + - - -
390A VAL* 4.7 2.0 - - + +
391A VAL* 1.3 83.4 - - - +
393A VAL* 1.3 67.4 + - - +
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Residues in contact with VAL 393 (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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287A VAL* 3.8 21.3 - - + -
288A ALA 3.0 11.2 + - - +
289A VAL* 3.4 7.4 - - - -
290A GLY* 2.7 33.1 + - - -
391A VAL* 4.1 14.6 - - + -
392A ARG* 1.3 80.0 - - - +
394A ALA* 1.3 57.4 + - - +
395A THR 3.6 19.7 - - - +
398A ASP* 4.0 17.3 - - + +
399A ALA* 3.8 14.1 - - + +
402A LEU* 4.6 7.0 - - + -
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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