Contacts of the strand formed by residues 388 - 392 (chain A) in PDB entry 4Z1H
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 ARG 388 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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315A TYR* 4.5 1.8 - - + -
318A VAL* 4.5 1.8 - - + -
319A ALA* 3.9 40.3 + - + +
343A PHE* 3.3 6.8 - - - -
344A TYR* 2.8 44.0 + - + +
346A PRO* 4.4 15.6 - - + +
362A SER* 3.6 27.9 + - - +
363A VAL* 4.2 4.7 - - - +
385A ARG 3.1 26.7 + - - -
386A PHE* 3.6 13.1 + - - +
387A ILE* 1.3 90.5 + - - +
389A GLY* 1.3 58.8 + - - +
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Residues in contact with GLY 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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314A PHE* 4.9 0.2 - - - -
318A VAL* 3.8 26.9 - - - +
342A ILE 3.3 6.5 - - - -
344A TYR* 4.2 6.5 - - - -
362A SER 4.0 4.1 + - - +
363A VAL* 3.3 10.5 - - - +
364A ALA* 2.9 25.7 + - - +
388A ARG* 1.3 79.4 - - - +
390A VAL* 1.3 62.1 + - - +
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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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299A TRP* 3.6 31.9 - - + -
314A PHE* 3.5 31.6 - - + -
341A SER* 3.2 4.9 - - - -
342A ILE* 2.9 44.7 + - + +
363A VAL* 4.1 1.9 - - - +
364A ALA* 3.4 6.7 - - + +
366A TYR* 3.5 38.8 - - + -
389A GLY* 1.3 75.3 - - - +
391A VAL* 1.3 72.8 + - - +
392A ASP 4.8 0.2 - - - +
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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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339A ILE* 4.8 5.6 - - + -
341A SER* 3.8 9.4 - - - -
343A PHE* 3.5 31.9 - - + -
363A VAL* 4.1 9.6 - - + -
364A ALA 2.9 8.9 + - - +
365A LEU* 3.6 21.7 - - + +
366A TYR 2.9 27.4 + - - +
379A ILE* 4.5 7.2 - - + -
380A LEU* 5.9 0.2 - - + -
390A VAL* 1.3 80.6 - - - +
392A ASP* 1.3 67.1 + - - +
393A SER* 4.9 2.0 - - - -
414A LEU* 4.6 13.9 - - + -
418A LEU* 3.8 21.1 - - + -
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Residues in contact with ASP 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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299A TRP* 3.1 23.1 + - + +
300A MET* 3.3 17.7 - - - +
338A ASN* 3.8 1.9 + - - +
339A ILE* 3.6 1.7 - - - -
340A ARG* 2.9 52.8 + - + +
366A TYR* 3.1 18.8 - - + +
367A SER* 3.3 0.3 - - - -
368A ARG 2.8 24.7 + - - -
369A LYS* 3.0 20.1 + - - -
391A VAL* 1.3 76.4 - - - +
393A SER* 1.3 64.9 + - - +
394A GLU* 4.9 0.3 + - - +
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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