Contacts of the strand formed by residues 339 - 344 (chain A) in PDB entry 4ZZH
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 LEU 339 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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254A LYS 5.3 0.2 - - - -
255A LYS* 5.3 0.2 - - - -
256A ILE* 3.5 19.1 - - + +
258A VAL* 3.7 22.4 - - + -
330A ILE* 3.9 25.6 - - + +
334A ASP* 3.6 43.9 - - + +
337A GLY 3.6 3.2 - - - +
338A LYS* 1.3 77.8 + - - +
340A LEU* 1.3 62.0 + - - +
341A ARG* 3.6 17.3 - - - +
342A ASN 4.0 3.8 - - - +
356A ILE* 3.9 6.5 - - + -
358A ARG* 3.4 41.1 + - - +
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Residues in contact with LEU 340 (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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255A LYS* 3.6 35.7 - - + +
256A ILE 2.8 12.7 + - - +
257A ILE* 3.6 23.6 - - + -
338A LYS 3.3 3.8 + - - -
339A LEU* 1.3 71.7 - - - +
341A ARG* 1.3 64.4 + - - +
358A ARG* 3.1 35.9 + - - +
428A TYR* 4.5 7.9 - - + -
429A ASP* 3.6 31.2 - - - +
432A GLU* 4.1 10.5 - - + -
433A VAL* 3.7 29.4 - - + +
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Residues in contact with ARG 341 (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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256A ILE 3.3 2.6 + - - +
257A ILE* 3.4 6.1 - - + +
258A VAL 2.9 24.4 + - - +
339A LEU* 3.4 7.5 - - - +
340A LEU* 1.3 79.7 - - + +
342A ASN* 1.3 64.6 + - - +
343A TYR* 3.4 26.4 + - + -
358A ARG* 3.0 52.4 - - - +
359A ILE 4.4 1.4 + - - -
360A ILE* 3.5 30.7 - - + +
421A GLN* 5.7 1.8 - - - +
425A ALA* 4.4 12.8 + - - +
428A TYR* 4.1 13.3 - - - -
429A ASP* 2.8 43.7 + - - +
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Residues in contact with ASN 342 (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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258A VAL 2.9 16.0 - - - +
260A THR* 3.5 15.2 + - - +
327A HIS* 6.0 0.2 - - - -
330A ILE* 3.6 42.8 - - + +
339A LEU* 4.0 7.4 - - + +
341A ARG* 1.3 72.3 - - - +
343A TYR* 1.3 69.5 + - - +
344A THR* 5.0 0.7 - - - -
351A GLU* 3.9 25.4 - - - +
356A ILE* 4.0 7.3 - - + +
358A ARG 3.1 11.2 + - - +
359A ILE* 3.4 10.2 - - + +
360A ILE 3.2 22.5 + - - +
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Residues in contact with TYR 343 (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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257A ILE* 3.9 28.3 - - + -
258A VAL 3.0 6.9 + - - +
259A LEU* 3.3 9.3 - - + +
260A THR 3.0 23.0 + - - -
341A ARG* 3.4 27.6 - - + -
342A ASN* 1.3 74.8 - - - +
344A THR* 1.3 60.5 + - - +
360A ILE* 3.6 22.4 - - + -
362A CYS* 4.2 5.2 - - - -
422A PHE* 3.8 39.9 - + - -
425A ALA* 3.4 3.8 - - + +
426A MET* 3.4 33.9 + - + -
429A ASP* 2.7 23.5 + - - +
448A VAL* 4.8 2.3 - - + +
451A ILE* 4.1 20.2 - - + -
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Residues in contact with THR 344 (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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260A THR* 3.3 23.6 + - - -
342A ASN* 4.4 2.0 - - - +
343A TYR* 1.3 73.9 - - - +
345A GLN* 1.3 62.7 + - - +
346A ASN* 2.7 31.2 + - - +
351A GLU* 4.1 11.3 + - + -
359A ILE* 4.1 15.9 - - + -
360A ILE 3.2 10.3 + - - +
361A GLN* 3.6 28.0 - - + -
362A CYS* 3.1 33.1 + - - +
448A VAL* 4.6 1.1 - - - -
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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