Contacts of the strand formed by residues 402 - 408 (chain A) in PDB entry 4GGA
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 402 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185A TYR* 3.1 10.3 + - - -
360A ALA* 3.6 10.8 + - + +
374A GLY* 3.7 19.8 - - - +
375A GLY 3.0 17.3 + - - +
380A ARG 4.4 0.9 - - - -
381A HIS 4.1 14.8 - - - +
382A ILE* 4.2 7.0 - - + -
398A ALA* 4.0 10.3 - - + -
400A SER 3.6 9.0 - - - +
401A GLN* 1.3 76.4 - - - +
403A CYS* 1.3 61.2 + - - +
404A SER 3.9 17.3 - - - +
405A ILE* 4.0 17.3 - - + -
416A SER* 4.0 10.3 - - - -
417A GLY 3.4 6.3 - - - +
418A HIS* 3.8 12.1 - - + -
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Residues in contact with CYS 403 (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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185A TYR* 3.6 24.9 + - + -
359A LYS* 3.4 29.4 - - + +
360A ALA* 3.8 4.0 + - - +
401A GLN* 3.9 3.8 - - - +
402A VAL* 1.3 75.5 - - - +
404A SER* 1.3 78.5 + - - +
417A GLY 3.1 18.7 + - - -
418A HIS* 5.3 0.4 - - - +
446A VAL* 3.5 41.7 - - - +
447A LEU* 3.6 17.0 - - - +
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Residues in contact with SER 404 (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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316A ARG* 6.4 0.4 - - - -
359A LYS* 6.1 0.2 - - - -
360A ALA* 3.7 7.0 - - - +
402A VAL* 3.6 2.4 - - - +
403A CYS* 1.3 96.9 - - - +
405A ILE* 1.3 69.3 + - - +
406A LEU* 5.9 0.7 - - - -
416A SER* 3.2 5.2 - - - -
417A GLY 3.0 23.2 + - - -
448A SER* 3.4 4.9 - - - -
449A LEU* 3.0 44.4 + - - +
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Residues in contact with ILE 405 (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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316A ARG* 5.8 0.5 + - - -
360A ALA* 3.9 11.8 - - + +
361A VAL 4.7 4.2 - - - +
362A ALA* 3.4 28.4 - - + +
372A ALA* 4.2 4.7 - - + +
373A THR* 3.6 40.8 - - - +
374A GLY* 3.7 7.4 - - - +
382A ILE* 4.2 15.5 - - + -
402A VAL* 4.0 8.7 - - + -
404A SER* 1.3 83.0 - - - +
406A LEU* 1.3 86.5 + - - +
407A TRP* 4.8 0.2 - - - +
414A LEU* 3.9 23.6 - - + -
415A ILE 3.2 8.7 - - - +
416A SER* 4.2 7.4 - - - -
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Residues in contact with LEU 406 (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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362A ALA* 4.6 2.9 - - - -
404A SER* 5.9 0.4 - - - -
405A ILE* 1.3 82.7 - - - +
407A TRP* 1.3 63.8 + - - +
414A LEU* 3.1 6.1 - - - +
415A ILE* 2.8 41.8 + - + -
449A LEU* 3.8 34.1 - - + +
450A THR* 3.7 29.2 - - - -
451A MET* 3.9 23.6 - - + +
458A VAL* 4.0 18.2 - - + -
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Residues in contact with TRP 407 (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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362A ALA* 2.9 33.8 + - + -
363A TRP 3.1 18.0 - - - -
364A CYS* 3.7 26.0 - - + -
365A PRO* 3.5 22.2 - - + +
366A TRP* 3.4 19.7 - + + -
370A VAL* 3.8 25.6 - - + -
372A ALA* 3.6 26.5 - - + +
384A ILE* 4.4 3.4 - - + -
405A ILE* 4.8 0.9 - - + -
406A LEU* 1.3 76.4 - - - +
408A SER* 1.3 59.8 + - - +
409A PRO* 4.1 4.4 - - - +
413A GLU 3.5 5.8 - - - -
414A LEU* 3.7 22.4 - - + +
430A TYR* 3.6 37.2 - + - -
451A MET* 3.3 18.2 - - - +
473A PHE* 5.7 0.2 - - - -
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Residues in contact with SER 408 (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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366A TRP* 3.8 4.1 - - - -
407A TRP* 1.3 74.5 - - - +
409A PRO* 1.3 65.4 - - - +
410A HIS* 3.4 19.2 + - - +
411A TYR 4.5 0.6 + - - -
412A LYS* 3.1 8.0 + - - -
413A GLU* 2.8 35.0 + - - -
414A LEU* 4.7 0.2 - - - +
451A MET* 4.2 2.8 - - - +
455A GLY 4.5 2.1 + - - -
473A PHE* 3.6 49.0 - - - +
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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