Contacts of the strand formed by residues 446 - 451 (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 446 (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* 5.3 0.5 - - - -
401A GLN* 3.9 10.7 - - - +
403A CYS* 3.5 28.1 - - - +
417A GLY* 4.2 1.8 - - - -
418A HIS 3.0 28.6 + - - +
423A ASN 3.7 19.5 - - - +
425A LEU* 4.0 10.5 - - + -
442A HIS* 3.7 20.6 - - + -
445A ARG* 1.3 78.5 - - - +
447A LEU* 1.3 63.0 + - - +
448A SER 4.0 2.5 - - - +
449A LEU* 3.9 24.7 - - + -
460A SER* 4.3 4.3 - - - -
461A ALA 3.7 11.9 - - - +
462A ALA* 4.0 2.0 - - - -
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Residues in contact with LEU 447 (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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181A ILE* 4.4 17.5 - - + -
182A ARG 4.0 16.8 - - - +
183A ASN* 3.6 21.1 - - - +
184A ASP 4.3 19.5 - - - +
185A TYR* 4.4 10.5 - - + -
187A LEU 5.8 0.2 - - - +
189A LEU* 5.3 4.3 - - + -
359A LYS* 2.7 31.0 + - - +
403A CYS* 3.6 15.3 - - - +
404A SER* 4.2 0.5 + - - -
445A ARG* 4.1 17.9 - - - +
446A VAL* 1.3 78.8 - - - +
448A SER* 1.3 61.1 + - - +
461A ALA* 2.7 14.6 + - + +
462A ALA 3.8 6.3 - - - +
463A ALA* 3.8 22.9 - - - +
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Residues in contact with SER 448 (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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187A LEU 4.2 1.2 + - - -
188A ASN* 4.3 4.3 + - - -
189A LEU* 4.0 17.0 + - - +
190A VAL* 3.6 25.8 - - - -
359A LYS* 3.9 10.0 + - - +
404A SER* 3.4 10.5 - - - -
446A VAL* 4.0 0.7 - - - +
447A LEU* 1.3 85.6 + - - +
449A LEU* 1.3 64.8 + - - +
459A ALA 3.8 0.3 - - - +
460A SER* 3.3 3.6 - - - -
461A ALA* 2.9 32.8 + - - +
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Residues in contact with LEU 449 (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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190A VAL* 5.0 1.0 - - - +
404A SER* 3.0 23.9 + - - +
406A LEU* 3.8 20.0 - - + +
415A ILE* 3.8 30.3 - - + +
416A SER 3.8 7.9 - - - +
417A GLY* 3.6 23.6 - - - +
425A LEU* 4.2 8.7 - - + -
446A VAL* 3.9 13.0 - - + -
448A SER* 1.3 88.9 - - - +
450A THR* 1.3 63.9 + - - +
458A VAL* 3.8 13.5 - - + -
459A ALA 3.3 3.4 - - - -
460A SER* 3.5 22.9 - - - -
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Residues in contact with THR 450 (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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190A VAL* 3.9 25.6 - - + -
191A ASP* 3.5 9.0 + - - -
192A TRP* 3.1 26.1 + - + +
198A LEU* 3.7 30.1 - - + -
406A LEU* 3.7 10.3 - - - -
449A LEU* 1.3 76.1 - - - +
451A MET* 1.3 61.4 + - - +
458A VAL* 3.5 3.5 - - - +
459A ALA* 2.9 43.7 + - + +
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Residues in contact with MET 451 (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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192A TRP* 3.3 23.8 - - - +
406A LEU* 3.9 22.8 - - + +
407A TRP 3.3 27.4 - - - +
408A SER* 4.2 5.2 - - - +
409A PRO* 5.6 1.6 - - + -
450A THR* 1.3 77.8 + - - +
452A SER* 1.3 74.5 + - - +
453A PRO 4.0 0.2 - - - -
455A GLY* 3.6 27.1 - - - +
457A THR 3.6 11.7 - - - +
458A VAL* 3.7 15.3 - - - -
473A PHE* 4.0 21.3 - - + -
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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