Contacts of the strand formed by residues 493 - 497 (chain A) in PDB entry 1GM5
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 493 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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384A MET* 5.0 5.8 - - - -
390A MET* 6.2 0.9 - - - -
409A ALA* 4.0 20.2 - - + +
410A ILE* 4.9 0.2 - - - -
413A ASN* 3.2 20.0 - - + +
419A GLN 4.0 0.4 + - - -
420A THR* 3.6 27.0 - - + +
421A ALA 3.2 15.9 + - - -
491A LEU* 3.4 7.4 - - - +
492A GLY* 1.3 83.1 - - - +
494A VAL* 1.3 119.0 + - - +
495A ILE* 3.2 18.2 - - + +
517A VAL* 3.0 9.4 - - - +
518A ASP* 2.8 22.2 - - + +
520A LEU* 5.4 5.2 - - + -
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Residues in contact with VAL 494 (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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421A ALA* 3.6 16.8 - - + +
423A MET* 4.3 13.0 - - + -
482A ILE* 5.9 0.4 - - + -
491A LEU* 4.3 3.6 - - + -
493A LEU* 1.3 92.2 - - - +
495A ILE* 1.3 65.5 + - - +
496A ILE* 4.5 10.0 - - + +
510A LEU* 3.3 37.7 - - + -
517A VAL* 3.7 16.4 - - + -
518A ASP 2.8 6.4 + - - +
519A THR* 3.7 12.6 - - + +
520A LEU* 2.9 27.4 + - - +
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Residues in contact with ILE 495 (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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406A ALA* 3.8 37.2 - - + +
409A ALA* 4.5 3.6 - - + -
410A ILE* 4.0 20.6 - - + -
420A THR* 4.9 1.3 - - - +
421A ALA 3.5 5.4 + - - +
422A PHE* 2.9 38.4 - - + -
423A MET* 3.0 23.9 + - - +
493A LEU* 3.2 20.0 - - + +
494A VAL* 1.3 73.2 - - - +
496A ILE* 1.3 74.6 + - - +
520A LEU* 3.3 20.0 - - + +
522A MET* 4.5 10.3 - - + -
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Residues in contact with ILE 496 (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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423A MET* 3.8 24.2 - - + -
494A VAL* 4.5 11.4 - - + +
495A ILE* 1.3 85.9 - - - +
497A ASP* 1.3 76.8 + - - +
498A GLU 3.6 9.2 - - - +
500A HIS* 4.1 14.8 - - + +
519A THR* 5.4 6.5 - - + -
520A LEU 2.7 17.2 + - - +
521A VAL* 4.0 16.8 - - + -
522A MET* 2.9 35.2 + - - +
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Residues in contact with ASP 497 (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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422A PHE* 4.4 3.1 - - - -
423A MET 3.3 7.3 + - - -
424A VAL* 4.0 17.3 - - + -
425A PRO* 3.2 11.8 - - + +
429A LEU* 6.3 0.9 - - + -
433A HIS* 3.3 18.8 - - + -
496A ILE* 1.3 75.7 - - - +
498A GLU* 1.3 81.0 + - + +
500A HIS* 2.9 23.2 + - - -
522A MET* 2.6 42.6 - - - +
651A VAL 5.8 0.2 - - - +
1757A MG 4.2 4.4 - - - -
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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