Contacts of the strand formed by residues 420 - 423 (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 THR 420 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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410A ILE* 3.9 40.3 - - + +
413A ASN* 3.8 16.2 - - - +
414A TYR* 4.8 1.8 - - + +
419A GLN* 1.3 82.4 - - - +
421A ALA* 1.3 68.7 + - - +
422A PHE* 4.2 1.9 + - - -
473A ASP 3.3 10.2 + - - +
474A VAL* 3.2 32.0 - - + +
475A VAL 3.5 1.2 + - - -
493A LEU* 3.6 31.8 - - - +
495A ILE* 4.9 1.6 - - - +
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Residues in contact with ALA 421 (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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420A THR* 1.3 81.1 + - - +
422A PHE* 1.3 62.8 + - - +
423A MET* 3.6 2.8 + - + +
475A VAL* 3.8 22.7 - - + +
481A LEU* 5.0 8.7 - - + -
491A LEU* 4.1 23.6 - - + -
493A LEU 3.2 7.0 + - - +
494A VAL* 3.6 14.5 - - + +
495A ILE 3.5 15.2 + - - -
510A LEU* 5.9 2.5 - - + -
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Residues in contact with PHE 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A ALA* 5.5 3.8 - - + -
410A ILE* 4.6 15.9 - - + -
420A THR* 4.2 3.7 + - - +
421A ALA* 1.3 72.2 - - - +
423A MET* 1.3 84.2 + - - +
424A VAL* 4.3 6.1 - - + -
433A HIS* 4.3 27.1 - + - -
437A THR* 4.1 19.1 - - + -
474A VAL* 5.2 3.0 - - + +
475A VAL 3.2 21.1 + - - +
476A ILE* 4.0 33.0 - - + -
477A GLY* 3.4 14.9 + - - +
481A LEU* 4.5 3.1 - - - +
495A ILE* 2.9 39.7 - - + -
496A ILE 4.6 0.9 - - - -
497A ASP* 4.4 9.2 - - - -
522A MET* 4.5 7.9 - - + -
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Residues in contact with MET 423 (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* 4.0 10.3 - - + +
422A PHE* 1.3 79.4 - - - +
424A VAL* 1.3 72.4 + - - +
477A GLY 3.6 3.8 - - - +
478A THR* 2.2 47.1 - - - +
479A HIS* 2.9 19.1 - - - +
481A LEU* 3.8 16.8 - - + -
482A ILE* 3.3 28.7 - - + -
494A VAL* 4.3 11.2 - - + -
495A ILE 3.0 15.1 + - - +
496A ILE* 3.8 19.0 - - + -
497A ASP 3.3 17.2 + - - -
500A HIS* 4.0 5.8 - - + -
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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