Contacts of the strand formed by residues 366 - 369 (chain T) in PDB entry 1G3I
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 ASN 366 (chain T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357T LYS* 4.5 16.3 + - - +
361T ALA* 5.7 4.6 - - - +
365T VAL* 1.3 78.1 + - - +
367T ILE* 1.3 79.8 + - - +
417T GLN 2.8 16.2 + - - +
418T THR* 3.5 33.4 + - - +
419T VAL 3.4 13.5 + - - -
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Residues in contact with ILE 367 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356T TYR 3.0 31.4 - - - +
357T LYS* 3.2 47.5 + - + +
360T MET* 3.5 16.6 - - + -
365T VAL* 4.7 3.4 - - + -
366T ASN* 1.3 88.0 + - - +
368T ALA* 1.3 60.0 + - - +
369T PHE* 3.9 16.9 + - + -
404T MET* 4.3 10.5 - - + -
407T ILE* 3.4 28.9 - - + -
418T THR* 5.9 0.7 - - - -
419T VAL* 3.8 9.0 - - + +
421T ILE* 5.2 7.0 - - + -
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Residues in contact with ALA 368 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357T LYS* 5.2 1.6 - - - +
366T ASN 4.4 0.2 - - - -
367T ILE* 1.3 72.7 - - - +
369T PHE* 1.3 61.5 + - - +
370T THR* 3.7 2.4 + - - +
418T THR* 5.3 7.4 - - + +
419T VAL 3.1 8.7 + - - +
420T ASN* 3.1 33.2 - - - +
421T ILE* 2.7 35.4 + - - +
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Residues in contact with PHE 369 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353T THR* 3.2 59.9 - - + -
356T TYR* 4.8 1.1 - - + -
357T LYS* 5.6 2.8 - - + +
367T ILE* 3.9 16.9 + - + -
368T ALA* 1.3 79.4 - - - +
370T THR* 1.3 68.1 + - - +
371T THR* 3.7 1.9 + - - +
373T ALA* 5.8 0.2 - - - -
374T VAL* 4.2 9.5 - - + +
377T ILE* 5.7 4.5 - - + -
400T MET* 3.9 14.8 - - + -
403T LEU* 5.3 1.6 - - + -
404T MET* 3.3 30.7 - - + -
421T ILE* 3.1 41.5 - - + -
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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