Contacts of the strand formed by residues 366 - 369 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361B ALA* 5.6 0.2 - - - +
364B GLY 3.6 2.3 + - - +
365B VAL* 1.3 73.4 - - - +
367B ILE* 1.3 69.4 + - - +
368B ALA* 5.1 3.6 - - - +
416B GLY 4.9 1.8 - - - +
417B GLN 3.2 5.8 + - - +
418B THR* 2.9 54.6 - - + +
419B VAL 2.9 5.0 + - - +
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Residues in contact with ILE 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356B TYR* 4.9 0.4 - - + -
357B LYS* 3.1 53.3 - - + +
360B MET* 3.9 22.2 - - + -
365B VAL* 4.5 5.2 - - + +
366B ASN* 1.3 82.5 + - - +
368B ALA* 1.3 69.9 + - - +
369B PHE* 3.8 14.1 - - + -
404B MET* 3.5 26.2 - - + -
407B ILE* 4.7 5.2 - - + -
419B VAL* 3.6 9.4 - - + +
421B ILE* 3.3 35.0 - - + -
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Residues in contact with ALA 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B LYS* 3.3 11.2 - - - +
366B ASN* 5.1 3.6 - - - +
367B ILE* 1.3 83.0 - - - +
369B PHE* 1.3 66.0 + - - +
370B THR* 4.0 0.4 + - - -
419B VAL 3.2 7.7 + - - +
420B ASN* 3.8 15.9 + - - +
421B ILE* 2.9 28.9 + - - +
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Residues in contact with PHE 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B THR* 6.3 0.2 - - + -
353B THR* 3.5 43.1 - - + -
356B TYR* 4.3 5.6 - - + -
357B LYS* 3.3 23.1 + - + +
367B ILE* 3.8 24.0 - - + -
368B ALA* 1.3 75.2 - - - +
370B THR* 1.3 62.9 + - - +
371B THR 3.9 0.9 + - - -
373B ALA* 4.7 2.7 - - + -
374B VAL* 4.4 18.2 - - + +
377B ILE* 4.4 15.5 - - + -
400B MET* 3.9 21.5 - - + -
403B LEU* 4.5 1.1 - - + -
404B MET* 3.8 14.4 - - - -
421B ILE* 3.5 35.7 - - + +
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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
------------------------------------------------------------
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