Contacts of the strand formed by residues 362 - 367 (chain B) in PDB entry 2G9Y
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 362 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B ASN* 3.2 34.0 + - + +
46B ILE* 4.2 14.6 - - + -
355B PHE* 3.6 12.4 - - + -
356B ALA* 3.9 33.7 + - + +
359B GLU* 2.8 20.3 + - - +
360B GLY 3.6 2.5 - - - +
361B ASN* 1.3 76.6 - - - +
363B LEU* 1.3 69.1 + - - +
364B VAL* 3.7 6.3 + - + -
422B TYR* 3.5 12.3 - - - +
423B GLY* 3.6 9.5 - - - -
424B PRO* 3.6 4.6 - - - +
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Residues in contact with LEU 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B ALA* 4.2 5.4 - - + +
44B ASN 2.9 7.0 + - - +
45B ILE* 3.2 23.2 - - + +
46B ILE 2.9 25.5 + - - +
361B ASN 4.2 0.4 - - - -
362B THR* 1.3 71.9 - - - +
364B VAL* 1.3 61.3 + - - +
365B ILE* 4.0 31.2 - - + -
421B ALA* 4.1 2.7 - - + -
422B TYR 3.4 13.7 - - - +
424B PRO* 3.4 29.6 - - + +
425B HIS* 4.6 1.1 - - + +
426B ALA* 4.0 19.5 - - + -
429B VAL* 6.2 0.2 - - + -
441B THR* 4.6 11.9 - - + +
442B MET* 5.1 0.2 - - - -
445B ALA* 3.9 22.9 - - + -
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Residues in contact with VAL 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B ILE* 3.4 9.9 - - + +
48B LEU* 3.7 25.6 - - + -
78B LEU* 3.7 6.6 - - + +
349B VAL* 5.4 0.4 - - + +
352B ALA* 4.2 14.6 - - + +
353B LEU* 3.9 26.7 - - + -
356B ALA* 3.4 32.5 - - + -
362B THR* 4.1 7.9 - - + +
363B LEU* 1.3 77.4 - - - +
365B ILE* 1.3 64.5 + - - +
366B VAL* 4.4 2.0 - - + -
421B ALA* 3.0 6.9 - - - +
422B TYR* 2.8 37.2 + - + +
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Residues in contact with ILE 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B ILE* 5.1 3.6 - - + -
46B ILE 3.0 8.9 + - - +
47B LEU* 3.7 18.8 - - + +
48B LEU* 2.8 32.9 + - - +
363B LEU* 4.0 26.9 - - + +
364B VAL* 1.3 79.8 - - - +
366B VAL* 1.3 66.3 + - - +
367B THR* 4.5 1.6 - - + -
419B ILE* 4.0 24.9 - - + -
420B ALA 3.3 9.2 - - - +
421B ALA* 3.8 12.8 - - + -
429B VAL* 4.6 7.0 - - + -
438B LEU* 3.5 25.8 - - + -
441B THR* 4.9 3.4 - - + -
442B MET* 4.4 12.1 - - + -
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Residues in contact with VAL 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B LEU* 3.4 16.8 - - + +
53B MET* 4.1 22.9 - - + -
75B ILE* 4.8 7.9 - - + -
78B LEU* 3.6 26.0 - - + -
345B LEU* 5.0 3.1 - - + -
349B VAL* 3.9 39.0 - - + -
364B VAL* 4.6 1.3 - - + -
365B ILE* 1.3 76.7 - - - +
367B THR* 1.3 64.3 + - - +
418B ARG* 4.3 12.9 + - - +
419B ILE* 3.5 1.4 - - - -
420B ALA* 2.9 33.9 + - - +
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Residues in contact with THR 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B LEU* 4.5 0.9 - - + -
48B LEU 3.1 3.9 + - - +
49B ILE* 3.4 23.1 - - + -
50B GLY* 2.9 23.7 + - - -
53B MET* 4.2 9.2 - - - +
84B TYR* 3.4 33.7 + - + +
365B ILE* 4.5 4.7 - - + -
366B VAL* 1.3 79.3 - - - +
368B ALA* 1.3 69.2 + - - +
418B ARG 2.9 22.9 + - - -
419B ILE* 3.7 13.7 - - + +
438B LEU* 4.4 13.9 - - + -
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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