Contacts of the strand formed by residues 417 - 422 (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 LEU 417 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A ASP* 5.4 0.2 - - - -
53B MET 4.7 2.5 - - - +
54B GLY* 4.1 14.1 - - - -
55B ASP* 3.5 11.7 - - - +
83B GLN* 3.4 7.4 - - - -
84B TYR* 3.0 36.3 + - + -
86B HIS* 3.8 11.4 - - + +
367B THR* 3.5 13.7 - - - +
368B ALA* 3.8 17.3 - - + +
370B HIS* 3.2 44.9 - - - +
371B ALA* 3.4 10.3 - - + +
415B SER 4.2 0.7 - - - +
416B GLN* 1.3 78.7 - - - +
418B ARG* 1.3 80.6 + - - +
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Residues in contact with ARG 418 (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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83A GLN* 3.4 31.3 + - - +
416A GLN* 4.1 9.0 - - - +
432A LEU* 5.6 7.2 - - - +
53B MET* 5.5 1.9 + - - +
54B GLY 5.7 0.2 - - - -
55B ASP* 3.0 24.3 + - - +
58B ILE* 3.9 21.9 - - + +
75B ILE* 2.9 45.4 + - - +
76B ASP* 4.0 15.3 + - - +
78B LEU* 4.1 8.1 + - - +
81B THR* 4.0 11.1 - - + +
82B GLY 3.4 7.6 - - - -
83B GLN* 5.0 0.4 - - - +
366B VAL* 4.7 10.9 + - - +
367B THR* 2.9 22.5 + - - -
417B LEU* 1.3 80.4 - - - +
419B ILE* 1.3 66.9 + - - +
420B ALA* 3.6 24.6 - - + +
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Residues in contact with ILE 419 (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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81B THR* 3.5 2.4 - - - -
82B GLY 3.0 37.4 + - - +
83B GLN 4.1 2.5 - - - +
84B TYR* 3.9 42.6 - - + +
365B ILE* 4.0 15.9 - - + -
366B VAL 3.5 5.4 - - - -
367B THR* 3.7 13.5 - - - +
418B ARG* 1.3 78.1 - - - +
420B ALA* 1.3 63.4 + - - +
429B VAL* 3.5 48.3 - - + +
433B THR* 4.8 2.0 - - - +
438B LEU* 4.3 14.4 - - + -
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Residues in contact with ALA 420 (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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78B LEU* 3.4 18.3 - - + +
80B LEU 3.2 9.9 - - - +
81B THR* 3.7 5.4 - - + -
365B ILE* 3.3 5.9 - - - +
366B VAL 2.9 32.4 + - - +
418B ARG* 3.6 36.8 - - - +
419B ILE* 1.3 78.2 - - - +
421B ALA* 1.3 63.1 + - - +
429B VAL* 4.1 2.2 - - - -
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Residues in contact with ALA 421 (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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78B LEU* 3.6 5.5 - - - +
79B PRO* 3.7 5.4 - - - +
80B LEU* 2.9 32.7 + - - +
363B LEU* 4.1 2.0 - - + -
364B VAL 3.0 12.8 - - - +
365B ILE* 3.8 15.9 - - + -
420B ALA* 1.3 79.2 - - - +
422B TYR* 1.3 62.4 + - - +
426B ALA* 3.7 21.8 - - + -
429B VAL* 3.8 16.2 - - + -
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Residues in contact with TYR 422 (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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2B PRO* 4.9 1.2 - - - +
4B MET* 2.5 47.4 + - + +
5B PRO 3.2 21.3 - - - -
6B VAL* 3.5 15.9 - - + -
36B SER* 5.9 1.3 - - - -
78B LEU* 4.6 2.0 - - + -
79B PRO* 4.1 18.4 - - + -
80B LEU* 5.8 0.2 - - - -
353B LEU* 4.0 30.3 - - + -
356B ALA* 4.0 32.5 + - + -
357B LYS* 3.6 20.1 + - - +
360B GLY* 5.8 1.4 - - - -
362B THR 3.5 3.4 - - - +
363B LEU* 3.4 4.2 - - - +
364B VAL* 2.8 31.9 + - + +
421B ALA* 1.3 76.4 - - - +
423B GLY* 1.3 69.8 + - - +
426B ALA* 3.9 4.0 - - - -
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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