Contacts of the helix formed by residues 663 - 672 (chain B) in PDB entry 2G5T
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 ASP 663 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201B TRP* 3.5 17.5 - - + -
202B VAL* 4.1 7.4 - - + -
206B GLU* 2.5 34.9 - - - +
256B TYR* 3.1 20.5 + - + +
257B PRO 3.1 14.1 - - - +
662B TYR* 1.3 94.8 - - - +
664B SER* 1.3 58.5 + - - +
665B VAL 3.5 1.0 + - - -
666B TYR* 2.9 26.5 + - - +
667B THR* 2.8 29.6 + - - -
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Residues in contact with SER 664 (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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257B PRO* 2.9 16.1 + - - +
258B LYS 3.8 12.5 - - - -
259B ALA* 4.1 5.4 - - - +
263B ASN* 2.6 32.5 + - - -
299B TYR* 4.4 0.2 - - - -
318B ARG* 3.8 2.9 - - - -
662B TYR 3.7 0.6 + - - -
663B ASP* 1.3 70.9 - - - +
665B VAL* 1.3 70.6 + - - +
668B GLU* 2.9 63.9 + - - +
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Residues in contact with VAL 665 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B VAL* 3.5 28.0 - - + +
203B TYR* 5.9 0.4 - - + -
206B GLU* 3.5 30.7 - - + +
207B VAL* 4.8 10.3 - - + -
263B ASN* 5.1 0.2 - - - +
299B TYR* 3.5 40.6 - - + +
316B LEU* 6.3 0.4 - - + -
320B GLN* 2.7 31.9 + - - +
663B ASP* 3.5 1.2 + - - -
664B SER* 1.3 83.4 + - - +
666B TYR* 1.3 59.5 - - - +
669B ARG* 3.4 18.9 + - - +
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Residues in contact with TYR 666 (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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206B GLU* 3.5 27.3 - - - +
357B PHE* 4.7 10.9 - + - -
547B TYR* 4.7 8.5 + - - -
549B GLY* 4.5 1.6 - - - -
550B PRO* 3.5 15.6 + - - +
598B LEU* 4.9 0.9 - - + -
631B TYR* 3.4 24.2 - + - -
659B TRP* 4.0 22.4 - + - -
662B TYR* 3.8 21.5 - + + -
663B ASP* 2.9 17.3 + - - +
665B VAL* 1.3 76.5 - - - +
667B THR* 1.3 69.8 + - - +
669B ARG* 3.1 25.7 + - - +
670B TYR* 3.1 50.1 - + - -
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Residues in contact with THR 667 (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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259B ALA* 3.9 5.6 - - + -
598B LEU* 5.7 0.4 - - - -
659B TRP* 3.4 40.7 - - + +
662B TYR* 3.3 25.6 - - - +
663B ASP 2.8 22.4 + - - -
664B SER 4.2 0.2 - - - -
666B TYR* 1.3 83.0 - - - +
668B GLU* 1.3 58.5 + - - +
669B ARG 3.2 0.7 + - - -
670B TYR* 3.2 5.5 + - - +
671B MET* 2.9 33.7 + - + +
683B TYR* 3.3 21.8 - - + +
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Residues in contact with GLU 668 (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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259B ALA* 4.6 1.1 - - - -
260B GLY* 2.6 32.2 + - - +
299B TYR* 3.9 2.4 + - - -
318B ARG* 2.6 54.2 + - - +
319B ILE* 5.8 1.2 - - - -
320B GLN* 4.3 7.1 + - - +
664B SER* 2.9 31.4 + - - +
667B THR* 1.3 70.6 - - - +
669B ARG* 1.3 62.8 + - - +
672B GLY* 2.9 46.3 + - - +
673B LEU* 4.0 13.1 - - + +
683B TYR* 4.0 6.7 - - - +
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Residues in contact with ARG 669 (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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206B GLU* 3.8 22.2 + - - -
316B LEU* 5.7 0.4 - - - +
320B GLN* 2.8 51.5 + - - +
353B TRP* 3.7 45.1 - - + +
354B VAL 5.4 1.8 - - - -
357B PHE* 2.9 47.1 + - - +
358B ARG* 5.4 0.4 - - - +
595B ASN* 4.3 4.2 + - - -
665B VAL* 3.4 17.0 + - - +
666B TYR* 3.1 31.0 + - - +
667B THR 3.1 0.6 - - - -
668B GLU* 1.3 79.2 - - - +
670B TYR* 1.3 86.2 + - + +
672B GLY 4.8 0.2 - - - -
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Residues in contact with TYR 670 (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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353B TRP* 3.5 47.1 - + + -
356B ARG 4.5 2.5 + - - -
357B PHE* 3.7 16.3 - - - -
550B PRO* 3.4 31.4 + - + +
594B ILE 5.0 2.0 - - - +
595B ASN* 3.9 6.9 + - - +
596B ARG* 2.5 36.4 + - - +
597B ARG 4.1 0.7 + - - -
598B LEU* 4.0 23.8 - - + -
666B TYR* 3.1 59.3 - + - -
667B THR 3.2 3.4 + - - -
669B ARG* 1.3 111.0 + - - +
671B MET* 1.3 56.5 + - - +
672B GLY 3.7 0.9 - - - -
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Residues in contact with MET 671 (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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596B ARG* 4.2 9.0 - - - -
597B ARG 4.3 0.2 - - - -
598B LEU* 3.5 48.2 - - + -
659B TRP* 4.2 7.6 - - + -
667B THR* 2.9 23.1 + - + +
670B TYR* 1.3 81.2 - - - +
672B GLY* 1.3 63.1 + - - +
679B ASN* 3.0 31.3 - - - +
682B HIS* 3.4 25.8 - - + -
683B TYR* 3.6 50.6 - - + +
686B SER* 4.0 7.4 - - - +
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Residues in contact with GLY 672 (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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319B ILE* 5.3 7.6 - - - -
596B ARG* 4.3 7.9 - - - +
668B GLU* 2.9 26.5 + - - +
670B TYR 3.7 1.2 - - - -
671B MET* 1.3 78.7 - - - +
673B LEU* 1.3 61.2 + - - -
678B ASP* 4.2 9.2 - - - -
683B TYR* 2.8 26.2 + - - -
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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