Contacts of the helix formed by residues 630 - 641 (chain A) 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 SER 630 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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547A TYR* 4.9 0.4 - - - -
629A TRP* 1.3 74.7 - - - +
631A TYR* 1.3 53.1 + - - -
633A GLY* 2.6 24.4 + - - -
634A TYR 2.9 10.0 + - - -
653A VAL 2.8 14.3 + - - -
654A ALA 3.0 15.7 - - - -
655A PRO* 3.5 6.1 - - - +
656A VAL 3.9 2.5 + - - -
711A VAL* 3.8 1.1 - - - +
740A HIS* 3.2 25.7 + - - -
800A ACF 1.4 77.3 - - - +
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Residues in contact with TYR 631 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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547A TYR* 3.2 36.8 - - + +
548A ALA 3.6 5.2 - - - -
549A GLY* 3.3 18.2 - - - -
550A PRO* 3.6 7.9 - - + +
594A ILE* 4.8 0.2 - - - +
598A LEU* 3.4 23.5 - - + +
599A GLY 4.3 0.2 + - - -
602A GLU* 2.7 23.6 + - - +
629A TRP 3.0 1.0 + - - -
630A SER* 1.3 80.9 + - - +
632A GLY* 1.3 57.5 + - - +
634A TYR* 3.2 11.7 + + - +
635A VAL* 3.0 43.8 + - + +
659A TRP* 3.5 34.8 - + - -
666A TYR* 3.4 26.0 - + - -
800A ACF 3.2 11.7 + - + -
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Residues in contact with GLY 632 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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546A VAL* 3.1 28.5 - - - +
547A TYR* 3.5 11.3 + - - +
628A GLY* 3.4 7.1 - - - -
629A TRP 2.8 11.8 + - - -
631A TYR* 1.3 80.7 - - - +
633A GLY* 1.3 55.5 + - - +
635A VAL* 4.6 0.4 - - - -
636A THR* 2.9 33.8 + - - -
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Residues in contact with GLY 633 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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628A GLY 3.3 21.0 - - - -
629A TRP 3.5 0.4 - - - -
630A SER 2.6 15.8 + - - -
632A GLY* 1.3 69.7 - - - +
634A TYR* 1.3 54.2 + - - -
636A THR* 4.2 0.7 - - - -
637A SER* 2.8 36.9 + - - -
652A ALA* 3.5 10.8 - - - +
653A VAL 4.2 1.6 - - - -
655A PRO* 3.3 17.4 - - - +
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Residues in contact with TYR 634 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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599A GLY* 3.4 33.7 - - - -
602A GLU* 4.4 3.8 - - - -
603A VAL* 5.3 0.2 - - + -
630A SER 2.9 5.9 + - - +
631A TYR* 3.4 20.9 - + - +
633A GLY* 1.3 76.5 - - - +
635A VAL* 1.3 61.4 + - + +
637A SER* 3.1 5.9 + - - -
638A MET* 2.8 52.8 + - + +
655A PRO* 3.5 1.2 - - - +
656A VAL* 3.1 48.2 - - + +
657A SER 4.5 7.2 - - - -
659A TRP* 3.4 38.2 + + + -
686A SER* 2.7 30.8 + - - -
688A VAL* 3.9 7.6 - - + -
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Residues in contact with VAL 635 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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546A VAL* 3.8 20.9 - - + -
547A TYR 3.7 8.5 - - - +
548A ALA* 4.2 3.6 - - + -
602A GLU* 4.1 13.5 - - + -
603A VAL* 4.2 23.1 - - + -
606A GLN* 4.3 6.1 - - + -
631A TYR* 3.0 46.1 + - + +
632A GLY 4.0 3.1 - - - +
634A TYR* 1.3 78.9 - - + +
636A THR* 1.3 59.2 + - - +
638A MET* 3.7 6.5 - - - +
639A VAL* 2.8 35.8 + - + +
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Residues in contact with THR 636 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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546A VAL* 3.4 6.2 - - - +
626A ILE* 3.5 27.7 - - + +
627A TRP* 3.1 6.9 - - - -
628A GLY 3.1 15.9 + - - -
632A GLY 2.9 23.3 + - - -
633A GLY* 3.7 6.1 - - - -
635A VAL* 1.3 75.4 - - - +
637A SER* 1.3 59.0 + - - +
639A VAL* 3.7 1.6 - - - +
640A LEU* 2.9 44.8 + - + +
651A ILE 3.5 25.4 - - - +
652A ALA* 4.3 3.8 - - + -
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Residues in contact with SER 637 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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633A GLY 2.8 22.8 + - - -
634A TYR* 3.5 4.0 - - - -
636A THR* 1.3 76.7 - - - +
638A MET* 1.3 60.0 + - - +
640A LEU* 3.4 0.6 + - - -
641A GLY* 3.0 23.2 + - - -
652A ALA* 3.5 5.9 - - - +
655A PRO* 4.2 4.3 - - - +
688A VAL* 3.7 30.5 - - - +
691A ARG* 5.2 0.2 - - - -
695A PHE* 3.2 16.3 - - - -
700A TYR* 2.8 27.9 + - - -
719A ILE* 4.3 0.9 - - - +
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Residues in contact with MET 638 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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599A GLY 3.7 15.5 - - - +
603A VAL* 4.1 20.2 - - + +
634A TYR* 2.8 64.3 + - + +
635A VAL* 3.7 4.0 - - - +
637A SER* 1.3 73.2 - - - +
639A VAL* 1.3 65.6 + - - +
641A GLY 3.3 2.6 + - - -
642A SER* 3.1 22.7 + - - -
686A SER* 3.5 9.6 - - - +
687A THR 3.7 17.7 - - - +
688A VAL* 3.9 7.9 - - + -
691A ARG* 3.3 47.3 + - - +
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Residues in contact with VAL 639 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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603A VAL* 3.7 31.6 - - + +
606A GLN* 4.2 4.3 - - + -
607A ILE* 3.8 11.0 - - + -
626A ILE* 3.8 22.2 - - + -
635A VAL* 2.8 26.0 + - + +
636A THR 3.7 2.9 - - - +
638A MET* 1.3 74.2 - - - +
640A LEU* 1.3 63.1 + - - +
641A GLY 3.0 4.0 - - - -
642A SER* 2.7 28.7 + - - -
643A GLY 4.4 0.3 + - - -
644A SER* 4.7 2.3 + - - -
647A PHE* 3.5 38.5 - - + -
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Residues in contact with LEU 640 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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626A ILE* 4.0 6.1 - - + -
636A THR* 2.9 25.9 + - + +
637A SER 3.9 3.4 - - - +
639A VAL* 1.3 76.4 - - - +
641A GLY* 1.3 57.2 + - - +
642A SER 3.4 0.4 + - - -
643A GLY* 4.5 3.0 + - - -
647A PHE* 3.9 26.0 - - + +
649A CYS 4.0 11.4 - - - +
650A GLY* 3.4 28.3 - - - +
694A ASN 3.7 16.1 - - - +
695A PHE* 4.0 12.6 - - + -
698A VAL* 3.8 39.2 - - + +
699A GLU 4.8 1.8 - - - +
700A TYR* 3.7 24.7 - - + -
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Residues in contact with GLY 641 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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637A SER 3.0 11.6 + - - -
638A MET 3.3 4.2 + - - -
639A VAL 3.0 0.6 - - - -
640A LEU* 1.3 77.3 - - - +
642A SER* 1.3 59.0 + - - +
643A GLY 3.3 2.5 - - - -
691A ARG* 3.3 23.5 - - - +
694A ASN* 3.0 25.1 - - - +
695A PHE* 3.5 24.9 - - - -
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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