Contacts of the helix formed by residues 634 - 639 (chain A) in PDB entry 3H0G
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 GLY 634 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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596A ARG* 6.1 0.4 - - - -
626A LYS 5.2 0.4 - - - -
627A THR* 4.4 3.4 - - - -
629A GLY 4.6 0.9 - - - -
631A SER* 3.5 30.7 - - - -
632A GLN 2.6 14.6 + - - -
633A GLY* 1.3 73.4 - - - +
635A LEU* 1.3 65.6 + - - -
636A VAL 3.0 3.6 - - - -
637A HIS* 2.8 13.2 + - - +
638A THR* 2.7 17.8 + - - -
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Residues in contact with LEU 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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588A ILE* 5.0 13.5 - - + -
589A PRO* 5.8 0.2 - - + -
592A ILE* 5.9 1.1 - - + -
594A LEU* 4.1 19.9 - - + +
611A MET* 5.4 4.0 - - + -
613A ILE* 4.6 25.1 - - + -
618A ILE* 6.2 0.9 - - + -
623A VAL* 6.1 3.6 - - + -
627A THR* 2.9 31.8 + - - +
628A VAL* 4.7 9.9 - - + -
633A GLY 3.8 1.0 + - - -
634A GLY* 1.3 71.5 - - - -
636A VAL* 1.3 62.9 + - - +
638A THR* 3.1 16.6 + - - -
639A ILE* 3.5 27.5 + - + +
651A PHE* 3.5 33.7 - - + -
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Residues in contact with VAL 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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517A ILE* 5.4 8.5 - - + +
518A VAL* 5.8 0.6 - - + +
525A PRO* 4.1 15.5 - - + -
527A MET 3.7 22.7 - - - +
528A GLY* 4.5 2.7 - - - -
529A ILE* 4.6 1.6 - - + -
627A THR 3.8 0.6 + - - -
628A VAL* 4.0 30.5 - - - +
629A GLY 4.3 7.6 - - - +
635A LEU* 1.3 81.5 - - - +
637A HIS* 1.3 62.0 + - - +
638A THR 3.4 0.3 + - - -
639A ILE* 3.8 11.6 + - - +
640A TRP* 4.0 10.9 - - - +
648A CYS* 5.1 1.7 - - - -
651A PHE* 4.5 15.3 - - + -
652A PHE* 3.8 27.1 - - + -
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Residues in contact with HIS 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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518A VAL* 4.2 13.2 - - + +
523A ASN 3.2 29.3 + - - -
524A LYS* 3.6 6.1 - - + +
525A PRO* 2.6 39.7 - - + +
632A GLN 3.5 22.4 + - - +
633A GLY* 5.1 3.1 - - - -
634A GLY* 2.8 13.6 + - - +
636A VAL* 1.3 80.7 - - - +
638A THR* 1.3 60.9 + - - +
639A ILE 3.4 0.5 + - - -
640A TRP* 3.5 6.6 - + - +
641A LYS* 3.3 27.8 - - + +
882A THR 5.8 0.9 - - - -
884A VAL 3.9 12.1 + - - -
885A GLU* 3.6 32.0 + - + +
965A ARG* 5.7 1.1 - - - -
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Residues in contact with THR 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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592A ILE* 4.6 12.2 - - + +
593A ASN 4.5 4.3 - - - +
594A LEU* 4.1 16.9 - - + +
633A GLY 3.7 10.2 + - - -
634A GLY 2.7 22.8 + - - -
635A LEU* 3.1 10.4 + - - -
637A HIS* 1.3 76.1 - - - +
639A ILE* 1.3 56.3 + - - +
641A LYS* 2.6 21.9 - - - +
642A GLU* 3.3 11.2 - - - +
885A GLU* 5.2 0.4 - - - -
965A ARG* 2.8 46.3 + - - +
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Residues in contact with ILE 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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589A PRO* 3.8 33.7 - - + -
592A ILE* 3.2 37.0 - - + -
635A LEU* 3.5 31.4 + - + +
636A VAL 4.2 5.4 - - - +
637A HIS 3.3 0.2 - - - -
638A THR* 1.3 79.9 - - - +
640A TRP* 1.3 58.6 + - - +
641A LYS 3.2 0.2 - - - -
642A GLU 2.8 14.8 - - - +
643A LYS 4.7 0.7 - - - +
648A CYS* 2.7 38.3 - - + +
651A PHE* 3.9 22.2 - - + -
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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