Contacts of the helix formed by residues 740 - 744 (chain A) in PDB entry 3GQL
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 VAL 740 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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738A HIS* 3.1 23.5 - - + +
739A ALA* 1.3 74.7 - - + +
741A PRO* 1.3 73.2 - - + +
742A SER* 3.1 25.6 - - - +
743A GLN* 3.0 15.1 + - + -
744A ARG* 3.7 4.3 + - - +
521C THR 5.0 0.9 - - - +
522C GLU* 4.2 31.2 - - + +
525C LEU* 3.6 30.5 - - + -
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Residues in contact with PRO 741 (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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670A GLU* 3.5 36.8 - - + +
678A THR* 5.5 0.4 - - - +
680A GLN* 3.4 36.0 - - + +
739A ALA 3.3 9.8 - - - +
740A VAL* 1.3 86.9 - - + +
742A SER* 1.3 61.3 + - - +
743A GLN 3.3 0.5 + - - -
744A ARG* 3.3 30.0 + - - +
463C TYR* 5.1 10.3 - - + +
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Residues in contact with SER 742 (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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680A GLN* 3.6 5.8 + - - +
740A VAL* 3.1 20.5 - - - +
741A PRO* 1.3 79.3 - - - +
743A GLN* 1.3 71.9 + - - +
744A ARG 3.3 2.6 + - - +
463C TYR 3.6 23.1 + - - -
464C GLU* 3.9 19.0 - - - +
465C LEU* 4.6 8.7 - - - +
525C LEU* 4.6 1.2 - - - +
554C ASP 5.5 0.2 + - - -
555C GLY 3.0 25.8 + - - +
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Residues in contact with GLN 743 (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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735A ASP* 4.8 1.0 - - - +
738A HIS* 3.4 38.8 + - + +
740A VAL* 3.0 9.4 + - + -
742A SER* 1.3 99.1 + - - +
744A ARG* 1.3 60.9 + - - +
745A PRO* 4.0 1.2 - - - +
465C LEU* 3.9 17.2 - - - +
516C LEU* 5.0 4.7 - - + +
525C LEU* 3.6 39.9 - - + +
552C THR* 5.7 1.0 + - - +
555C GLY 4.0 6.7 + - - -
556C PRO* 3.2 20.2 - - + +
557C LEU* 2.6 35.0 + - - +
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Residues in contact with ARG 744 (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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668A ALA* 3.9 3.2 - - - +
669A PRO* 3.9 2.6 - - - +
670A GLU* 2.8 43.2 + - - -
680A GLN* 3.1 32.6 + - + +
681A SER* 3.5 4.8 - - - +
683A VAL* 4.4 3.8 - - + -
684A TRP* 3.7 17.3 - - - +
735A ASP 3.6 2.2 - - - +
736A CYS* 2.8 24.4 + - - +
738A HIS* 2.8 36.8 + - + -
739A ALA 3.7 7.1 + - - -
740A VAL 3.8 1.1 - - - +
741A PRO* 3.6 26.0 - - - +
742A SER 3.3 4.0 - - - +
743A GLN* 1.3 82.1 - - - +
745A PRO* 1.3 81.6 - - + +
746A THR* 4.6 0.9 - - - +
555C GLY* 3.5 16.8 + - - -
556C PRO* 4.6 0.7 - - - -
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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