Contacts of the helix formed by residues 755 - 763 (chain A) in PDB entry 3GTL
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 PHE 755 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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727A ASP* 3.9 21.8 - - - -
730A GLY* 3.6 7.4 - - - -
731A ARG* 3.3 51.1 - - + -
734A GLU* 3.7 32.5 - - + +
747A VAL* 4.6 1.7 - - - +
754A SER* 1.3 76.7 + - - +
756A ILE* 1.3 79.4 + - + +
757A ASN 3.1 2.5 - - - -
758A ILE* 2.8 31.7 + - + +
759A ALA* 3.0 33.0 + - + -
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Residues in contact with ILE 756 (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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726A ARG* 3.8 27.6 - - - +
727A ASP* 5.3 0.7 - - - +
754A SER* 3.1 14.1 + - - +
755A PHE* 1.3 93.1 - - + +
757A ASN* 1.3 67.9 + - - +
759A ALA* 3.8 16.2 - - + -
760A GLN* 2.9 60.5 + - + +
1021B MET* 6.0 0.9 - - - -
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Residues in contact with ASN 757 (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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747A VAL* 5.9 0.7 - - + -
753A GLY* 3.5 9.4 - - - -
754A SER* 3.0 40.4 + - - +
756A ILE* 1.3 83.4 - - - +
758A ILE* 1.3 56.4 + - + +
761A MET* 2.9 38.6 + - + +
1018B PRO* 2.8 33.4 - - + +
1019B SER* 3.9 9.6 - - - +
1021B MET* 3.4 20.9 - - - +
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Residues in contact with ILE 758 (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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669A THR* 5.8 2.7 - - + -
730A GLY 4.9 6.7 - - - +
733A ALA* 4.7 11.0 - - + +
734A GLU* 5.0 17.9 - - + +
737A LEU* 4.4 23.1 - - + -
743A VAL* 3.6 31.0 - - + -
744A LYS* 4.2 21.1 - - + -
747A VAL* 4.7 6.7 - - + -
754A SER 4.1 12.1 - - - +
755A PHE* 2.8 17.3 + - + +
757A ASN* 1.3 69.5 - - + +
759A ALA* 1.3 69.0 + - - +
760A GLN 2.9 3.8 + - - -
761A MET* 3.1 6.8 + - - -
762A SER* 3.0 31.9 + - - +
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Residues in contact with ALA 759 (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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726A ARG* 4.6 6.4 - - + +
730A GLY* 3.5 30.3 - - - -
733A ALA* 6.0 0.2 - - - -
755A PHE* 3.0 29.9 + - + -
756A ILE* 3.1 15.5 + - + +
758A ILE* 1.3 81.6 - - - +
760A GLN* 1.3 60.1 + - - +
763A ALA* 3.3 11.1 + - - +
764A CYS 3.0 26.2 + - - +
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Residues in contact with GLN 760 (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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726A ARG* 4.9 0.9 - - - -
756A ILE* 2.9 38.6 + - + +
758A ILE 2.9 0.4 + - - -
759A ALA* 1.3 77.8 - - - +
761A MET* 1.3 69.9 + - - +
762A SER 2.8 2.1 + - - -
763A ALA 3.3 6.1 + - - -
764A CYS 2.9 17.0 + - - +
765A VAL* 2.7 41.9 + - - +
768A GLN* 5.6 3.2 - - - +
803A SER* 3.7 6.4 - - - -
804A TYR* 3.8 22.9 + - + -
1021B MET* 3.9 24.3 - - - +
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Residues in contact with MET 761 (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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669A THR* 3.7 31.0 - - + -
743A VAL* 4.4 15.0 - - + -
757A ASN 2.9 31.6 + - - +
758A ILE* 3.1 4.2 + - - +
760A GLN* 1.3 78.5 - - - +
762A SER* 1.3 55.7 + - - +
803A SER* 3.6 2.1 - - - -
804A TYR* 3.3 14.2 + - + -
805A LEU* 3.3 29.9 + - - +
1017B ILE* 4.6 10.1 - - + +
1018B PRO* 3.9 31.9 - - + +
1021B MET* 4.2 22.0 - - + -
1023B VAL* 3.7 29.3 - - + +
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Residues in contact with SER 762 (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 ASP 4.9 0.2 + - - -
669A THR* 3.0 41.1 + - - +
670A ILE 3.4 9.8 + - - -
671A ALA* 4.7 10.0 - - - +
676A MET* 3.8 20.8 - - - +
679A ILE* 5.4 0.2 - - - +
733A ALA* 4.8 10.3 - - - -
737A LEU* 5.5 5.3 - - - +
758A ILE* 3.0 21.1 + - - -
760A GLN 2.8 3.6 + - - -
761A MET* 1.3 70.3 - - - +
763A ALA* 1.3 57.1 + - - +
803A SER* 3.6 10.3 - - - -
805A LEU* 5.0 4.3 - - - +
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Residues in contact with ALA 763 (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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676A MET* 5.1 2.2 - - - +
679A ILE* 3.9 32.6 - - + +
683A ILE* 5.7 0.5 - - - +
729A ALA* 4.0 20.4 - - + +
730A GLY* 4.5 0.9 - - - +
733A ALA* 4.1 14.4 - - + -
759A ALA 3.3 11.0 + - - +
760A GLN 3.3 1.2 + - - -
762A SER* 1.3 80.5 - - - +
764A CYS* 1.3 65.5 - - - +
801A GLU 4.7 2.8 - - - +
802A ASN 4.7 0.5 - - - -
803A SER* 3.6 14.3 + - - -
806A ARG* 4.9 6.4 + - - -
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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