Contacts of the helix formed by residues 782 - 787 (chain B) 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 LEU 782 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194B GLU* 5.0 0.9 - - - +
195B CYS* 3.6 22.7 - - + +
197B PHE* 4.9 0.7 - - + -
198B ASP* 3.9 21.5 - - + +
485B ARG* 3.5 29.6 - - - +
488B TYR* 4.5 13.7 - - + -
780B VAL* 3.5 5.1 - - - +
781B PHE* 1.3 109.9 + - + +
783B THR* 1.3 59.5 + - - +
784B ASN* 2.9 24.0 - - - +
785B TYR* 3.3 25.4 - - - +
788B ARG* 3.5 18.6 - - - +
817B LEU* 3.9 10.5 - - + -
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Residues in contact with THR 783 (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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190B TYR* 5.0 1.3 - - + -
195B CYS* 3.5 18.6 - - - -
196B PRO* 4.8 1.1 - - - -
197B PHE* 3.8 15.1 - - - -
780B VAL* 4.9 2.5 - - - +
782B LEU* 1.3 71.1 - - - +
784B ASN* 1.3 57.0 + - - +
785B TYR* 3.0 19.6 + - - -
786B ASN* 4.3 3.5 + - - +
817B LEU* 4.3 7.4 - - - +
56J LEU* 5.6 1.6 - - + +
59J LYS* 3.7 30.7 - - + +
60J PHE* 3.8 24.9 - - + -
63J TYR* 3.2 35.9 - - + +
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Residues in contact with ASN 784 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B GLN* 4.8 2.4 + - - -
193B LYS 3.5 25.5 + - - +
194B GLU* 4.1 8.1 + - - -
195B CYS* 3.3 15.3 - - - +
782B LEU* 2.9 30.9 - - - +
783B THR* 1.3 68.4 - - - +
785B TYR* 1.3 54.4 + - - -
786B ASN* 3.0 6.5 - - - -
787B VAL* 2.8 28.2 + - + -
788B ARG* 2.9 40.5 + - - +
63J TYR* 3.2 23.3 + - + +
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Residues in contact with TYR 785 (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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780B VAL* 6.0 1.6 - - + -
781B PHE* 3.4 29.2 - - + -
782B LEU 3.3 20.3 + - - +
783B THR 3.0 10.8 + - - -
784B ASN* 1.3 77.2 + - - +
786B ASN* 1.3 72.6 + - + +
787B VAL 3.4 0.3 + - - -
788B ARG* 3.7 22.2 + - - +
793B ALA* 5.9 0.9 - - + -
795B ILE* 3.6 42.2 - - + +
854B LEU* 5.1 5.7 - - + +
856B PHE* 4.1 25.8 - + - -
967B ARG* 3.9 7.3 + - - -
57C VAL 4.4 14.0 + - - -
58C LEU* 5.8 0.5 - - - -
1J MET* 3.5 21.8 - - - +
60J PHE* 3.7 27.8 - + - -
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Residues in contact with ASN 786 (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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783B THR 4.3 3.5 + - - +
784B ASN 3.0 0.8 - - - -
785B TYR* 1.3 94.9 - - + +
787B VAL* 1.3 65.0 + - + +
856B PHE* 5.1 3.8 - - - -
950B ASP* 5.5 1.9 - - - +
951B GLN* 3.8 15.9 + - - +
967B ARG* 2.9 34.5 + - - +
56C THR 4.8 4.4 + - - -
57C VAL* 4.5 30.3 - - + +
63J TYR* 6.1 2.7 - - + -
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Residues in contact with VAL 787 (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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115B GLN* 3.3 17.6 + - - +
119B LEU* 4.0 12.9 - - + +
193B LYS* 3.4 51.6 - - + +
784B ASN* 2.8 25.5 + - + +
786B ASN* 1.3 83.0 - - + +
788B ARG* 1.3 65.3 + - - +
789B MET* 4.7 1.1 - - - +
951B GLN* 5.8 1.8 - - - +
63J TYR* 4.6 19.5 - - + -
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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