Contacts of the helix formed by residues 718 - 729 (chain B) in PDB entry 4GT4
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 PRO 718 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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686B PHE* 3.6 25.1 - - + -
716B ASP 3.6 8.0 - - - +
717B CYS* 1.3 89.6 - - - +
719B ALA* 1.3 66.3 + - - +
720B TRP* 3.3 26.5 - - + +
721B VAL* 3.2 21.2 + - + +
722B TYR* 3.3 9.7 + - - +
802B NO3 4.1 3.4 - - - +
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Residues in contact with ALA 719 (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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717B CYS 3.6 2.7 + - - -
718B PRO* 1.3 72.9 - - - +
720B TRP* 1.3 57.6 + - - +
722B TYR* 3.3 7.6 + - - +
723B ALA* 2.9 28.5 + - - +
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Residues in contact with TRP 720 (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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593B VAL* 4.4 20.9 - - + -
686B PHE* 6.0 0.4 - + - -
718B PRO* 3.7 21.8 - - + +
719B ALA* 1.3 79.1 - - - +
721B VAL* 1.3 82.6 + - + +
723B ALA* 3.4 8.9 + - - +
724B LEU* 2.9 34.3 + - + +
745B ARG* 5.6 1.8 - - + -
746B LEU* 3.5 34.1 - - + -
749B TRP* 3.6 80.3 - + + +
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Residues in contact with VAL 721 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
682B LEU* 4.5 10.0 - - + +
686B PHE* 3.7 39.3 - - + -
717B CYS* 3.8 4.9 - - - -
718B PRO* 3.2 21.0 + - + +
720B TRP* 1.3 112.2 - - + +
722B TYR* 1.3 61.2 + - - +
724B LEU* 3.1 8.9 + - + +
725B MET* 2.9 44.9 + - + +
746B LEU* 6.1 0.2 - - + -
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Residues in contact with TYR 722 (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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710B VAL* 3.8 9.5 - - - +
711B LEU 2.7 26.0 + - - -
712B PRO* 3.6 4.9 - - - +
713B CYS* 3.4 59.8 + - + -
714B PRO* 4.2 1.3 - - + -
717B CYS* 4.2 2.7 - - - -
718B PRO 3.3 5.4 + - - +
719B ALA* 3.3 9.2 + - - +
721B VAL* 1.3 76.5 - - - +
723B ALA* 1.3 61.9 + - - +
725B MET* 3.1 21.5 + - - +
726B ILE* 2.9 52.1 + - + +
729B TRP* 4.2 11.0 - + - -
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Residues in contact with ALA 723 (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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719B ALA 2.9 18.1 + - - +
720B TRP* 3.5 10.3 - - - +
722B TYR* 1.3 75.6 - - - +
724B LEU* 1.3 57.8 + - - +
726B ILE* 3.2 11.1 + - - +
727B GLU* 2.9 39.1 + - - +
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Residues in contact with LEU 724 (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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682B LEU* 3.8 23.3 - - + -
720B TRP* 2.9 23.6 + - + +
721B VAL* 3.2 12.1 - - + +
723B ALA* 1.3 74.4 - - - +
725B MET* 1.3 59.4 + - - +
727B GLU* 3.2 9.8 + - - +
728B CYS* 2.9 38.0 + - - -
737B PRO* 4.7 3.1 - - + -
742B ILE* 4.4 20.6 - - + +
745B ARG* 4.1 33.4 - - + +
746B LEU* 3.9 31.9 - - + -
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Residues in contact with MET 725 (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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679B GLY* 3.9 2.7 - - - +
682B LEU* 3.7 29.2 - - + +
683B TRP* 3.6 38.8 - - - +
686B PHE* 4.5 0.7 - - + -
714B PRO* 4.4 7.4 - - + -
717B CYS* 4.0 16.6 - - - -
721B VAL* 2.9 37.3 + - + +
722B TYR* 3.3 20.2 - - + +
724B LEU* 1.3 77.0 - - - +
726B ILE* 1.3 56.8 + - - +
728B CYS* 3.1 6.8 + - - +
729B TRP* 2.9 62.9 + - + -
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Residues in contact with ILE 726 (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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710B VAL* 4.1 18.8 - - + -
722B TYR* 2.9 54.2 + - + +
723B ALA* 3.2 10.1 + - - +
725B MET* 1.3 74.2 - - - +
727B GLU* 1.3 65.3 + - + +
729B TRP* 3.0 26.3 + - + +
730B ASN* 3.5 2.6 + - - +
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Residues in contact with GLU 727 (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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723B ALA* 2.9 26.4 + - + +
724B LEU* 3.4 10.1 + - - +
726B ILE* 1.3 77.8 - - + +
728B CYS* 1.3 62.3 + - - +
729B TRP 3.3 0.5 + - - -
730B ASN* 3.4 19.6 + - - +
735B ARG 4.8 0.2 - - - +
736B ARG* 3.8 0.7 - - - -
737B PRO* 3.2 27.7 - - + +
745B ARG* 2.8 43.3 + - - -
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Residues in contact with CYS 728 (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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675B ILE* 3.6 25.1 - - - +
676B TRP* 3.6 12.6 + - - -
678B TYR* 4.2 11.9 - - - -
679B GLY* 3.8 15.0 - - - -
682B LEU* 4.6 1.6 - - - -
724B LEU* 2.9 23.4 + - - -
725B MET 3.1 9.4 + - - +
727B GLU* 1.3 76.3 - - - +
729B TRP* 1.3 58.2 + - - +
730B ASN 3.3 0.9 - - - -
736B ARG* 3.4 21.9 + - - -
737B PRO* 4.1 10.1 - - - -
742B ILE* 3.9 27.4 - - - -
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Residues in contact with TRP 729 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
676B TRP* 3.2 61.4 + + + +
679B GLY* 3.5 24.0 - - - -
680B VAL* 3.5 17.3 - - + +
683B TRP* 4.3 1.8 - + + -
710B VAL* 3.5 37.9 - - + +
711B LEU* 3.6 48.7 - - + -
722B TYR* 4.2 6.7 - + - -
725B MET* 2.9 46.7 + - + +
726B ILE* 3.0 14.5 + - + +
728B CYS* 1.3 80.5 - - + +
730B ASN* 1.3 62.8 + - - +
731B GLU 3.6 1.4 + - - -
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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