Contacts of the helix formed by residues 725 - 738 (chain B) in PDB entry 1GGE
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 ASP 725 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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618B ALA* 4.4 10.5 - - - -
721B ALA* 4.7 5.2 - - - +
723B SER* 3.4 24.0 + - - +
724B ALA* 1.3 84.2 - - - +
726B GLY* 1.3 63.3 + - - +
727B SER* 2.6 35.6 + - - +
728B PHE* 2.8 12.7 + - - +
729B MET* 3.2 16.7 + - - +
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Residues in contact with GLY 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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618B ALA* 5.2 1.2 - - - +
622B ALA* 6.2 0.7 - - - -
725B ASP* 1.3 78.6 - - - +
727B SER* 1.3 60.2 + - - +
729B MET* 3.4 6.0 + - - +
730B ASP* 3.0 32.3 + - - +
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Residues in contact with SER 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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725B ASP* 2.6 19.6 + - - +
726B GLY* 1.3 72.3 - - - +
728B PHE* 1.3 58.9 + - - -
730B ASP* 3.4 7.5 + - - +
731B GLU* 3.3 36.4 + - - +
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Residues in contact with PHE 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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666B ILE* 4.2 11.2 - - + -
696B ALA* 3.5 33.9 - - + -
697B LEU 3.5 25.1 - - - -
698B ALA* 3.9 16.4 - - + -
719B VAL* 3.5 33.7 - - + +
721B ALA* 3.7 24.0 - - + -
723B SER 3.8 10.5 - - - +
724B ALA* 3.7 22.0 - - + -
725B ASP* 2.8 19.9 + - - +
727B SER* 1.3 73.3 - - - +
729B MET* 1.3 81.9 + - - +
731B GLU* 3.5 4.6 + - - -
732B LEU* 3.1 19.6 + - - +
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Residues in contact with MET 729 (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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618B ALA 4.0 9.0 - - - +
619B ILE* 3.8 32.5 - - - +
622B ALA* 3.7 26.0 - - + -
623B LEU* 3.8 22.9 - - + -
666B ILE* 4.0 15.5 - - + -
724B ALA 3.8 7.2 - - - +
725B ASP 3.2 16.6 + - - +
726B GLY* 4.0 5.6 - - - +
728B PHE* 1.3 100.6 - - - +
730B ASP* 1.3 60.0 + - - +
732B LEU* 3.3 10.8 + - + +
733B LEU* 3.0 37.2 + - + +
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Residues in contact with ASP 730 (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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622B ALA* 6.1 0.2 - - - +
626B LYS* 5.2 6.7 + - - +
726B GLY 3.0 23.3 + - - +
727B SER* 3.4 6.7 + - - +
729B MET* 1.3 76.0 - - - +
731B GLU* 1.3 54.0 + - + +
733B LEU* 3.5 10.3 + - - +
734B THR* 2.7 38.8 + - - +
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Residues in contact with GLU 731 (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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718B ILE 5.3 0.7 - - - +
719B VAL* 3.7 28.9 - - + +
720B GLU 5.0 4.3 + - - +
727B SER* 3.3 27.0 + - - +
728B PHE* 3.5 9.3 - - - +
730B ASP* 1.3 80.7 - - + +
732B LEU* 1.3 57.3 + - - +
734B THR* 3.3 8.3 + - - -
735B LEU* 3.0 31.8 + - + +
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Residues in contact with LEU 732 (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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603B VAL* 4.7 3.1 - - + -
623B LEU* 4.8 0.9 - - + -
664B ALA* 4.3 8.5 - - + -
666B ILE* 4.1 24.0 - - + -
694B PRO* 3.7 28.3 - - + -
696B ALA* 4.0 26.5 - - + +
719B VAL* 3.9 14.4 - - + -
728B PHE 3.1 14.8 + - - +
729B MET* 3.3 17.2 + - + +
731B GLU* 1.3 79.0 - - - +
733B LEU* 1.3 61.6 + - + +
735B LEU* 3.1 5.9 + - - +
736B MET* 2.9 53.2 + - - +
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Residues in contact with LEU 733 (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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598B VAL* 4.0 10.7 - - + +
622B ALA* 3.9 23.6 - - + +
623B LEU* 4.2 13.7 - - + -
626B LYS* 3.8 42.0 - - + +
628B VAL* 3.9 27.6 - - + -
729B MET* 3.0 27.1 + - + +
730B ASP* 3.9 9.9 - - - +
732B LEU* 1.3 78.3 - - + +
734B THR* 1.3 63.3 + - - +
736B MET* 3.4 11.6 + - - +
737B ALA* 3.0 23.0 + - - +
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Residues in contact with THR 734 (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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730B ASP* 2.7 26.6 + - - +
731B GLU* 3.5 9.0 - - - -
732B LEU 3.2 0.2 - - - -
733B LEU* 1.3 74.3 - - - +
735B LEU* 1.3 68.9 + - + +
737B ALA* 3.3 14.9 + - - +
738B ALA* 3.4 11.4 + - - +
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Residues in contact with LEU 735 (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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694B PRO* 3.7 26.7 - - + +
695B ILE 5.1 0.2 - - - +
716B GLU* 5.9 2.2 - - + +
717B GLY* 3.8 40.6 - - - +
718B ILE 4.5 0.4 - - - +
719B VAL* 3.5 32.1 - - + -
731B GLU 3.0 14.8 + - - +
732B LEU* 3.1 6.7 + - - +
734B THR* 1.3 78.4 - - + +
736B MET* 1.3 61.9 + - - +
738B ALA* 3.0 19.6 + - + +
739B HIS 3.3 8.8 + - - -
740B ARG* 4.7 1.4 + - - +
741B VAL* 4.8 7.1 - - + +
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Residues in contact with MET 736 (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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597B ASP 5.7 0.5 - - - +
598B VAL* 3.7 13.1 - - + +
601B ARG* 3.8 40.0 + - + +
602B VAL 4.4 0.4 - - - +
603B VAL* 3.5 33.9 - - + -
623B LEU* 5.0 0.2 - - - -
628B VAL* 3.8 14.8 - - + -
663B ASP* 4.0 16.2 - - + +
664B ALA* 3.9 17.0 - - + -
694B PRO* 4.3 8.1 - - + -
732B LEU* 2.9 34.3 + - + +
733B LEU* 3.8 13.2 - - - +
734B THR 3.3 0.2 - - - -
735B LEU* 1.3 76.2 - - - +
737B ALA* 1.3 57.1 + - - +
739B HIS* 2.9 22.6 + - - +
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Residues in contact with ALA 737 (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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596B GLY* 3.3 36.6 + - - +
597B ASP 5.0 0.4 - - - +
598B VAL* 3.5 15.8 - - + +
733B LEU 3.0 13.9 + - - +
734B THR* 3.3 11.6 + - - +
736B MET* 1.3 75.7 - - - +
738B ALA* 1.3 58.6 + - - +
739B HIS* 3.2 2.0 + - - +
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Residues in contact with ALA 738 (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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591B TYR* 5.4 1.6 - - - -
734B THR* 3.4 8.8 + - + +
735B LEU* 3.0 13.7 + - + +
737B ALA* 1.3 75.1 - - - +
739B HIS* 1.3 64.3 + - - +
740B ARG 2.9 20.1 + - - +
742B TRP* 4.1 11.0 + - + +
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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