Contacts of the helix formed by residues 679 - 694 (chain C) 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 HIS 679 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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615C ALA* 3.6 37.7 + - + +
618C LYS* 4.4 7.7 - - - -
619C CYS 2.9 35.4 + - - -
620C ILE* 3.9 14.1 - - + +
678C THR* 1.3 75.5 - - - +
680C GLN* 1.3 64.8 + - - +
682C ASP* 3.2 23.9 + - - +
683C VAL* 3.2 13.7 + - - +
747C PHE* 3.6 8.7 - - + -
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Residues in contact with GLN 680 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
678C THR* 3.0 30.0 + - - +
679C HIS* 1.3 84.5 - - - +
681C SER* 1.3 56.2 + - - +
682C ASP 2.8 9.0 + - - -
683C VAL* 3.1 20.1 + - + +
684C TRP 3.1 6.2 + - - -
741C PRO* 3.4 47.1 + - + +
742C SER* 4.8 4.7 + - - +
744C ARG* 3.0 21.6 + - + +
745C PRO 5.6 0.7 - - - +
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Residues in contact with SER 681 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
667C MET* 5.6 0.2 - - - -
668C ALA* 4.0 19.1 + - - +
670C GLU* 4.3 4.9 - - - -
671C ALA* 4.0 9.6 - - - +
676C ILE 3.7 16.2 - - - -
677C TYR* 3.3 10.9 - - - +
678C THR* 2.8 30.9 + - - -
680C GLN* 1.3 77.3 - - - +
682C ASP* 1.3 61.4 + - - +
684C TRP* 3.8 8.6 - - - +
685C SER* 3.6 14.4 + - - -
744C ARG* 3.4 11.9 - - - +
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Residues in contact with ASP 682 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611C MET* 4.5 7.1 - - - +
619C CYS 5.4 0.2 - - - +
620C ILE* 3.9 7.6 - - - +
621C HIS* 3.2 33.2 + - - +
622C ARG* 3.5 23.1 + - - -
624C LEU* 4.2 7.8 - - + +
677C TYR* 5.2 0.9 - - - -
678C THR 3.4 12.7 - - - +
679C HIS* 3.2 18.0 + - - +
680C GLN 2.8 0.2 - - - -
681C SER* 1.3 85.0 + - - +
683C VAL* 1.3 58.5 + - - +
684C TRP 3.1 1.6 - - - -
685C SER* 3.1 8.1 + - - +
686C PHE* 2.9 23.2 + - - +
747C PHE* 3.7 18.4 - - + -
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Residues in contact with VAL 683 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679C HIS 3.3 15.9 - - - +
680C GLN* 3.5 12.1 - - + +
682C ASP* 1.3 74.1 - - - +
684C TRP* 1.3 66.8 + - - +
686C PHE* 3.0 3.3 + - - +
687C GLY 2.9 18.7 + - - -
736C CYS* 3.2 30.5 - - + +
744C ARG* 4.8 3.1 - - + -
745C PRO* 3.3 34.5 - - + +
746C THR* 4.5 1.1 - - - -
747C PHE* 3.6 29.2 - - + +
750C LEU* 3.7 11.4 - - + -
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Residues in contact with TRP 684 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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665C LYS 4.5 2.0 + - - -
666C TRP 3.3 21.7 + - - -
667C MET 3.5 10.9 + - - -
668C ALA* 3.5 28.3 - - + -
669C PRO* 3.4 30.5 - - + -
680C GLN 3.1 4.9 + - - -
681C SER 3.8 4.0 - - - +
683C VAL* 1.3 76.5 - - - +
685C SER* 1.3 56.8 + - - +
687C GLY* 2.9 18.5 + - - -
688C VAL* 3.1 22.0 + - + +
701C TYR* 4.2 15.2 + - - -
713C LEU* 4.2 14.6 - - + -
718C ARG* 3.9 18.4 - - - -
736C CYS 3.3 15.6 + - - +
737C TRP* 3.0 54.7 + + + -
738C HIS 4.2 1.8 - - - -
739C ALA* 4.7 0.7 - - - -
744C ARG* 3.5 25.8 - - - +
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Residues in contact with SER 685 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622C ARG 5.6 2.6 + - - -
623C ASP* 5.7 0.9 - - - -
624C LEU* 3.4 35.0 + - - +
666C TRP* 2.4 33.3 + - - +
667C MET* 4.6 0.9 - - - -
681C SER 3.6 10.3 + - - -
682C ASP* 3.1 11.2 + - - -
684C TRP* 1.3 75.8 - - - +
686C PHE* 1.3 61.1 + - - +
688C VAL* 3.4 7.2 + - - +
689C LEU* 2.9 26.6 + - - +
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Residues in contact with PHE 686 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604C ALA* 3.6 25.6 - - - -
607C VAL* 4.0 26.7 - - + -
608C ALA* 4.0 9.4 - - + -
624C LEU* 4.1 8.7 - - + +
682C ASP 2.9 12.8 + - - +
683C VAL* 3.0 8.9 + - - +
685C SER* 1.3 76.3 - - - +
687C GLY* 1.3 53.4 + - - +
689C LEU* 2.8 15.1 + - + +
690C LEU* 2.7 65.4 + - + +
736C CYS* 4.2 3.4 - - - -
747C PHE* 3.7 22.0 - + + -
750C LEU* 3.5 29.2 - - + -
754C LEU* 3.7 19.3 - - + -
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Residues in contact with GLY 687 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
683C VAL 2.9 10.7 + - - -
684C TRP 2.9 4.9 + - - -
686C PHE* 1.3 77.7 - - - +
688C VAL* 1.3 56.5 + - - +
690C LEU* 3.0 22.0 + - - +
691C TRP* 3.0 10.4 + - - +
733C MET* 3.8 11.2 - - - +
736C CYS* 3.8 21.8 - - - -
737C TRP* 3.6 15.3 - - - -
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Residues in contact with VAL 688 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
665C LYS 3.8 19.1 - - - +
666C TRP* 3.6 25.1 - - + +
684C TRP* 3.1 22.3 + - + +
685C SER* 3.6 7.6 - - - +
686C PHE 3.3 0.2 - - - -
687C GLY* 1.3 73.5 - - - +
689C LEU* 1.3 58.6 + - - +
691C TRP* 3.6 5.3 - - - +
692C GLU* 3.3 22.8 + - - +
700C PRO* 3.7 26.0 - - + -
701C TYR* 4.8 2.5 - - - +
719C MET* 4.0 7.4 - - + -
737C TRP* 3.0 29.4 - - + +
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Residues in contact with LEU 689 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
569C LEU* 4.2 10.1 - - + -
607C VAL* 4.0 20.2 - - + -
624C LEU* 3.6 36.3 - - + -
625C ALA* 3.9 17.3 - - - +
626C ALA* 4.0 11.4 - - - +
629C VAL* 4.1 4.9 - - + -
685C SER 2.9 12.2 + - - +
686C PHE* 2.8 17.6 + - + +
688C VAL* 1.3 76.9 - - - +
690C LEU* 1.3 63.7 + - - +
691C TRP 3.1 1.3 - - - -
692C GLU* 3.0 13.9 + - - +
693C ILE* 3.0 44.1 + - + +
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Residues in contact with LEU 690 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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604C ALA* 3.6 30.7 - - + -
686C PHE* 2.7 47.9 + - + +
687C GLY* 3.3 9.0 - - - +
689C LEU* 1.3 72.0 - - - +
691C TRP* 1.3 58.1 + - - +
693C ILE* 2.9 23.7 + - + +
694C PHE* 2.9 33.8 + - + -
729C LEU* 5.0 1.3 - - + +
732C MET* 4.0 24.2 - - + -
733C MET* 3.9 33.9 - - + +
736C CYS* 5.0 0.7 - - - -
754C LEU* 4.6 7.6 - - + -
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Residues in contact with TRP 691 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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687C GLY 3.0 8.7 + - - +
688C VAL* 3.6 10.3 - - - +
690C LEU* 1.3 80.9 - - - +
692C GLU* 1.3 64.4 + - + +
693C ILE 3.4 0.2 + - - -
694C PHE* 3.6 1.8 + - - +
695C THR* 2.9 47.5 + - + +
698C GLY* 3.6 14.6 - - - -
699C SER 3.3 19.3 - - - -
700C PRO* 3.2 35.2 - - + -
702C PRO* 3.7 20.6 - - + -
719C MET* 3.5 28.3 - - + +
720C ASP 3.6 18.6 + - - -
722C PRO* 4.1 22.1 - - + +
730C TYR* 5.6 0.2 - + - -
733C MET* 4.1 12.9 - - - +
737C TRP* 4.0 17.7 - + + -
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Residues in contact with GLU 692 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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570C ARG* 3.3 15.3 + - - +
573C LEU* 3.7 1.4 - - - +
626C ALA* 3.1 44.1 + - + +
627C ARG* 4.9 1.2 + - - -
666C TRP* 3.1 39.0 + - - -
688C VAL 3.3 9.6 + - - +
689C LEU* 3.0 16.9 + - - +
691C TRP* 1.3 79.8 - - + +
693C ILE* 1.3 61.3 + - + +
695C THR* 3.1 8.7 + - - -
697C GLY* 2.8 33.4 + - - -
698C GLY 3.7 15.0 - - - +
700C PRO* 4.3 7.6 - - + -
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Residues in contact with ILE 693 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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569C LEU* 4.0 15.7 - - + -
573C LEU* 3.5 12.5 - - + +
600C LEU* 3.8 35.8 - - + +
603C CYS* 4.2 10.3 - - - +
604C ALA* 3.5 35.7 - - + +
607C VAL* 5.2 0.4 - - + -
689C LEU* 3.0 37.6 + - + +
690C LEU* 2.9 11.9 + - - +
692C GLU* 1.3 77.9 - - + +
694C PHE* 1.3 70.4 + - + +
695C THR 3.0 5.8 + - - -
696C LEU* 3.1 21.8 + - - +
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Residues in contact with PHE 694 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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597C SER* 5.2 1.3 - - - -
600C LEU* 3.5 50.3 - - + -
601C VAL* 4.3 8.1 - - + -
604C ALA* 4.7 4.7 - - + -
690C LEU* 2.9 43.0 + - + +
692C GLU 3.4 0.2 - - - -
693C ILE* 1.3 83.1 - - + +
695C THR* 1.3 65.2 + - - +
696C LEU* 3.5 3.6 - - - -
722C PRO* 3.5 23.9 - - + +
723C SER 3.9 10.7 - - - +
725C CYS* 4.2 16.8 - - + +
729C LEU* 3.4 40.8 - - + -
733C MET* 3.9 15.5 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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