Contacts of the helix formed by residues 673 - 688 (chain C) in PDB entry 3QHE
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 SER 673 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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727A ARG* 6.1 0.7 - - - +
629C LEU* 3.9 18.7 - - - +
633C GLU* 3.1 20.1 + - - -
671C SER* 3.0 11.2 + - - -
672C HIS* 1.3 78.3 - - - +
674C LEU* 1.3 63.8 + - - +
675C THR* 3.5 2.9 + - - -
676C ILE* 3.2 28.1 + - - +
677C VAL* 3.1 25.1 + - - +
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Residues in contact with LEU 674 (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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726A LEU* 4.2 20.0 - - + -
727A ARG* 4.2 24.7 - - + +
730A MET* 3.7 37.5 - - + -
672C HIS 3.7 4.3 + - - +
673C SER* 1.3 71.8 + - - +
675C THR* 1.3 54.7 + - - +
677C VAL* 3.2 5.3 + - + +
678C SER* 2.8 37.1 + - - -
713C SER* 5.5 1.8 - - - +
715C HIS* 4.4 18.4 - - + +
718C ILE* 3.8 21.8 - - + +
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Residues in contact with THR 675 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
711A ILE* 3.9 23.2 - - - +
712A HIS* 4.6 2.8 + - - +
593C TRP* 3.7 31.9 - - + -
633C GLU* 3.8 19.7 + - + -
673C SER* 3.2 8.3 - - - -
674C LEU* 1.3 75.0 - - - +
676C ILE* 1.3 67.0 + - - +
678C SER* 3.4 5.3 + - - -
679C ASN* 2.9 40.3 + - - +
715C HIS* 6.0 0.4 - - - -
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Residues in contact with ILE 676 (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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629C LEU* 4.1 27.8 - - + -
632C ILE* 3.8 24.7 - - + -
633C GLU* 3.7 15.3 - - + +
668C HIS* 3.7 36.3 + - + +
671C SER* 3.5 28.7 - - - +
673C SER* 3.2 22.8 + - - +
675C THR* 1.3 78.4 - - - +
677C VAL* 1.3 64.2 - - - +
679C ASN* 3.2 8.2 + - - +
680C ALA* 3.0 21.8 + - - +
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Residues in contact with VAL 677 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668C HIS 3.7 19.1 - - - +
669C LEU* 4.1 8.7 - - - +
671C SER* 3.3 24.0 - - - +
673C SER 3.1 16.4 + - - +
674C LEU* 3.5 9.4 - - + +
676C ILE* 1.3 74.1 - - - +
678C SER* 1.3 58.8 + - - +
680C ALA* 3.2 6.0 + - - +
681C CYS* 2.9 28.8 + - - -
710C LEU* 3.9 32.5 - - + -
718C ILE* 3.7 23.6 - - + -
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Residues in contact with SER 678 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
640C ARG* 3.0 25.7 + - - -
674C LEU 2.8 21.2 + - - -
675C THR* 3.7 6.7 - - - -
677C VAL* 1.3 71.4 - - - +
679C ASN* 1.3 65.5 + - - +
681C CYS* 3.4 5.8 + - - +
682C GLY 3.0 17.3 + - - -
715C HIS* 3.8 17.7 - - - -
717C MET* 3.4 27.2 - - - +
718C ILE* 3.8 9.6 - - - +
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Residues in contact with ASN 679 (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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593C TRP* 4.1 8.3 + - - -
633C GLU* 3.0 30.5 + - - +
636C GLY* 3.7 17.1 - - - +
637C GLY* 3.3 16.8 - - - +
640C ARG* 3.2 28.7 + - - +
665C LEU* 5.6 0.2 - - - -
668C HIS* 6.2 0.7 - - - +
675C THR* 2.9 35.2 + - - +
676C ILE* 3.5 5.9 - - - +
678C SER* 1.3 74.8 - - - +
680C ALA* 1.3 54.2 + - - +
682C GLY 3.2 1.2 + - - -
683C THR* 2.8 37.3 + - - -
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Residues in contact with ALA 680 (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 LEU* 3.6 39.9 - - + +
668C HIS* 3.7 14.8 + - + +
669C LEU* 3.9 8.5 - - + -
676C ILE 3.0 13.3 + - - +
677C VAL* 3.4 9.4 - - - +
679C ASN* 1.3 74.9 - - - +
681C CYS* 1.3 58.4 + - - +
683C THR* 3.4 1.2 + - - -
684C LEU* 2.9 36.7 + - - +
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Residues in contact with CYS 681 (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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669C LEU* 3.8 18.6 - - - -
677C VAL* 2.9 19.0 + - - +
678C SER* 3.8 7.2 - - - +
680C ALA* 1.3 76.5 - - - +
682C GLY* 1.3 57.8 + - - +
684C LEU* 3.5 6.1 + - - +
685C TRP* 2.8 30.1 + - - +
707C LEU* 4.8 2.0 - - - -
710C LEU* 4.1 10.5 - - - -
717C MET 4.7 0.7 - - - +
718C ILE* 4.1 16.2 - - - +
721C GLY* 3.8 12.2 - - - +
722C SER* 3.8 37.5 - - - +
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Residues in contact with GLY 682 (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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640C ARG* 3.6 31.8 - - - +
678C SER 3.0 10.7 + - - -
679C ASN 3.2 1.3 + - - -
680C ALA 3.2 0.2 - - - -
681C CYS* 1.3 77.4 - - - +
683C THR* 1.3 60.8 + - - +
685C TRP* 3.2 26.5 - - - +
686C ASN* 3.3 15.6 + - - -
721C GLY* 5.3 1.1 - - - -
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Residues in contact with THR 683 (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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636C GLY 4.4 1.7 + - - -
639C LEU* 4.2 20.1 - - + +
640C ARG* 3.2 18.1 + - - +
643C SER* 3.8 25.1 - - - -
646C ILE* 6.3 0.2 - - + -
656C LEU* 5.6 0.7 - - + -
665C LEU* 3.7 27.1 - - + +
679C ASN 2.8 18.8 + - - -
680C ALA* 3.9 3.7 - - - -
682C GLY* 1.3 72.7 - - - +
684C LEU* 1.3 61.2 + - - +
686C ASN* 3.0 4.3 + - - +
687C LEU* 2.9 43.0 + - + +
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Residues in contact with LEU 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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662C LEU* 4.2 18.6 - - + +
665C LEU* 3.9 30.7 - - + +
666C LEU* 3.9 28.9 - - + -
669C LEU* 3.9 27.1 - - + -
680C ALA 2.9 24.6 + - - +
681C CYS* 3.8 4.5 - - - +
683C THR* 1.3 72.8 - - - +
685C TRP* 1.3 55.8 + - - +
687C LEU* 4.4 3.1 - - + +
688C SER* 2.7 44.1 + - - +
697C ALA* 6.0 4.7 - - + -
703C ALA* 6.2 0.4 - - + -
707C LEU* 4.3 10.8 - - + -
725C ALA* 4.0 9.6 - - + -
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Residues in contact with TRP 685 (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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681C CYS 2.8 15.1 + - - +
682C GLY* 3.2 20.0 - - - +
684C LEU* 1.3 76.1 - - - +
686C ASN* 1.3 69.2 + - - +
688C SER* 3.4 1.0 - - - -
689C ALA* 3.8 1.8 + - + +
717C MET 5.7 0.2 - - - -
720C MET* 3.7 45.8 - - + -
721C GLY* 3.8 22.0 - - - +
724C ALA* 3.5 27.2 - - + +
725C ALA* 3.9 11.5 - - - +
728C ASN* 3.2 26.2 + - - +
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Residues in contact with ASN 686 (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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640C ARG 4.1 4.8 + - - -
643C SER* 2.5 43.2 + - - +
644C SER* 3.5 26.6 - - - +
647C ALA* 3.6 19.6 - - + +
653C ARG* 3.7 0.7 + - - -
682C GLY 3.3 11.5 + - - -
683C THR 3.0 4.8 + - - +
685C TRP* 1.3 83.8 - - - +
687C LEU* 1.3 67.0 + - - +
689C ALA* 3.1 17.8 + - - +
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Residues in contact with LEU 687 (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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643C SER* 4.6 8.5 - - - +
646C ILE* 4.1 27.8 - - + -
647C ALA 4.6 5.2 - - - +
653C ARG* 3.2 40.3 + - + +
656C LEU* 3.8 22.2 - - + -
661C CYS* 4.8 0.7 - - - -
662C LEU* 3.9 25.8 - - + -
665C LEU* 3.8 28.9 - - + -
683C THR* 2.9 22.8 + - + +
684C LEU* 4.3 2.7 - - + +
686C ASN* 1.3 76.2 - - - +
688C SER* 1.3 61.9 + - - +
689C ALA 4.2 0.9 - - - -
694C ASP* 5.1 6.6 + - - +
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Residues in contact with SER 688 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684C LEU* 2.7 25.9 + - - +
685C TRP 3.4 1.8 - - - -
687C LEU* 1.3 76.9 - - - +
689C ALA* 1.3 57.2 + - - +
694C ASP* 2.8 27.6 - - - +
725C ALA* 3.5 20.7 + - - +
728C ASN* 3.4 37.0 - - - +
729C LEU* 4.3 12.7 - - - +
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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