Contacts of the helix formed by residues 611 - 620 (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 GLY 611 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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577C LEU* 4.0 7.6 - - - +
609C VAL 3.3 1.0 + - - -
610C ASP* 1.3 79.6 + - - +
612C ALA* 1.3 61.9 + - - +
613C LEU 3.5 2.9 - - - -
614C ALA* 3.6 11.0 + - - +
615C PHE* 3.0 23.7 + - - +
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Residues in contact with ALA 612 (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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573C MET* 3.7 26.0 - - + -
577C LEU* 4.2 10.5 - - - -
606C ILE* 3.4 23.1 - - + +
609C VAL* 3.1 22.2 + - + +
610C ASP 3.3 2.0 + - - -
611C GLY* 1.3 77.4 - - - +
613C LEU* 1.3 58.6 + - + +
615C PHE* 3.2 2.4 + - - +
616C LEU* 2.8 35.3 + - - +
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Residues in contact with LEU 613 (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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606C ILE* 5.3 0.7 - - + -
607C CYS* 4.2 28.3 - - + +
609C VAL 4.7 0.4 + - - -
611C GLY 3.5 0.4 - - - -
612C ALA* 1.3 73.9 - - - +
614C ALA* 1.3 65.6 + - - +
616C LEU* 3.2 20.9 + - + +
617C VAL* 2.9 29.9 + - - +
639C LEU* 4.6 4.2 - - + +
642C VAL* 4.4 1.6 - - + -
646C ILE* 3.8 26.9 - - + -
652C HIS* 3.6 52.5 - - + +
655C ILE* 4.3 19.5 - - + -
656C LEU* 4.5 5.8 - - + -
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Residues in contact with ALA 614 (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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611C GLY* 3.6 13.1 + - - +
612C ALA 3.4 0.4 - - - -
613C LEU* 1.3 77.7 - - - +
615C PHE* 1.3 57.0 + - - +
617C VAL* 3.4 4.3 + - - +
618C GLY* 2.9 25.1 + - - -
655C ILE* 3.9 11.4 - - + +
659C ASN* 3.9 32.5 - - - +
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Residues in contact with PHE 615 (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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573C MET* 4.0 15.5 - - + -
576C ALA* 3.5 32.1 - - + -
577C LEU* 3.6 26.9 - - + -
579C VAL 6.0 1.1 - - - -
585C LEU* 3.7 27.1 - - + -
589C LEU* 4.4 4.9 - - + -
611C GLY 3.0 18.6 + - - +
612C ALA 3.4 3.8 - - - +
613C LEU 3.2 0.2 - - - -
614C ALA* 1.3 76.8 - - - +
616C LEU* 1.3 65.0 + - + +
618C GLY* 3.1 4.5 + - - -
619C THR* 3.0 42.7 + - + +
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Residues in contact with LEU 616 (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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573C MET* 4.4 17.0 - - + -
589C LEU* 4.7 4.3 - - + -
592C LEU* 4.7 0.7 - - + -
606C ILE* 3.9 20.2 - - + -
612C ALA 2.8 23.5 + - - +
613C LEU* 3.2 20.2 + - + +
615C PHE* 1.3 78.5 - - + +
617C VAL* 1.3 60.0 + - - +
619C THR* 2.6 24.5 + - + +
620C LEU* 3.6 9.9 + - - +
635C GLY* 4.4 11.4 - - - +
638C ILE* 3.8 47.3 - - + -
639C LEU* 4.2 18.2 - - + -
642C VAL* 4.8 2.5 - - + -
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Residues in contact with VAL 617 (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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613C LEU 2.9 21.3 + - - +
614C ALA* 3.7 4.9 - - - +
616C LEU* 1.3 72.0 - - - +
618C GLY* 1.3 66.6 + - - +
620C LEU* 3.1 27.3 + - + +
621C THR* 4.2 4.0 + - - +
639C LEU* 4.6 6.1 - - + -
655C ILE 5.4 0.4 - - - +
656C LEU* 4.0 23.6 - - + -
659C ASN* 3.6 36.6 - - + +
661C CYS* 3.9 36.6 - - + -
664C THR* 5.6 2.6 - - - +
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Residues in contact with GLY 618 (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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614C ALA 2.9 15.9 + - - -
615C PHE* 3.1 6.2 + - - -
617C VAL* 1.3 75.5 - - - +
619C THR* 1.3 60.9 + - - +
621C THR* 3.2 20.7 + - - -
622C TYR* 3.6 8.3 + - - +
659C ASN* 5.9 0.2 - - - +
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Residues in contact with THR 619 (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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585C LEU* 5.1 2.0 - - + -
589C LEU* 4.1 16.6 - - + -
615C PHE* 3.0 40.5 + - + +
616C LEU* 2.6 20.3 + - + +
618C GLY* 1.3 75.8 - - - +
620C LEU* 1.3 61.7 + - - +
621C THR 3.1 1.5 + - - -
622C TYR* 3.2 25.0 + - + +
631C ILE* 4.1 18.8 - - + -
632C ILE* 3.5 13.0 - - - +
635C GLY* 3.3 20.9 - - - -
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Residues in contact with LEU 620 (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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616C LEU 3.8 10.1 - - - +
617C VAL* 3.1 21.6 + - + +
619C THR* 1.3 77.9 + - - +
621C THR* 1.3 60.5 + - - +
622C TYR 3.6 0.2 - - - -
632C ILE* 3.9 13.6 - - - +
635C GLY 4.4 0.2 - - - -
636C GLY* 3.7 33.0 - - - +
639C LEU* 3.9 26.2 - - + -
661C CYS* 4.1 15.5 - - - -
664C THR* 3.7 19.5 - - + -
665C LEU* 4.1 15.0 - - + -
668C HIS* 2.9 42.1 + - + +
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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