Contacts of the helix formed by residues 611 - 620 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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577A LEU* 3.9 7.6 - - - +
609A VAL 3.1 1.2 + - - -
610A ASP* 1.3 79.5 + - - +
612A ALA* 1.3 63.6 + - - +
613A LEU 3.4 2.2 - - - -
614A ALA* 3.7 11.4 + - - +
615A PHE* 3.1 24.1 + - - +
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Residues in contact with ALA 612 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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573A MET* 3.8 33.4 - - + -
577A LEU* 4.3 2.6 - - - +
606A ILE* 3.2 30.3 - - + +
607A CYS* 5.1 1.6 - - - +
609A VAL* 3.0 14.6 + - + +
610A ASP 3.3 1.6 + - - -
611A GLY* 1.3 76.5 - - - +
613A LEU* 1.3 59.9 + - - +
615A PHE* 3.3 4.0 + - - +
616A LEU* 2.8 33.0 + - - +
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Residues in contact with LEU 613 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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606A ILE* 5.3 0.4 - - + -
607A CYS* 4.0 27.6 + - + +
609A VAL 4.8 0.4 + - - -
611A GLY 3.4 0.4 - - - -
612A ALA* 1.3 73.6 - - + +
614A ALA* 1.3 67.8 + - - +
616A LEU* 3.1 20.8 + - + +
617A VAL* 2.9 29.5 + - - +
639A LEU* 4.9 2.0 - - + +
642A VAL* 4.5 1.3 - - + -
646A ILE* 3.8 27.8 - - + -
652A HIS* 3.5 51.8 - - + +
655A ILE* 4.0 18.8 - - + -
656A LEU* 4.2 9.4 - - + -
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Residues in contact with ALA 614 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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611A GLY* 3.7 13.6 + - - +
612A ALA 3.4 0.2 - - - -
613A LEU* 1.3 78.0 - - - +
615A PHE* 1.3 65.8 + - - +
617A VAL* 3.3 3.5 + - - +
618A GLY* 2.9 19.8 + - - -
655A ILE* 4.0 8.9 - - + +
659A ASN* 4.0 30.3 - - - +
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Residues in contact with PHE 615 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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573A MET* 3.7 24.9 - - + -
576A ALA* 3.9 13.9 - - + -
577A LEU* 3.4 20.9 - - + -
585A LEU* 3.9 31.9 - - + -
589A LEU* 3.9 18.6 - - + -
611A GLY 3.1 18.8 + - - +
612A ALA 3.4 2.5 - - - +
614A ALA* 1.3 76.9 - - - +
616A LEU* 1.3 67.0 + - + +
618A GLY* 2.9 18.6 + - - -
619A THR* 3.1 38.7 + - + +
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Residues in contact with LEU 616 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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573A MET* 4.7 6.3 - - + -
589A LEU* 5.0 0.2 - - + -
606A ILE* 4.1 18.8 - - + -
612A ALA 2.8 22.6 + - - +
613A LEU* 3.7 12.6 - - + +
615A PHE* 1.3 90.9 - - + +
617A VAL* 1.3 61.7 + - - +
619A THR* 2.7 24.0 + - - -
620A LEU* 3.6 9.1 + - - +
635A GLY* 3.9 20.6 - - - +
638A ILE* 3.7 38.6 - - + -
639A LEU* 4.4 19.2 - - + +
642A VAL* 4.3 14.8 - - + -
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Residues in contact with VAL 617 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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613A LEU 2.9 19.2 + - - +
614A ALA* 3.7 6.5 - - - +
616A LEU* 1.3 75.8 - - - +
618A GLY* 1.3 62.9 + - - +
620A LEU* 3.0 30.0 + - + +
621A THR* 4.1 4.0 + - - +
639A LEU* 4.8 5.6 - - + -
655A ILE 5.2 0.4 - - - +
656A LEU* 4.0 34.5 - - + -
659A ASN* 3.5 38.4 - - + +
660A ASN 4.9 0.2 - - - -
661A CYS* 4.1 22.7 - - + -
664A THR* 5.5 2.0 - - - +
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Residues in contact with GLY 618 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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614A ALA 2.9 9.9 + - - -
615A PHE* 2.9 10.2 + - - -
617A VAL* 1.3 77.6 - - - +
619A THR* 1.3 61.2 + - - +
621A THR* 3.1 22.6 + - - -
622A TYR* 3.3 8.5 + - - -
659A ASN* 5.9 0.2 - - - +
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Residues in contact with THR 619 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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585A LEU* 5.7 0.2 - - + -
589A LEU* 4.5 1.3 - - + -
615A PHE* 3.1 46.8 + - + +
616A LEU* 2.7 18.7 + - - +
618A GLY* 1.3 74.2 - - - +
620A LEU* 1.3 62.1 + - - +
621A THR 3.1 0.9 + - - -
622A TYR* 3.2 23.9 + - + +
631A ILE* 4.0 24.7 - - + -
632A ILE* 3.4 15.5 - - - +
635A GLY* 3.2 26.4 - - - -
636A GLY 3.9 0.5 + - - -
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Residues in contact with LEU 620 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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616A LEU 3.8 7.6 - - - +
617A VAL* 3.0 22.6 + - + +
619A THR* 1.3 78.6 + - - +
621A THR* 1.3 57.8 + - - +
632A ILE* 3.7 12.9 - - - +
636A GLY* 3.7 31.4 - - - +
639A LEU* 3.8 25.8 - - + -
661A CYS* 4.1 12.1 - - - -
664A THR* 3.7 19.7 - - + -
665A LEU* 4.1 19.5 - - + -
668A HIS* 2.8 45.0 + - + +
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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