Contacts of the helix formed by residues 649 - 658 (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 ASN 649 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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645C LEU 3.5 13.7 + - - +
646C ILE 2.9 11.1 + - - +
647C ALA 3.4 0.4 - - - -
648C THR* 1.3 78.3 - - - +
650C GLU* 1.3 58.3 + - - +
651C ASP* 3.2 11.8 + - - +
652C HIS* 2.8 60.2 + - + -
653C ARG* 2.9 27.7 + - - +
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Residues in contact with GLU 650 (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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648C THR 4.1 2.0 + - - -
649C ASN* 1.3 69.9 + - - +
651C ASP* 1.3 64.8 + - - +
653C ARG* 3.3 17.8 + - - +
654C GLN* 2.8 29.7 + - + +
657C ARG* 2.8 38.0 + - - -
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Residues in contact with ASP 651 (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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649C ASN* 3.2 8.6 + - - +
650C GLU* 1.3 77.5 - - - +
652C HIS* 1.3 63.6 + - + +
654C GLN* 3.3 8.1 + - - +
655C ILE* 3.1 35.2 + - + +
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Residues in contact with HIS 652 (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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607C CYS* 3.6 39.0 + - + +
608C ALA* 5.6 0.8 - - - -
613C LEU* 3.6 27.5 - - + +
645C LEU* 5.3 1.3 - - + -
646C ILE* 4.0 18.2 - - + -
649C ASN* 2.8 43.4 + - + +
651C ASP* 1.3 79.2 - - + +
653C ARG* 1.3 64.6 + - - +
655C ILE* 3.3 13.3 + - + +
656C LEU* 3.2 26.9 + - - +
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Residues in contact with ARG 653 (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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646C ILE* 3.6 17.2 - - + +
647C ALA* 2.9 38.3 + - - +
649C ASN 2.9 16.2 + - - +
650C GLU* 3.5 21.8 - - - +
652C HIS* 1.3 75.2 - - - +
654C GLN* 1.3 62.4 + - - +
656C LEU* 3.2 9.7 + - + +
657C ARG* 3.1 50.8 + - - +
662C LEU* 6.2 2.0 - - - +
686C ASN 3.7 8.9 + - - -
687C LEU* 3.2 42.7 + - + +
689C ALA 4.0 14.1 - - - -
694C ASP 6.1 0.6 - - - +
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Residues in contact with GLN 654 (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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650C GLU* 2.8 19.2 + - + +
651C ASP* 3.5 9.6 - - - +
652C HIS 3.2 0.4 - - - -
653C ARG* 1.3 72.8 - - - +
655C ILE* 1.3 64.9 + - + +
657C ARG* 2.7 44.1 + - - +
658C GLU* 3.1 55.3 + - - +
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Residues in contact with ILE 655 (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* 4.3 15.7 - - + -
614C ALA* 3.9 26.2 - - + +
651C ASP* 3.1 19.2 + - + +
652C HIS* 3.3 19.5 + - + +
654C GLN* 1.3 74.5 - - - +
656C LEU* 1.3 60.9 + - + +
658C GLU* 3.6 9.6 + - - +
659C ASN* 2.5 44.9 + - - +
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Residues in contact with LEU 656 (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* 4.5 14.8 - - + -
617C VAL* 4.0 17.7 - - + -
639C LEU* 4.8 6.3 - - + -
646C ILE* 3.9 39.3 - - + -
652C HIS 3.2 17.0 + - - +
653C ARG* 3.3 11.0 - - - +
654C GLN 3.2 0.2 - - - -
655C ILE* 1.3 78.7 - - - +
657C ARG* 1.3 62.7 + - + +
659C ASN* 3.1 8.5 + - - +
661C CYS* 3.0 50.2 + - + +
662C LEU* 6.4 0.9 - - + -
683C THR* 5.6 0.9 - - + -
687C LEU* 3.8 30.7 - - + -
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Residues in contact with ARG 657 (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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650C GLU* 2.8 29.6 + - - -
653C ARG* 3.1 38.4 + - - +
654C GLN* 2.7 47.1 + - - +
656C LEU* 1.3 71.0 - - + +
658C GLU* 1.3 58.6 + - - +
659C ASN 2.9 5.2 - - - -
660C ASN* 2.9 28.6 + - - +
661C CYS* 4.8 2.5 - - - +
662C LEU* 5.1 17.8 - - + +
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Residues in contact with GLU 658 (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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654C GLN* 3.1 48.9 + - - +
655C ILE* 3.9 11.3 - - - +
656C LEU 3.3 0.2 - - - -
657C ARG* 1.3 74.9 - - + +
659C ASN* 1.3 66.0 + - - +
660C ASN* 3.5 5.9 + - - +
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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