Contacts of the helix formed by residues 670 - 675 (chain C) in PDB entry 2HYE
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 670 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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463C VAL* 3.0 34.0 - - - +
575C HIS* 4.1 8.9 - - - +
590C GLN* 3.3 22.9 + - - +
591C VAL 3.1 3.5 - - - -
592C SER* 2.8 36.7 + - - -
595C GLN* 3.8 4.0 + - - -
668C LYS* 3.2 30.7 + - + +
669C ILE* 1.3 73.4 - - - +
671C GLN* 1.3 63.4 + - - +
672C ILE* 3.2 2.2 - - - -
673C GLN* 3.0 26.4 + - - +
674C MET* 4.2 1.0 + - - +
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Residues in contact with GLN 671 (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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635C LYS* 5.3 5.0 + - - -
668C LYS* 2.6 63.1 + - - +
669C ILE* 2.7 17.6 + - - +
670C ASN* 1.3 72.3 - - - +
672C ILE* 1.3 62.6 + - + +
674C MET* 2.9 19.7 + - - +
675C LYS* 3.8 22.3 - - - +
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Residues in contact with ILE 672 (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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592C SER* 6.1 0.4 - - - +
595C GLN* 3.8 11.7 - - + +
623C GLU* 5.2 6.5 - - - +
626C ARG* 3.3 42.3 + - + +
627C THR* 4.0 9.9 - - + +
630C SER* 2.8 41.3 - - - +
669C ILE 4.2 6.5 - - - +
670C ASN 3.2 0.6 + - - -
671C GLN* 1.3 77.1 - - + +
673C GLN* 1.3 65.9 + - + +
674C MET 3.1 1.6 + - - -
675C LYS* 3.4 23.6 + - + +
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Residues in contact with GLN 673 (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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459C LYS* 3.5 23.5 + - - +
463C VAL* 3.7 27.0 - - + +
571C THR 5.2 0.2 + - - -
572C THR 3.2 25.1 + - - -
573C LEU* 4.5 1.2 - - - +
574C GLY 3.0 19.4 + - - +
575C HIS* 3.5 14.9 - - - +
592C SER* 3.1 33.5 - - - -
593C LEU 4.6 0.2 - - - +
594C PHE* 5.6 4.2 - - - -
670C ASN* 3.0 23.9 + - - +
672C ILE* 1.3 78.8 - - + +
674C MET* 1.3 60.1 + - - +
675C LYS 3.7 0.7 - - - -
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Residues in contact with MET 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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414C ASP* 5.2 0.4 - - - +
418C ARG* 3.0 61.5 + - + +
456C ASP 5.1 1.8 - - - +
459C LYS* 3.8 35.4 - - + +
460C ARG* 4.1 20.0 - - + -
463C VAL* 3.4 32.5 - - + +
464C GLY* 5.1 2.7 - - - +
465C LYS 5.9 0.7 - - - +
668C LYS* 4.7 10.1 - - - +
670C ASN 5.0 2.5 - - - +
671C GLN* 2.9 10.4 + - - +
673C GLN* 1.3 83.7 - - + +
675C LYS* 1.3 67.7 + - - +
676C GLU 4.1 0.9 + - - -
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Residues in contact with LYS 675 (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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418C ARG* 4.8 10.9 - - - +
459C LYS* 4.7 5.0 + - - -
671C GLN* 3.8 28.9 - - + +
672C ILE* 3.4 14.9 + - - +
673C GLN 3.7 0.5 - - - +
674C MET* 1.3 85.3 + - - +
676C GLU* 1.3 63.3 + - - +
677C THR* 3.5 8.3 + - - +
680C GLU* 3.6 7.2 - - - +
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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