Contacts of the helix formed by residues 646 - 651 (chain B) in PDB entry 6IEH
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 LYS 646 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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642B GLU 3.9 8.3 + - - +
643B TYR* 3.3 16.2 + - - +
644B ILE 3.3 1.8 - - - -
645B HIS* 1.3 79.0 - - - +
647B PRO* 1.3 75.3 - - + +
648B LYS* 3.1 2.8 + - + +
649B TYR* 3.2 18.5 + - + +
650B CYS* 3.1 18.4 + - - -
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Residues in contact with PRO 647 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A TRP* 3.7 20.4 - - + -
645B HIS 3.8 4.5 - - - +
646B LYS* 1.3 87.3 - - + +
648B LYS* 1.3 63.3 + - - +
650B CYS* 4.0 9.4 - - - -
651B LEU* 3.1 30.3 + - + +
694B TYR* 3.7 35.7 - - + -
733B VAL* 4.3 11.7 - - + -
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Residues in contact with LYS 648 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A TRP* 3.8 38.9 - - + +
646B LYS* 3.1 3.1 + - + +
647B PRO* 1.3 81.0 - - - +
649B TYR* 1.3 79.5 + - + +
652B PRO* 3.2 20.3 - - - +
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Residues in contact with TYR 649 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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643B TYR* 3.7 23.6 - - + +
644B ILE* 4.7 0.4 - - - +
646B LYS* 3.2 16.4 + - + +
648B LYS* 1.3 91.2 - - + +
650B CYS* 1.3 60.3 + - - +
652B PRO* 3.9 2.7 - - - +
653B PHE* 3.4 22.9 - - - -
783B MET* 3.5 27.2 - - + +
784B GLY 4.8 1.6 - - - -
785B ILE* 3.4 43.3 - - + +
786B GLN* 4.3 8.6 + - - +
787B ASP* 4.4 20.0 + - + +
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Residues in contact with CYS 650 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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644B ILE 3.5 15.5 - - - +
645B HIS* 3.8 12.6 - - - -
646B LYS 3.1 23.0 + - - -
647B PRO* 4.0 2.7 - - - -
649B TYR* 1.3 73.9 - - - +
651B LEU* 1.3 67.9 + - - +
652B PRO 3.2 2.9 - - - -
653B PHE* 3.0 14.4 + - - +
654B LEU* 3.2 19.9 + - + +
733B VAL* 3.5 32.8 - - - -
736B LEU* 4.8 2.9 - - + -
739B ILE* 3.9 16.8 - - + -
783B MET* 4.4 3.1 - - - -
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Residues in contact with LEU 651 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A ASN* 3.2 31.3 + - - +
174A TRP* 3.8 22.7 - - + +
177A LYS* 5.1 2.2 - - - +
647B PRO* 3.1 21.9 + - + +
650B CYS* 1.3 78.4 - - - +
652B PRO* 1.3 71.1 - - + +
654B LEU* 3.4 30.0 + - + +
677B PHE* 3.6 28.9 - - + -
694B TYR* 3.3 40.6 - - + -
733B VAL* 4.6 4.5 - - + -
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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