Contacts of the strand formed by residues 649 - 652 (chain C) in PDB entry 6IWQ
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 TRP 649 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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537C ILE* 4.0 17.9 - - + -
538C ARG 3.4 22.2 - - - +
539C GLY* 4.1 5.8 - - - -
540C PHE* 4.1 1.3 - - - +
546C ILE* 3.8 22.9 - - + -
559C LEU* 3.9 15.9 - - + -
610C TYR* 4.5 6.0 + - - -
615C HIS* 2.6 41.4 + - - +
617C PHE* 4.0 28.9 - + + -
626C LEU* 3.2 39.4 + - + +
627C ASP* 3.7 27.1 - - - -
628C ARG* 3.4 37.9 - - + -
635C VAL* 4.5 4.7 - - + -
647C GLN* 3.7 10.6 - - - +
648C LYS* 1.3 78.1 - - - +
650C GLU* 1.3 61.6 + - - +
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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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536C GLU 3.6 0.2 - - - +
537C ILE* 3.5 4.7 - - - +
538C ARG* 2.9 52.0 + - - +
540C PHE* 4.1 20.9 - - + -
541C GLU* 3.8 18.5 + - - -
610C TYR* 4.0 5.4 - - - +
615C HIS* 4.5 11.9 - - + +
617C PHE* 5.4 0.2 - - - -
649C TRP* 1.3 76.3 - - - +
651C MET* 1.3 60.9 - - - +
652C ASN* 3.0 30.4 + - - +
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Residues in contact with MET 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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533C ASP* 4.0 17.9 - - - +
534C TRP* 4.0 10.8 - - - +
535C GLY 4.3 2.2 - - - +
536C GLU 3.1 11.0 - - - +
537C ILE* 3.7 30.5 - - + -
571C PHE* 3.9 25.8 - - + +
572C ARG* 4.0 3.4 - - - +
573C ILE* 3.7 39.7 - - + -
579C LEU* 4.3 1.3 - - + -
610C TYR* 3.2 21.0 + - + +
612C LYS* 3.7 18.0 + - - -
617C PHE* 3.8 17.7 - - + -
650C GLU* 1.3 73.2 - - - +
652C ASN* 1.3 66.7 + - - +
653C ASN* 5.0 1.0 + - - -
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Residues in contact with ASN 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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534C TRP 3.7 2.5 - - - -
535C GLY* 3.0 0.3 - - - -
536C GLU* 2.8 62.7 + - + +
538C ARG* 4.1 9.3 - - - +
612C LYS* 5.5 0.3 + - - -
650C GLU* 3.0 38.0 + - - +
651C MET* 1.3 83.4 - - - +
653C ASN* 1.3 68.3 + - - +
654C ILE* 3.2 1.0 + - + +
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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