Contacts of the strand formed by residues 640 - 644 (chain C) in PDB entry 1M7X
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 ILE 640 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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628C TRP* 3.3 4.7 - - - -
629C LEU* 3.2 16.7 + - + -
630C VAL* 3.0 52.7 + - + +
638C VAL* 3.6 14.1 - - + +
639C LEU* 1.3 81.5 - - - +
641C PHE* 1.3 69.3 + - - +
652C ILE* 4.0 20.6 - - + -
653C VAL 3.6 12.3 - - - +
654C ALA* 4.2 11.7 - - + -
665C TYR* 3.6 17.5 - - + -
667C PHE* 3.6 29.6 - - + -
715C LEU* 4.4 4.5 - - + -
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Residues in contact with PHE 641 (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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556C TRP* 3.5 38.1 - + - -
559C ALA* 3.9 17.3 - - + -
560C PHE* 4.3 6.3 - + - -
626C PHE* 3.3 32.1 - + + -
627C GLU 3.2 15.0 - - - +
628C TRP* 3.7 27.6 - + + -
629C LEU* 3.8 9.6 - - - +
640C ILE* 1.3 76.2 - - - +
642C VAL* 1.3 72.6 + - - +
643C ARG* 3.8 15.5 - - + -
652C ILE* 3.8 4.9 - - - +
653C VAL* 3.2 60.2 + - + +
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Residues in contact with VAL 642 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
626C PHE* 3.5 4.7 - - - -
627C GLU* 2.6 40.6 + - + +
629C LEU* 3.7 16.4 - - + -
641C PHE* 1.3 76.2 - - - +
643C ARG* 1.3 64.5 + - - +
644C ARG* 4.0 9.2 - - - +
650C GLU* 3.1 49.1 - - + +
651C ILE 3.8 8.3 - - - +
652C ILE* 3.4 33.4 - - + -
670C ASN* 4.7 1.1 - - - +
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Residues in contact with ARG 643 (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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559C ALA 3.3 27.9 + - - +
561C PRO* 3.5 16.5 - - - +
615C ALA* 3.8 15.2 - - - +
616C MET* 3.6 41.9 + - + +
617C HIS* 5.1 0.2 - - - +
618C GLU 5.5 0.8 - - - +
619C LEU 3.8 6.0 + - - +
620C ASP* 2.5 46.9 + - - +
625C GLY 3.3 13.1 + - - -
626C PHE* 3.6 24.5 - - - -
641C PHE* 3.8 10.8 - - + -
642C VAL* 1.3 73.6 - - - +
644C ARG* 1.3 64.3 + - - +
650C GLU* 3.0 3.7 - - - -
651C ILE 2.9 34.6 + - - +
653C VAL* 4.6 1.1 - - + -
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Residues in contact with ARG 644 (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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615C ALA* 3.8 6.3 - - - -
616C MET 5.3 0.2 + - - -
619C LEU* 3.5 6.9 + - - +
624C TYR* 2.8 65.6 + - - +
625C GLY* 2.6 30.4 + - - +
626C PHE 4.1 3.2 + - - -
627C GLU* 3.2 36.3 + - - +
642C VAL* 4.0 4.1 + - + +
643C ARG* 1.3 78.6 + - - +
645C ASP* 1.3 73.7 + - - +
648C GLY* 3.7 15.9 - - - -
649C ASN 3.0 14.1 - - - +
650C GLU* 2.6 34.1 + - + -
670C ASN* 4.4 1.8 - - - +
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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