Contacts of the strand formed by residues 650 - 656 (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 GLU 650 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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615C ALA* 4.3 1.1 - - - -
629C LEU* 5.6 0.3 - - - +
642C VAL* 3.1 29.2 - - + +
643C ARG 3.0 14.1 - - - +
644C ARG* 2.6 38.0 + - + -
648C GLY 4.6 1.7 - - - +
649C ASN* 1.3 77.0 - - - +
651C ILE* 1.3 63.2 + - - +
652C ILE* 5.9 0.2 - - - +
669C ILE* 5.5 0.3 - - - +
670C ASN* 3.1 39.8 + - - +
671C GLN* 2.9 31.7 + - - +
675C TRP* 3.0 31.8 - - + -
724C VAL* 5.9 0.2 - - - +
725C ARG* 4.8 3.1 + - - +
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Residues in contact with ILE 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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613C HIS* 4.9 13.5 - - + +
615C ALA* 3.6 22.4 - - + +
616C MET* 3.3 26.2 - - - -
642C VAL* 3.8 1.4 - - - +
643C ARG* 2.9 25.7 + - - +
649C ASN* 6.3 0.4 - - + -
650C GLU* 1.3 76.2 - - - +
652C ILE* 1.3 78.1 + - - +
653C VAL* 3.6 16.3 + - + +
678C ILE* 4.7 7.0 - - + -
722C TRP* 3.9 20.0 - - + -
723C LEU 3.1 15.3 - - - +
724C VAL* 4.6 16.6 - - + +
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Residues in contact with ILE 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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629C LEU* 4.3 3.8 - - + -
640C ILE* 4.0 18.8 - - + -
641C PHE 3.8 8.7 - - - +
642C VAL* 3.4 22.4 - - + -
650C GLU* 5.9 0.2 - - - +
651C ILE* 1.3 74.5 - - - +
653C VAL* 1.3 63.3 + - - +
654C ALA* 4.6 1.6 - - + +
667C PHE* 4.3 9.4 - - + -
669C ILE* 3.8 29.6 - - + -
675C TRP* 3.5 35.9 - - + -
711C LEU* 4.1 10.3 - - + -
722C TRP* 3.1 5.5 - - - -
723C LEU* 2.6 54.6 + - + +
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Residues in contact with VAL 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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555C GLY 4.4 1.6 - - - +
556C TRP* 5.1 2.0 - - + -
559C ALA* 3.4 36.8 - - + -
616C MET* 4.0 6.1 - - + -
639C LEU 4.3 0.3 - - - +
640C ILE* 3.6 3.1 - - - +
641C PHE* 3.2 56.0 + - + +
643C ARG* 4.6 0.4 - - + -
651C ILE* 3.6 26.0 - - + +
652C ILE* 1.3 73.6 - - - +
654C ALA* 1.3 60.3 + - - +
655C SER* 4.2 5.5 + - - +
720C THR* 4.0 12.6 - - - +
721C ILE 3.3 3.1 - - - -
722C TRP* 4.0 13.9 - - + +
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Residues in contact with ALA 654 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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639C LEU 4.0 3.8 - - - -
640C ILE* 4.2 18.4 - - + -
652C ILE* 4.0 3.0 + - + -
653C VAL* 1.3 73.2 - - - +
655C SER* 1.3 62.8 + - - +
667C PHE* 5.7 1.3 - - + -
713C LEU* 5.3 2.0 - - + -
715C LEU* 3.5 30.3 - - + +
719C ALA 4.2 0.5 - - - +
720C THR* 3.1 2.1 - - - -
721C ILE* 2.7 50.3 + - + +
723C LEU* 4.9 4.7 - - + -
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Residues in contact with SER 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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556C TRP* 3.0 25.4 - - - +
637C SER 3.5 1.9 - - - +
638C VAL* 3.3 8.2 - - - +
639C LEU* 3.0 33.7 + - - +
640C ILE* 4.9 0.2 - - - +
653C VAL* 4.2 3.0 + - - +
654C ALA* 1.3 72.1 - - - +
656C ASN* 1.3 59.4 + - - +
657C PHE* 3.3 32.0 - - - -
715C LEU* 5.8 0.9 - - - -
719C ALA 3.9 3.8 - - - -
720C THR* 2.9 22.5 + - - -
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Residues in contact with ASN 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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636C ARG 3.6 7.3 + - - -
637C SER 3.8 1.6 - - - -
638C VAL* 4.2 5.1 - - + +
654C ALA 4.3 0.6 + - - -
655C SER* 1.3 71.4 - - - +
657C PHE* 1.3 62.3 + - - +
658C THR* 2.9 40.5 + - - +
660C VAL 3.1 17.9 - - - +
662C ARG* 3.6 10.4 - - - +
715C LEU* 2.9 32.8 - - + +
716C PRO 3.2 19.5 - - - +
718C LEU* 3.2 20.8 - - - -
719C ALA 3.0 12.2 + - - +
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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