Contacts of the helix formed by residues 641 - 646 (chain C) in PDB entry 6T8O
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 LEU 641 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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609C GLU* 3.3 40.4 - - + +
610C GLU* 4.4 20.6 - - + +
613C ALA* 4.4 17.3 - - + +
616C ALA* 5.7 1.7 - - - +
639C THR* 3.3 1.2 + - - -
640C GLY* 1.3 77.7 - - - +
642C ILE* 1.3 63.3 + - - +
644C ALA* 3.3 16.8 - - - +
645C ASN* 4.3 2.8 + - - +
601D MET 5.8 0.4 - - - +
602D MET* 3.7 43.8 - - + +
632D ARG* 4.5 4.9 - - - +
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Residues in contact with ILE 642 (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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463C LEU* 3.8 31.1 - - + +
597C PHE* 4.6 10.3 - - + -
601C MET* 4.8 7.9 - - - -
609C GLU* 4.2 20.9 - - + +
612C ILE* 3.7 31.9 - - + -
613C ALA* 4.9 1.8 - - - +
616C ALA* 5.6 0.2 - - - +
628C LEU* 4.3 5.6 - - + -
637C VAL 4.2 11.2 - - - +
638C ILE* 5.0 2.5 - - - -
639C THR* 3.4 22.5 + - - +
640C GLY 3.3 0.2 - - - -
641C LEU* 1.3 80.1 - - - +
643C LYS* 1.3 61.3 + - + +
644C ALA 3.1 1.3 + - - -
646C ILE* 3.4 36.5 + - + +
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Residues in contact with LYS 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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463C LEU* 4.6 3.8 - - + -
638C ILE* 3.7 24.3 + - + -
639C THR 3.3 24.1 + - - +
640C GLY* 3.6 7.9 - - - +
641C LEU 3.4 0.2 - - - -
642C ILE* 1.3 75.9 - - - +
644C ALA* 1.3 64.8 + - - +
645C ASN 3.5 0.4 - - - -
646C ILE 4.3 8.5 - - - +
647C PRO* 5.5 0.7 - - - +
649C ARG* 3.4 35.7 + - - +
661C ARG 4.6 1.2 + - - -
662C THR* 3.3 31.8 + - - +
663C ILE 4.8 0.7 - - - +
665C ASP* 3.4 15.4 + - - +
632D ARG* 4.8 4.2 - - - +
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Residues in contact with ALA 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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640C GLY 2.9 13.9 + - - +
641C LEU 3.3 14.4 - - - +
642C ILE 3.1 1.0 - - - -
643C LYS* 1.3 79.3 - - - +
645C ASN* 1.3 68.9 + - - +
646C ILE 3.6 0.4 + - - -
647C PRO* 5.8 1.4 - - - +
602D MET* 3.7 17.7 - - - -
631D GLN* 4.3 12.6 - - - +
632D ARG* 3.5 38.0 + - - +
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Residues in contact with ASN 645 (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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460C PRO* 4.9 2.9 - - - +
461C HIS* 3.8 12.6 - - - -
613C ALA 4.2 0.9 - - - +
616C ALA* 3.3 30.8 - - + +
617C GLN* 3.7 12.7 + - - -
641C LEU 4.3 2.1 + - - +
642C ILE 3.9 1.8 + - - -
644C ALA* 1.3 85.3 + - - +
646C ILE* 1.3 65.2 + - - +
647C PRO* 3.3 12.9 - - - +
500D LYS* 3.1 36.2 - - - +
599D ASP* 3.4 10.6 + - - +
602D MET* 3.3 28.1 - - - +
631D GLN* 5.2 1.0 + - - -
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Residues in contact with ILE 646 (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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461C HIS* 3.7 17.7 - - + -
462C LEU* 3.5 29.8 - - - +
463C LEU* 3.8 20.5 - - + +
612C ILE* 4.7 5.6 - - + -
616C ALA* 3.9 19.1 - - + -
626C LEU* 5.4 2.2 - - + -
628C LEU* 3.8 27.1 - - + -
642C ILE* 3.4 30.8 + - + +
643C LYS* 4.4 3.3 - - - +
644C ALA 3.6 1.4 - - - -
645C ASN* 1.3 83.2 - - - +
647C PRO* 1.3 58.8 - - - +
648C THR 4.2 2.2 - - - +
649C ARG* 3.2 21.7 + - - -
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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