Contacts of the helix formed by residues 639 - 645 (chain F) in PDB entry 6T8G
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 THR 639 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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601F MET* 4.2 2.7 - - + -
609F GLU* 2.3 42.8 + - - +
635F VAL* 3.3 22.2 - - - +
636F ASP* 3.3 16.6 - - - +
637F VAL 3.2 5.1 + - - +
638F ILE* 1.3 76.9 - - - +
640F GLY* 1.3 65.2 + - - +
641F LEU 3.6 4.2 + - - -
642F ILE* 3.4 11.6 - - - +
643F LYS* 3.1 23.7 + - - +
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Residues in contact with GLY 640 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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635F VAL* 5.6 2.4 - - - +
639F THR* 1.3 74.7 - - - +
641F LEU* 1.3 61.8 + - - +
643F LYS* 3.2 9.3 + - - +
644F ALA* 2.9 34.0 + - - +
10G T 5.8 5.4 + - - -
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Residues in contact with LEU 641 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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602A MET* 6.2 3.1 - - + -
632A ARG* 3.4 59.2 - - + +
634A SER* 5.6 4.3 - - - -
636A ASP* 4.8 7.6 - - - +
609F GLU* 4.2 19.5 - - + +
610F GLU* 6.0 4.5 - - + -
613F ALA* 4.1 26.7 - - + +
616F ALA* 5.6 0.7 - - - +
617F GLN* 4.8 3.4 - - - +
639F THR* 3.3 1.4 + - - -
640F GLY* 1.3 75.6 - - - +
642F ILE* 1.3 68.2 + - + +
643F LYS 3.4 0.3 + - - -
644F ALA* 5.5 0.7 - - - -
645F ASN* 2.9 33.6 + - - +
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Residues in contact with ILE 642 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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463F LEU* 4.4 10.6 - - + +
597F PHE* 3.9 33.7 - - + -
609F GLU* 3.9 24.5 - - + +
612F ILE* 4.2 18.6 - - + -
613F ALA* 4.8 3.8 - - - +
628F LEU* 4.0 21.8 - - + -
637F VAL 4.4 0.7 - - - +
638F ILE* 4.4 11.4 - - + -
639F THR* 3.4 30.1 - - - +
640F GLY 3.3 0.4 - - - -
641F LEU* 1.3 80.3 - - + +
643F LYS* 1.3 63.7 + - - +
646F ILE* 3.5 25.2 - - + +
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Residues in contact with LYS 643 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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655A SER* 4.8 6.2 + - - -
656A SER* 5.4 10.8 - - - -
463F LEU* 5.0 0.9 - - - -
635F VAL* 6.6 0.7 - - + -
638F ILE* 3.7 23.8 - - + +
639F THR 3.1 23.8 + - - +
640F GLY* 3.6 8.3 - - - +
641F LEU 3.2 0.2 - - - -
642F ILE* 1.3 77.1 - - - +
644F ALA* 1.3 60.7 + - + +
645F ASN 2.9 8.1 + - - -
646F ILE 3.0 25.3 + - - +
649F ARG* 3.3 30.7 + - - +
661F ARG 4.3 4.2 + - - -
662F THR* 3.5 21.5 + - + +
665F ASP* 3.1 24.4 + - - -
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Residues in contact with ALA 644 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467A THR* 4.1 15.1 - - + +
468A THR 5.6 0.2 + - - -
631A GLN 5.1 4.5 - - - +
632A ARG* 6.1 4.9 - - + -
633A PRO* 6.0 2.0 - - + -
655A SER* 3.6 32.9 + - - +
656A SER* 5.6 0.9 - - - +
659A ASP* 3.7 23.3 - - - +
640F GLY 2.9 19.5 + - - +
641F LEU* 5.2 0.9 - - - +
643F LYS* 1.3 72.3 - - + +
645F ASN* 1.3 67.8 + - - +
646F ILE 5.2 0.4 - - - -
647F PRO* 5.9 0.4 - - - -
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Residues in contact with ASN 645 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467A THR* 6.1 1.2 - - - +
468A THR* 4.2 16.1 + - + +
631A GLN* 4.3 24.0 + - - +
632A ARG* 4.6 3.4 - - - +
461F HIS* 4.5 5.4 - - - -
613F ALA* 4.7 3.3 - - - +
616F ALA* 3.9 32.2 + - + +
617F GLN* 3.8 33.5 + - - +
641F LEU* 2.9 32.8 + - - +
643F LYS 2.9 1.0 + - - -
644F ALA* 1.3 85.0 + - - +
646F ILE* 1.3 64.3 + - + +
647F PRO* 3.4 11.5 - - - +
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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