Contacts of the helix formed by residues 639 - 646 (chain B) 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 THR 639 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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601B MET* 5.4 0.2 - - + -
609B GLU* 2.7 30.3 + - - +
635B VAL* 3.3 20.0 - - - +
636B ASP* 3.4 17.7 - - - +
637B VAL 3.7 2.5 + - - -
638B ILE* 1.3 77.2 - - - +
640B GLY* 1.3 62.7 + - - +
641B LEU* 3.1 19.4 + - + +
642B ILE* 3.7 4.6 + - - +
643B LYS* 3.3 26.8 + - - +
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Residues in contact with GLY 640 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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639B THR* 1.3 74.0 - - - +
641B LEU* 1.3 58.4 + - - +
642B ILE 3.2 0.7 - - - -
643B LYS* 3.6 18.8 - - - +
644B ALA 2.9 24.9 + - - -
602C MET* 3.3 36.2 - - - +
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Residues in contact with LEU 641 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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606B LYS* 5.8 3.8 - - + -
609B GLU* 3.3 36.1 - - + +
610B GLU* 5.8 4.0 - - - +
613B ALA* 4.4 15.1 - - + +
639B THR* 3.1 8.2 + - + +
640B GLY* 1.3 78.2 - - - +
642B ILE* 1.3 63.6 + - - +
644B ALA* 3.8 13.7 - - - +
645B ASN* 4.4 4.7 + - - +
602C MET* 4.0 11.9 - - + +
603C ILE* 3.7 43.3 - - + +
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Residues in contact with ILE 642 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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463B LEU* 4.1 22.1 - - + +
597B PHE* 5.5 6.7 - - + -
601B MET* 5.0 4.5 - - - -
609B GLU* 3.7 40.4 - - + +
612B ILE* 4.1 22.7 - - + -
613B ALA* 4.7 5.8 - - + +
628B LEU* 4.4 6.5 - - + -
637B VAL 4.8 9.9 - - - +
638B ILE* 5.1 5.2 - - + -
639B THR* 3.7 11.0 + - - +
640B GLY 3.2 0.2 - - - -
641B LEU* 1.3 77.7 - - - +
643B LYS* 1.3 66.2 + - - +
644B ALA 3.1 2.1 + - - -
645B ASN* 3.9 1.8 + - - +
646B ILE* 3.7 40.9 + - + +
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Residues in contact with LYS 643 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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463B LEU* 5.1 3.6 - - + -
638B ILE* 4.7 5.2 - - + -
639B THR 3.3 13.6 + - - +
640B GLY* 3.1 25.2 + - - +
642B ILE* 1.3 75.5 - - - +
644B ALA* 1.3 64.9 + - - +
646B ILE 3.6 6.0 - - - +
647B PRO* 5.2 0.5 - - - +
649B ARG* 3.0 39.0 + - - +
661B ARG 4.0 14.1 + - - +
662B THR* 3.3 29.9 - - - +
663B ILE* 5.3 0.2 - - - -
665B ASP* 5.5 4.7 + - - -
602C MET* 5.6 3.4 - - - -
632C ARG* 4.2 22.5 - - - +
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Residues in contact with ALA 644 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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640B GLY 2.9 14.5 + - - +
641B LEU* 3.8 11.2 - - - +
642B ILE 3.1 1.0 - - - -
643B LYS* 1.3 80.3 - - - +
645B ASN* 1.3 71.1 + - - +
646B ILE 3.4 1.7 + - - -
647B PRO* 4.7 2.1 - - - +
500C LYS* 3.8 21.8 + - - -
599C ASP* 3.3 30.9 - - + +
602C MET* 3.8 7.0 - - + -
603C ILE* 6.0 4.7 - - + -
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Residues in contact with ASN 645 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460B PRO* 5.0 2.3 - - - +
461B HIS* 4.1 12.3 - - - -
613B ALA* 3.5 23.9 - - - +
616B ALA* 3.6 25.5 + - + +
617B GLN* 3.5 35.6 - - - +
620B ARG* 5.3 6.4 + - - +
641B LEU 4.4 4.0 + - - +
642B ILE 3.9 3.4 + - - +
644B ALA* 1.3 84.1 - - - +
646B ILE* 1.3 62.2 + - + +
647B PRO* 3.3 10.9 - - - +
499C PRO* 4.2 8.7 + - - +
500C LYS* 4.6 14.9 - - - +
599C ASP* 5.4 1.8 + - - -
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Residues in contact with ILE 646 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461B HIS* 3.4 48.0 - - + +
462B LEU 5.1 0.4 - - - +
463B LEU* 3.8 27.8 - - + +
612B ILE* 5.8 0.7 - - + -
616B ALA* 4.4 12.1 - - + -
626B LEU* 5.3 0.2 - - + -
628B LEU* 3.8 28.7 - - + -
642B ILE* 3.7 22.7 + - + +
643B LYS* 3.6 2.9 - - - +
644B ALA 3.3 1.6 - - - -
645B ASN* 1.3 81.7 - - - +
647B PRO* 1.3 51.5 - - - +
648B THR 3.7 12.6 - - - +
649B ARG* 2.4 37.0 + - - +
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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