Contacts of the helix formed by residues 608 - 616 (chain X) in PDB entry 1T6B
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 ASP 608 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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595X ARG 4.2 5.0 + - - -
597X HIS* 3.2 22.3 + - - -
607X ALA* 1.3 77.6 - - - +
609X GLU* 1.3 65.1 + - - +
610X SER* 3.9 12.1 - - - +
611X VAL* 3.2 19.4 + - + +
612X VAL* 3.0 20.6 + - - +
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Residues in contact with GLU 609 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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607X ALA 3.5 1.2 + - - +
608X ASP* 1.3 72.1 - - - +
610X SER* 1.3 56.3 + - - +
612X VAL* 3.3 1.9 + - - +
613X LYS* 2.8 53.3 + - - +
722X LYS* 5.0 12.7 + - + +
723X LYS 5.0 5.2 - - - +
724X ILE* 3.9 38.3 - - + +
725X LEU 5.5 0.3 + - - -
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Residues in contact with SER 610 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608X ASP* 3.2 8.6 - - - +
609X GLU* 1.3 75.2 - - - +
611X VAL* 1.3 61.6 + - - +
613X LYS* 3.3 9.0 + - - +
614X GLU* 2.9 35.5 + - - +
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Residues in contact with VAL 611 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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595X ARG* 4.3 29.8 - - + +
607X ALA* 4.1 11.7 - - + -
608X ASP* 3.2 25.6 + - + +
610X SER* 1.3 77.1 - - - +
612X VAL* 1.3 65.0 + - - +
614X GLU* 3.4 6.1 + - - +
615X ALA* 2.9 23.7 + - - +
635X ILE* 3.7 24.7 - - + -
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Residues in contact with VAL 612 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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607X ALA* 3.8 26.7 - - + +
608X ASP 3.0 15.3 + - - +
609X GLU 3.7 4.0 - - - +
611X VAL* 1.3 76.2 - - + +
613X LYS* 1.3 63.0 + - - +
615X ALA* 3.4 7.2 + - - +
616X HIS* 2.7 40.4 + - + -
635X ILE* 5.1 3.8 - - + -
638X ILE* 4.5 12.3 - - + -
639X LEU* 4.6 4.9 - - + -
700X ALA* 4.1 8.7 - - + -
702X THR* 4.6 2.0 - - + -
724X ILE* 3.8 27.1 - - + -
726X ILE* 3.9 17.4 - - + +
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Residues in contact with LYS 613 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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609X GLU* 2.8 41.7 + - - +
610X SER* 3.8 8.1 - - - +
612X VAL* 1.3 77.1 - - - +
614X GLU* 1.3 60.8 - - + +
616X HIS* 3.3 13.3 + - - +
617X ARG* 3.6 10.7 + - - +
724X ILE* 4.0 5.8 - - + -
725X LEU* 2.6 55.1 + - - +
726X ILE* 4.2 10.0 - - - +
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Residues in contact with GLU 614 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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610X SER* 2.9 19.7 + - - +
611X VAL* 3.8 5.6 - - - +
613X LYS* 1.3 75.8 - - + +
615X ALA* 1.3 63.6 + - - +
616X HIS 3.0 1.4 + - - -
617X ARG* 3.1 56.3 + - - +
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Residues in contact with ALA 615 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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611X VAL 2.9 17.5 + - - +
612X VAL 3.9 3.4 - - - +
613X LYS 3.3 0.8 - - - -
614X GLU* 1.3 75.2 - - - +
616X HIS* 1.3 60.7 + - - +
617X ARG 3.5 0.2 - - - -
618X GLU* 4.9 1.7 + - - +
630X ASN 3.8 18.4 - - - +
631X ILE* 4.1 11.3 - - + +
632X ASP* 5.0 4.8 + - + +
635X ILE* 3.7 39.7 - - + -
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Residues in contact with HIS 616 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612X VAL* 2.7 32.7 + - + -
613X LYS 3.3 7.8 + - - +
614X GLU 3.1 0.8 - - - -
615X ALA* 1.3 78.8 - - - +
617X ARG* 1.3 63.2 + - - +
618X GLU* 3.3 4.4 + - - -
619X VAL* 3.7 15.9 - - - +
629X LEU* 3.8 25.5 - - + +
631X ILE* 3.8 10.0 - - + +
635X ILE* 4.2 11.9 - - + -
639X LEU* 3.8 20.4 - - + -
642X TYR* 2.9 29.4 + + - -
700X ALA* 4.7 0.2 - - + -
726X ILE* 3.5 52.0 - - + +
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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