Contacts of the helix formed by residues 632 - 638 (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 632 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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545X LYS* 5.6 2.8 + - - -
595X ARG* 2.9 29.1 + - - -
615X ALA* 5.0 4.7 + - + +
630X ASN 4.2 0.6 + - - -
631X ILE* 1.3 76.1 - - - +
633X LYS* 1.3 71.2 + - - +
634X ASP* 2.8 32.2 + - - +
635X ILE* 2.9 26.9 + - + +
636X ARG* 3.3 8.7 + - - +
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Residues in contact with LYS 633 (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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495X GLY 5.7 0.6 + - - -
496X LYS 4.1 15.5 + - - -
497X ASP* 5.3 9.1 - - + +
631X ILE 3.6 4.1 + - - -
632X ASP* 1.3 75.1 + - - +
634X ASP* 1.3 81.8 + - - +
636X ARG* 3.6 13.7 + - - +
637X LYS* 3.4 20.4 + - - +
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Residues in contact with ASP 634 (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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495X GLY 5.5 3.0 - - - +
496X LYS 4.8 0.7 - - - +
497X ASP* 4.3 17.4 - - - +
498X LEU* 4.0 16.7 - - + +
545X LYS* 4.2 7.4 - - - -
593X ASP* 4.4 1.0 - - - +
595X ARG* 3.1 24.6 + - - +
596X PHE* 3.5 29.7 - - + -
632X ASP* 2.8 17.7 + - - +
633X LYS* 1.3 92.6 + - - +
635X ILE* 1.3 65.9 + - - +
637X LYS* 3.2 21.0 + - - +
638X ILE* 3.7 2.6 + - - +
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Residues in contact with ILE 635 (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 10.3 - - - +
596X PHE* 3.9 17.5 - - + -
607X ALA* 4.9 4.3 - - + -
611X VAL* 3.7 31.9 - - + +
612X VAL* 5.1 4.3 - - - -
615X ALA* 3.7 25.8 - - + -
616X HIS* 4.2 4.7 - - + -
631X ILE* 3.9 17.9 - - + -
632X ASP* 2.9 21.2 + - + +
634X ASP* 1.3 74.5 - - - +
636X ARG* 1.3 64.4 + - - +
638X ILE* 2.9 30.2 + - + +
639X LEU* 3.6 19.5 - - + +
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Residues in contact with ARG 636 (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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631X ILE* 4.1 22.9 - - + +
632X ASP 3.3 9.4 + - - +
633X LYS* 3.6 13.7 - - - +
634X ASP 3.3 0.4 - - - -
635X ILE* 1.3 77.9 - - - +
637X LYS* 1.3 61.9 + - - +
638X ILE 3.1 1.2 + - - -
639X LEU* 3.2 27.9 + - - +
642X TYR* 5.7 2.4 + - - +
666X SER* 3.3 20.9 + - - -
667X SER* 4.1 7.5 - - - +
668X LEU* 3.6 44.0 - - - +
674X THR* 2.7 50.7 + - - +
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Residues in contact with LYS 637 (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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296X SER* 5.4 5.4 - - - -
497X ASP* 3.5 30.0 + - - +
498X LEU* 4.1 14.1 - - + -
499X ASN* 3.4 30.3 + - - +
604X ALA* 5.1 1.2 - - + +
633X LYS 3.4 9.2 + - - +
634X ASP* 3.2 15.2 + - - +
635X ILE 3.1 0.6 + - - -
636X ARG* 1.3 79.2 - - - +
638X ILE* 1.3 62.4 + - + +
639X LEU 3.5 2.0 + - - +
703X LYS* 4.3 12.8 - - - +
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Residues in contact with ILE 638 (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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498X LEU* 4.5 2.5 - - + -
596X PHE* 3.6 27.8 - - + -
604X ALA* 3.6 42.8 - - + +
606X GLY 4.0 13.7 - - - +
607X ALA* 4.1 21.3 - - + -
612X VAL* 4.5 6.1 - - + -
634X ASP 4.4 2.5 - - - +
635X ILE* 2.9 29.9 + - + +
637X LYS* 1.3 83.4 - - + +
639X LEU* 1.3 71.3 + - + +
702X THR* 3.3 12.6 - - + -
703X LYS* 3.0 30.0 + - - -
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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