Contacts of the helix formed by residues 633 - 637 (chain R) in PDB entry 1HI0
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 633 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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288R GLN* 5.0 7.6 + - - -
291R ARG* 5.3 2.4 - - - -
292R ASN* 5.7 0.3 + - - -
295R TYR* 3.8 29.7 - - + -
303R HIS* 4.3 12.1 - - + +
628R LEU* 4.4 6.7 - - - -
632R TRP* 1.3 76.7 + - - +
634R GLU* 1.3 56.1 + - - +
635R ALA* 3.2 27.4 - - + +
636R ASP* 2.6 52.5 + - - +
637R VAL* 3.6 5.4 + - - +
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Residues in contact with GLU 634 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144R LYS* 3.4 37.0 + - - +
288R GLN* 5.3 14.7 + - - +
628R LEU* 4.4 3.7 + - - +
633R THR* 1.3 74.8 + - - +
635R ALA* 1.3 64.4 + - - +
637R VAL* 3.1 24.0 + - - +
642R HIS* 3.3 43.6 + - + +
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Residues in contact with ALA 635 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292R ASN* 6.1 0.7 - - - +
303R HIS* 5.4 2.7 - - + +
633R THR* 2.8 15.1 + - + +
634R GLU* 1.3 82.3 - - - +
636R ASP* 1.3 60.4 + - - +
637R VAL 3.2 6.5 + - - +
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Residues in contact with ASP 636 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303R HIS* 3.2 25.3 + - - -
304R HIS 4.6 2.1 - - - +
305R THR* 3.3 20.6 - - + +
615R THR* 5.1 2.6 + - - +
617R ILE* 3.4 37.6 - - + +
618R ASP* 4.7 0.9 - - - +
632R TRP* 3.9 12.5 - - + -
633R THR* 2.6 47.6 + - - +
635R ALA* 1.3 73.4 - - - +
637R VAL* 1.3 57.6 + - - -
638R SER 4.4 0.3 + - - -
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Residues in contact with VAL 637 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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617R ILE* 3.9 17.0 - - + -
618R ASP* 3.7 11.0 - - - +
621R VAL* 4.0 13.9 - - + -
628R LEU* 3.8 25.8 - - + -
632R TRP* 5.1 0.9 - - + -
633R THR 4.1 3.8 - - - +
634R GLU 3.1 17.4 + - - +
635R ALA 3.2 4.0 - - - +
636R ASP* 1.3 84.0 - - + +
638R SER* 1.3 79.3 + - - +
639R ALA* 3.2 4.3 + - - -
641R ILE* 4.1 8.7 - - + -
642R HIS* 3.7 27.4 - - + +
645R LEU* 6.5 0.2 - - + -
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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