Contacts of the strand formed by residues 357 - 359 (chain D) in PDB entry 1V1H
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 ILE 357 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336D ILE* 3.8 34.5 - - + -
338D ALA* 4.3 6.7 - - + -
342D LEU* 4.2 24.0 - - + -
343D GLU 3.6 11.4 - - - +
344D PHE* 3.8 17.9 - - + -
356D PRO* 1.3 73.9 - - - +
358D LYS* 1.3 64.7 + - - +
326E GLY* 3.7 5.6 - - - +
336E ILE* 3.9 22.0 - - + -
337E ASN 2.9 15.8 + - - +
338E ALA* 4.3 0.7 - - - -
339E GLY 2.6 32.7 + - - -
342E LEU* 3.4 19.9 - - + +
357E ILE* 4.7 2.0 - - + -
357F ILE* 4.6 2.5 - - + -
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Residues in contact with LYS 358 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342D LEU* 3.5 6.8 - - - +
343D GLU* 2.6 68.0 + - + +
345D ASP* 3.6 41.5 - - + +
357D ILE* 1.3 76.0 - - - +
359D THR* 1.3 72.7 + - - +
360D LYS* 4.5 1.2 - - - +
361D ILE* 5.0 2.6 - - - +
367D TYR* 3.2 31.2 + - - -
339E GLY* 4.2 1.1 - - - -
340E LYS* 3.2 32.8 - - + +
342E LEU* 3.7 9.0 - - - -
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Residues in contact with THR 359 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341D GLY 3.3 9.0 - - - +
342D LEU* 4.0 7.2 - - + -
343D GLU* 4.5 0.4 - - - -
358D LYS* 1.3 90.9 + - - +
360D LYS* 1.3 61.9 + - - +
361D ILE* 3.9 1.0 - - - +
367D TYR* 2.8 46.7 + - - -
373D MET* 3.3 26.5 - - + -
340E LYS 3.0 5.8 + - - -
341E GLY 3.4 26.0 - - - +
342E LEU* 3.8 13.5 - - + -
359E THR* 4.5 1.1 - - + -
359F THR* 4.5 4.0 - - + -
373F MET* 3.9 6.3 - - + -
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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