Contacts of the strand formed by residues 351 - 355 (chain D) in PDB entry 4OMD
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 351 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122D TRP* 4.5 2.2 - - + -
123D TYR* 3.5 40.8 - - + +
201D GLU* 3.5 32.8 - - + +
341D TYR 4.1 8.1 - - - +
342D SER* 4.0 25.4 - - - +
350D GLN* 1.3 82.1 - - - +
352D VAL* 1.3 65.4 + - - +
353D THR* 4.8 0.2 - - + -
361D THR 3.8 1.4 - - - +
362D GLU 3.4 7.9 - - - -
364D HIS* 3.1 44.5 + - + +
369D ALA* 3.5 20.9 - - + -
373D LEU* 4.5 2.0 - - + -
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Residues in contact with VAL 352 (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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117D LYS* 3.8 31.9 - - + -
120D GLN* 3.9 31.6 - - + +
121D GLN* 3.2 22.9 + - + +
123D TYR* 3.0 23.4 + - - +
200D GLY 5.7 0.2 - - - +
201D GLU* 5.3 2.6 - - - +
211D CYS* 4.3 8.3 - - - -
212D GLY 4.8 0.7 - - - +
350D GLN 3.8 5.1 + - - +
351D ILE* 1.3 73.0 - - - +
353D THR* 1.3 67.4 + - - +
360D CYS* 4.4 0.2 - - - -
361D THR 3.3 10.8 - - - +
362D GLU* 3.9 24.9 - - + +
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Residues in contact with THR 353 (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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121D GLN* 5.3 0.4 - - - +
197D ARG* 2.8 36.2 + - - +
200D GLY* 3.2 17.1 - - - -
201D GLU* 3.2 11.5 + - + -
211D CYS* 3.6 13.5 - - - -
212D GLY* 6.4 0.4 - - - -
351D ILE* 4.8 0.7 - - + -
352D VAL* 1.3 78.4 - - - +
354D THR* 1.3 66.0 + - - +
361D THR* 2.9 49.3 + - + +
364D HIS* 3.8 23.3 - - + -
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Residues in contact with THR 354 (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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160D HIS* 3.5 22.4 - - + +
162D ASP* 3.4 37.0 - - + +
163D LEU* 3.9 14.7 - - + +
196D THR* 2.9 26.9 + - - +
197D ARG* 3.1 25.6 + - - +
200D GLY* 3.3 17.1 + - - -
204D ALA* 4.4 3.8 - - + +
211D CYS* 4.6 4.3 - - - -
353D THR* 1.3 79.7 + - - +
355D ASP* 1.3 59.6 + - - +
359D LYS 3.9 4.0 - - - -
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Residues in contact with ASP 355 (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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160D HIS* 3.1 11.8 - - - -
193D ARG* 3.6 13.2 + - - +
196D THR* 3.9 5.6 - - - -
197D ARG* 2.8 42.4 + - - +
353D THR 3.7 0.4 + - - -
354D THR* 1.3 74.6 - - - +
356D LEU* 1.3 86.7 + - - +
359D LYS* 2.8 41.0 + - + +
360D CYS 4.3 0.2 - - - -
361D THR* 3.6 18.6 - - + +
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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