Contacts of the strand formed by residues 296 - 300 (chain A) in PDB entry 1U7V
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 SER 296 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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294A GLN* 3.0 19.1 - - - +
295A PRO* 1.3 88.2 - - - +
297A LEU* 1.3 67.8 + - - +
298A THR* 5.6 0.7 + - - -
309A GLU* 3.8 20.7 + - - +
337A ARG* 5.2 7.2 + - - +
338A LEU 3.6 7.2 - - - -
339A TYR* 5.1 12.8 - - - -
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Residues in contact with LEU 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274A TRP* 3.7 22.7 - - + +
275A CYS* 4.6 0.2 - - - -
277A ILE* 3.5 22.2 - - + -
290A PHE* 3.3 33.2 - - + -
292A ALA* 3.6 24.5 - - + -
294A GLN* 5.3 0.4 - - + +
296A SER* 1.3 81.8 + - - +
298A THR* 1.3 64.9 + - - +
299A VAL* 4.3 8.5 - - + -
308A SER 4.7 1.8 - - - +
309A GLU* 3.0 16.2 - - - +
311A PHE* 4.4 4.5 - - + +
336A VAL 4.1 0.3 - - - +
337A ARG* 3.8 2.3 - - - +
338A LEU* 3.0 46.0 + - + +
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Residues in contact with THR 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296A SER* 5.6 0.7 + - - -
297A LEU* 1.3 78.2 + - - +
299A VAL* 1.3 65.6 + - - +
300A ASP* 3.7 12.1 + - - +
309A GLU 2.7 13.1 + - - -
310A ARG* 3.3 9.5 - - - +
311A PHE 2.9 24.1 + - - -
334A ARG 3.0 28.3 - - - +
336A VAL 3.1 17.0 - - - +
337A ARG* 3.9 20.1 + - - +
350A LEU* 3.9 9.5 - - + +
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Residues in contact with VAL 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A ILE* 3.9 31.0 - - + -
297A LEU* 4.3 2.9 - - + -
298A THR* 1.3 73.9 - - - +
300A ASP* 1.3 57.0 + - - +
311A PHE* 3.6 24.7 - - + +
313A LEU* 3.8 23.8 - - + -
335A GLY* 3.2 3.6 - - - -
336A VAL* 2.9 42.4 + - + -
338A LEU* 4.4 8.1 - - + -
418A PHE* 3.7 22.0 - - + -
438A ILE* 4.2 11.2 - - + -
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Residues in contact with ASP 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298A THR* 3.7 9.5 + - + +
299A VAL* 1.3 75.5 - - - +
301A GLY* 1.3 58.9 + - - +
302A PHE* 2.7 41.9 + - + +
310A ARG* 3.1 29.8 + - - +
311A PHE 3.4 3.0 + - - -
312A CYS* 3.4 14.9 - - - -
313A LEU* 3.0 30.5 + - - +
332A ILE* 3.6 5.4 - - - -
333A GLY 3.2 15.5 - - - +
334A ARG* 3.4 15.3 - - - +
335A GLY* 3.9 3.6 - - - -
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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