Contacts of the strand formed by residues 256 - 263 (chain A) in PDB entry 1C5G
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 LEU 256 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A ASN* 4.9 2.5 - - + -
112A ASP* 4.0 19.4 + - + +
114A ILE* 4.1 13.7 - - + -
194A PHE* 3.8 25.4 - - + -
250A PRO* 4.0 1.6 - - - +
251A TYR* 3.1 41.1 + - + +
254A ASP 4.6 2.2 - - - +
255A THR* 1.3 87.9 + - - +
257A SER* 1.3 62.8 + - - +
385A VAL* 4.7 5.6 - - + -
386A ARG* 3.1 23.6 - - - +
387A HIS* 3.6 30.3 - - + +
388A ASN* 3.9 1.3 - - - -
394A LEU* 4.4 20.0 - - + -
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Residues in contact with SER 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A GLU* 2.9 37.0 + - - -
249A LEU 3.6 10.1 - - - -
250A PRO* 3.9 6.7 - - - -
251A TYR* 3.6 8.9 - - - -
256A LEU* 1.3 76.2 - - - +
258A MET* 1.3 60.1 + - - +
259A PHE* 3.1 17.5 + - - -
384A VAL 3.6 0.9 - - - +
385A VAL* 3.5 1.2 - - - -
386A ARG* 2.9 29.5 + - - -
388A ASN* 3.0 12.1 + - - -
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Residues in contact with MET 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A TRP* 3.6 16.8 - - + -
247A LEU 3.8 0.5 - - - +
248A GLU 3.7 0.2 - - - -
249A LEU* 2.8 40.4 + - + +
251A TYR* 3.0 33.5 - - - +
257A SER* 1.3 72.5 - - - +
259A PHE* 1.3 72.5 + - - +
260A ILE* 3.9 14.2 + - + +
298A LEU* 5.0 6.7 - - - -
301A PHE* 5.7 2.0 - - - -
349A ILE* 5.3 0.2 - - + -
351A VAL* 4.0 17.0 - - + -
356A THR* 3.4 16.4 - - + +
381A PHE* 6.0 1.1 - - - -
383A PHE* 4.0 24.9 - - + -
384A VAL 3.0 12.1 - - - +
385A VAL* 4.2 12.6 - - + +
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Residues in contact with PHE 259 (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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246A ILE* 4.4 5.8 - - + -
247A LEU 3.4 5.4 - - - -
248A GLU* 4.1 9.6 - - + -
257A SER* 3.1 27.6 - - - -
258A MET* 1.3 77.8 - - - +
260A ILE* 1.3 62.1 + - - +
282A ILE* 4.6 8.5 - - + -
285A TRP* 4.3 17.5 - + + -
286A LYS* 3.3 44.4 - - + -
289A MET* 4.0 26.7 - - + -
382A LEU 4.0 0.2 - - - +
383A PHE* 3.1 7.6 - - - +
384A VAL* 2.7 46.1 + - + +
386A ARG* 4.1 23.1 - - + -
388A ASN* 3.8 11.2 - - - -
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Residues in contact with ILE 260 (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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245A ASP 4.4 0.9 - - - -
246A ILE* 3.3 7.5 - - - +
247A LEU* 2.8 42.4 + - + +
249A LEU* 3.8 30.1 - - + -
258A MET* 4.2 15.5 - - + +
259A PHE* 1.3 79.3 - - - +
261A ALA* 1.3 67.8 + - - +
262A ALA* 5.0 4.3 - - + +
285A TRP* 6.0 0.2 - - - -
296A LEU* 4.6 14.8 - - + -
298A LEU* 3.8 27.1 - - + -
381A PHE* 3.8 25.6 - - + -
382A LEU 3.5 3.4 - - - +
383A PHE* 4.9 1.8 - - + -
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Residues in contact with ALA 261 (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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244A TYR* 5.3 0.9 - - + -
245A ASP 3.6 5.8 - - - -
246A ILE* 3.8 21.3 - - + -
260A ILE* 1.3 77.7 - - - +
262A ALA* 1.3 62.4 + - - +
270A LEU* 4.5 4.5 - - - +
273A LEU* 4.0 20.6 - - + -
285A TRP* 4.3 10.5 - - + -
381A PHE* 3.8 3.8 - - - +
382A LEU* 3.1 40.5 + - + +
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Residues in contact with ALA 262 (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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244A TYR* 3.4 4.1 - - - -
245A ASP* 2.9 42.0 + - - +
260A ILE* 5.0 5.1 - - + +
261A ALA* 1.3 76.6 - - - +
263A PRO* 1.3 73.6 - - + +
381A PHE* 4.5 5.2 - - + -
401A GLU* 3.3 26.5 - - - +
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Residues in contact with PRO 263 (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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243A TYR 3.5 0.4 - - - +
244A TYR* 3.4 34.1 - - + -
245A ASP* 4.9 2.9 - - - +
261A ALA 4.7 1.1 - - - +
262A ALA* 1.3 92.3 - - + +
264A TYR* 1.3 67.6 + - - +
265A GLU* 3.8 8.5 - - - +
268A VAL* 3.7 19.7 - - + +
270A LEU* 4.8 9.0 - - + +
379A ARG* 3.2 39.0 - - - +
380A PRO 5.1 1.8 - - - +
401A GLU* 4.6 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