Contacts of the strand formed by residues 242 - 250 (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 HIS 242 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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237A THR* 3.0 7.6 - - - +
238A THR* 2.8 45.4 + - - +
240A ASP* 3.0 40.4 + - - +
241A GLY* 1.3 82.4 - - - +
243A TYR* 1.3 61.6 + - - +
244A TYR* 3.5 13.5 - - + -
265A GLU* 5.8 0.2 - - - -
268A VAL* 3.1 33.6 - - + +
269A PRO* 3.8 24.2 - - + -
272A ALA* 3.7 8.0 - - + +
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Residues in contact with TYR 243 (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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233A TYR* 5.0 4.0 - - - -
235A GLU* 2.9 52.2 + - + +
236A PHE 3.3 2.7 - - - -
237A THR* 3.0 31.6 - - + -
241A GLY 4.2 1.2 + - - -
242A HIS* 1.3 71.6 - - - +
244A TYR* 1.3 64.1 + - - +
245A ASP* 5.9 0.7 - - + -
263A PRO* 3.5 5.0 - - - +
264A TYR* 2.8 69.9 + + + +
265A GLU* 3.5 13.1 + - - +
268A VAL* 4.6 0.5 - - - +
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Residues in contact with TYR 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A GLU* 3.7 2.1 - - - -
236A PHE* 2.7 42.0 + + + +
238A THR* 3.4 36.8 - - + -
242A HIS* 3.5 17.9 - - + -
243A TYR* 1.3 76.4 - - - +
245A ASP* 1.3 60.3 + - - +
246A ILE* 4.0 14.8 - - + -
262A ALA* 3.4 11.4 - - - +
263A PRO* 3.4 41.1 - - + -
264A TYR* 4.1 1.3 - - - +
268A VAL* 3.3 9.3 - - + +
269A PRO 2.6 28.1 + - - -
270A LEU* 4.3 7.4 - - + -
272A ALA* 3.0 13.5 - - - +
273A LEU* 3.6 28.4 + - + -
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Residues in contact with ASP 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A TYR* 3.4 34.1 + - + +
234A THR 3.8 2.7 - - - -
235A GLU* 5.1 0.2 - - - -
243A TYR* 5.9 0.9 - - + -
244A TYR* 1.3 72.4 - - - +
246A ILE* 1.3 62.8 + - - +
247A LEU* 3.9 2.4 + - - +
260A ILE 3.7 1.7 - - - +
261A ALA* 3.6 2.3 - - - -
262A ALA* 2.9 44.8 + - - +
263A PRO 4.9 3.4 - - - +
264A TYR* 4.8 16.7 - - + -
294A ARG* 4.3 14.0 + - - -
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Residues in contact with ILE 246 (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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233A TYR* 3.4 6.6 - - - -
234A THR* 3.0 49.9 + - + +
236A PHE* 3.9 26.2 - - + -
244A TYR* 4.2 8.7 - - + -
245A ASP* 1.3 77.4 - - - +
247A LEU* 1.3 60.8 + - - +
259A PHE* 4.4 6.7 - - + -
260A ILE 3.3 10.5 - - - +
261A ALA* 3.8 19.3 - - + -
273A LEU* 4.9 0.9 - - + -
285A TRP* 3.5 43.7 - - + +
289A MET* 3.5 19.6 - - + +
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Residues in contact with LEU 247 (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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231A PHE* 3.7 30.3 - - + -
232A ASN 3.5 10.1 - - - +
233A TYR* 4.8 3.8 - - + -
245A ASP 3.9 2.7 + - - +
246A ILE* 1.3 75.2 - - - +
248A GLU* 1.3 72.3 + - - +
249A LEU* 4.5 3.8 - - + +
258A MET 3.8 0.7 - - - +
259A PHE* 3.4 2.9 - - - +
260A ILE* 2.8 47.8 + - + +
289A MET* 4.7 3.1 - - - -
294A ARG* 3.5 39.7 - - + +
296A LEU* 3.6 35.0 - - + -
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Residues in contact with GLU 248 (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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231A PHE* 4.2 3.5 - - - +
232A ASN* 3.0 50.0 + - + +
247A LEU* 1.3 80.4 - - - +
249A LEU* 1.3 62.0 + - - +
250A PRO* 3.3 17.8 - - + +
257A SER* 2.9 34.5 + - - +
258A MET 3.8 2.5 - - - -
259A PHE* 4.1 9.6 - - + +
286A LYS* 3.0 44.9 + - - +
289A MET* 3.9 10.6 - - - +
388A ASN* 3.9 2.3 - - - +
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Residues in contact with LEU 249 (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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198A TRP* 3.5 51.0 - - + -
200A THR* 4.9 7.4 - - - +
202A PHE* 4.0 15.5 - - + -
227A GLN* 4.8 3.1 - - - +
231A PHE* 4.6 12.8 - - + -
247A LEU* 4.0 2.9 + - + -
248A GLU* 1.3 74.1 - - - +
250A PRO* 1.3 69.4 - - + +
251A TYR* 4.4 0.2 - - - -
257A SER* 3.6 0.8 - - - -
258A MET* 2.8 38.2 + - + +
260A ILE* 3.8 20.9 - - + -
296A LEU* 3.6 33.0 - - + -
298A LEU* 4.0 4.7 - - + -
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Residues in contact with PRO 250 (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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198A TRP* 3.5 12.3 - - - -
199A LYS* 3.0 43.0 + - + +
200A THR* 4.7 2.8 + - - +
231A PHE* 5.2 6.5 - - + -
232A ASN* 5.6 4.5 - - - +
248A GLU* 3.3 26.5 - - + +
249A LEU* 1.3 90.3 - - + +
251A TYR* 1.3 63.3 + - - +
254A ASP* 4.7 6.5 - - - +
256A LEU 4.0 1.6 - - - +
257A SER* 3.9 9.2 - - - -
291A ARG* 5.6 8.5 - - - +
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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