Contacts of the strand formed by residues 237 - 244 (chain A) in PDB entry 3CWM
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 237 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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231A HIS* 3.6 9.6 + - - -
232A CSD 2.9 33.3 + - - +
235A LEU* 2.8 27.3 + - - -
236A SER* 1.3 75.1 + - - +
238A TRP* 1.3 69.0 + - - +
239A VAL* 3.7 6.4 + - - +
253A PHE* 4.6 0.9 - - - -
254A LEU 3.3 13.7 - - - -
255A PRO* 3.3 12.8 - - - +
263A LEU* 3.4 18.8 - - - +
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Residues in contact with TRP 238 (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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229A ILE* 4.0 21.3 - - + -
230A GLN* 3.5 25.8 - - - -
231A HIS* 3.7 38.6 - + + -
237A SER* 1.3 74.0 - - - +
239A VAL* 1.3 58.4 + - - +
240A LEU 4.2 0.2 - - - -
252A PHE 3.5 1.1 - - - +
253A PHE* 3.3 5.5 - - - -
254A LEU* 2.8 64.3 + - + +
256A ASP* 5.1 2.7 + - - -
282A ARG* 6.2 1.8 - - - -
362A PRO* 5.0 13.0 - - + -
363A GLU 5.7 0.2 - - - -
364A VAL* 3.8 38.7 - - + +
366A PHE* 4.6 5.1 - - + -
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Residues in contact with VAL 239 (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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229A ILE* 3.4 2.4 - - - -
230A GLN* 2.6 51.2 + - - +
232A CSD 4.3 7.9 - - + -
235A LEU* 4.5 3.1 - - + -
237A SER* 4.0 11.4 - - - +
238A TRP* 1.3 76.5 - - - +
240A LEU* 1.3 59.9 + - - +
241A LEU* 3.8 9.4 - - + -
251A ILE* 3.6 31.4 - - + -
252A PHE 3.3 2.7 - - - -
253A PHE* 3.6 22.2 - - + -
275A PHE* 3.8 33.9 - - + -
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Residues in contact with LEU 240 (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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227A PHE* 4.1 26.7 - - + -
228A ASN 3.5 10.8 - - - +
229A ILE* 4.1 14.6 - - + -
238A TRP 4.2 0.4 - - - -
239A VAL* 1.3 74.7 - - - +
241A LEU* 1.3 66.5 + - - +
242A MET* 3.9 23.1 - - + -
250A ALA 3.5 1.0 - - - +
251A ILE* 3.1 4.7 - - - +
252A PHE* 2.7 59.6 + - + +
286A LEU* 3.8 30.3 - - + -
288A LEU* 4.8 4.0 - - + -
366A PHE* 3.8 21.3 - - + -
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Residues in contact with LEU 241 (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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228A ASN* 3.1 38.6 + - - +
230A GLN* 4.0 2.7 - - - +
239A VAL* 3.8 11.4 - - + -
240A LEU* 1.3 78.0 - - - +
242A MET* 1.3 57.8 + - - +
249A THR* 4.1 8.5 - - + -
250A ALA 3.1 5.6 - - - +
251A ILE* 3.7 28.3 - - + -
275A PHE* 3.4 37.7 - - + +
276A LEU* 3.8 24.2 - - + +
278A ASN 5.2 0.2 - - - +
500A CIT 2.5 36.6 - - - +
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Residues in contact with MET 242 (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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194A TRP* 3.4 50.0 - - + -
196A ARG 5.2 3.8 - - - +
198A PHE* 4.0 10.5 - - + -
227A PHE* 4.3 9.2 - - - -
240A LEU* 3.9 12.7 - - + +
241A LEU* 1.3 78.4 - - - +
243A LYS* 1.3 60.5 + - - +
244A TYR 4.0 0.2 + - - -
249A THR* 4.2 1.8 - - - -
250A ALA* 2.8 40.8 + - - +
252A PHE* 4.1 6.7 - - + -
286A LEU* 4.1 20.9 - - - -
288A LEU* 3.6 22.4 - - + -
500A CIT 2.9 27.6 - - + +
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Residues in contact with LYS 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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194A TRP* 3.6 5.5 - - - -
195A GLU* 3.0 34.0 + - + +
242A MET* 1.3 73.1 - - - +
244A TYR* 1.3 62.2 + - - +
248A ALA 3.7 7.4 - - - +
249A THR* 3.9 15.5 - - + +
279A GLU* 4.3 27.3 + - - +
281A ARG* 4.7 8.4 - - - +
377A GLN* 4.0 14.7 - - - +
500A CIT 2.6 63.8 - - + +
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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
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110A LEU* 4.6 6.3 - - + -
190A PHE* 3.5 30.5 - + - -
192A GLY* 3.5 36.6 + - - -
193A LYS 3.3 6.7 - - - +
194A TRP* 3.4 43.7 - + - -
195A GLU* 3.7 12.5 - - - +
243A LYS* 1.3 76.8 - - - +
245A LEU* 1.3 63.7 + - - +
246A GLY 2.6 21.5 - - - +
248A ALA* 2.9 30.9 + - + +
250A ALA* 3.8 19.1 - - + -
338A LEU* 4.8 1.4 - - - +
339A THR 5.1 1.8 + - - -
340A ILE* 4.0 6.5 - - - +
374A MET* 3.4 26.8 - - + +
377A GLN* 5.2 0.7 - - - +
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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