Contacts of the strand formed by residues 282 - 289 (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 ARG 282 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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226A MET* 4.2 7.4 - - - -
227A PHE* 2.7 40.0 + - - +
229A ILE* 3.0 36.7 + - + +
230A GLN* 4.4 21.5 + - - +
238A TRP* 6.2 1.8 - - - -
278A ASN* 4.8 1.4 + - - -
280A ASP* 3.7 30.0 + - - +
281A ARG* 1.3 82.2 + - - +
283A SER* 1.3 69.8 + - - +
284A ALA* 3.5 2.8 + - - +
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Residues in contact with SER 283 (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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224A LEU* 4.8 0.7 - - - +
225A GLY 3.7 6.0 + - - -
226A MET* 4.1 8.0 - - - +
229A ILE* 5.2 0.2 - - - +
282A ARG* 1.3 76.8 - - - +
284A ALA* 1.3 65.4 + - - +
356A ILE* 4.2 12.6 - - - +
357A PRO* 4.4 20.5 - - - +
359A SER* 4.8 7.3 + - - -
360A ILE 6.0 0.2 - - - -
361A PRO* 3.3 25.7 - - - +
362A PRO* 3.4 19.6 - - - +
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Residues in contact with ALA 284 (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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224A LEU* 3.6 1.5 - - - -
225A GLY 2.9 35.1 + - - +
227A PHE* 3.4 17.7 - - + -
229A ILE* 4.0 30.5 - - + -
282A ARG 4.3 0.2 - - - +
283A SER* 1.3 79.3 + - - +
285A SER* 1.3 62.1 + - - +
286A LEU* 3.8 1.3 - - + +
361A PRO* 3.9 7.2 - - - +
362A PRO* 3.6 13.2 - - + +
364A VAL* 5.0 4.5 - - + -
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Residues in contact with SER 285 (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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223A ARG 3.8 5.4 + - - -
224A LEU* 4.3 17.6 + - - +
284A ALA* 1.3 72.0 - - - +
286A LEU* 1.3 60.7 + - - +
287A HIS* 3.8 10.4 + - - -
361A PRO* 4.1 9.0 - - - +
362A PRO 2.8 16.2 + - - -
363A GLU* 3.1 26.0 + - - -
364A VAL 3.0 24.0 + - - +
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Residues in contact with LEU 286 (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 PHE* 3.9 23.1 - - + -
221A MET 3.7 0.5 - - - +
222A LYS* 3.3 6.4 - - - -
223A ARG 3.1 30.5 + - - +
227A PHE* 3.8 40.4 - - + -
229A ILE* 4.5 10.3 - - + -
240A LEU* 3.8 23.1 - - + -
242A MET* 4.1 2.9 - - - -
284A ALA* 3.8 1.5 + - + -
285A SER* 1.3 70.0 - - - +
287A HIS* 1.3 78.0 + - - +
288A LEU* 4.5 4.5 - - + +
364A VAL* 3.5 7.4 - - - +
366A PHE* 3.6 36.3 - - + -
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Residues in contact with HIS 287 (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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206A GLU* 5.2 2.9 - - + +
220A MET* 3.7 20.5 - - + +
221A MET 3.3 3.4 - - - -
222A LYS* 3.6 42.6 - - + +
285A SER* 3.9 13.9 + - - -
286A LEU* 1.3 81.1 - - - +
288A LEU* 1.3 59.7 + - - +
363A GLU* 4.0 16.6 + - + -
364A VAL 3.0 6.5 + - - -
365A LYS* 3.6 48.2 - - + +
366A PHE* 2.7 36.5 + - - +
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Residues in contact with LEU 288 (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 PHE* 4.1 11.2 - - + -
220A MET* 3.6 2.9 - - - -
221A MET* 2.7 55.6 + - + +
240A LEU* 4.8 4.5 - - + -
242A MET* 3.6 31.2 - - + -
252A PHE* 4.1 32.5 - - + -
286A LEU* 4.2 5.1 - - + -
287A HIS* 1.3 74.0 - - - +
289A PRO* 1.3 81.6 - - + +
340A ILE* 4.3 8.5 - - + -
366A PHE* 3.9 23.6 - - + -
370A PHE* 4.6 4.7 - - + -
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Residues in contact with PRO 289 (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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208A PHE* 4.5 7.6 - - + -
218A VAL* 4.3 17.9 - - + -
219A PRO 3.5 10.5 - - - +
220A MET* 3.5 5.8 - - - -
221A MET* 3.5 8.6 - - - +
288A LEU* 1.3 97.1 - - + +
290A LYS* 1.3 69.4 + - - +
291A LEU* 3.5 16.3 + - + +
340A ILE* 4.0 7.1 - - - +
366A PHE* 3.2 26.5 - - + +
370A PHE* 4.0 19.1 - - + -
391A PRO* 4.6 6.1 - - + -
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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