Contacts of the strand formed by residues 354 - 365 (chain A) in PDB entry 1W57
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 GLY 354 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218A VAL* 5.6 0.2 - - - -
219A HIS 3.0 15.5 - - - -
220A GLU* 4.0 1.8 - - - -
221A PHE* 3.5 20.1 - - - -
309A ALA* 5.3 0.3 - - - -
348A PHE* 4.1 15.7 + - - -
349A ILE* 3.9 22.2 - - - +
352A LYS 3.4 0.4 - - - -
353A GLU* 1.3 78.0 - - - +
355A MET* 1.3 62.2 + - - +
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Residues in contact with MET 355 (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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217A ASP 3.9 0.7 - - - +
218A VAL* 3.5 4.8 - - - -
219A HIS 2.8 31.2 + - - +
221A PHE* 4.0 18.7 - - + -
227A LEU* 4.6 6.3 - - + -
229A LEU* 3.6 23.6 - - + -
240A LEU* 4.3 12.0 - - + +
248A VAL* 3.8 27.7 - - + +
307A VAL* 3.1 35.2 - - + -
308A MET 3.5 9.6 - - - +
309A ALA* 3.4 24.5 - - + -
311A SER 5.3 0.4 - - - +
312A PRO* 5.9 1.1 - - + -
314A LEU* 4.5 2.7 - - + -
349A ILE* 4.7 2.5 - - - -
354A GLY* 1.3 75.3 - - - +
356A ALA* 1.3 64.7 + - - +
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Residues in contact with ALA 356 (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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216A PHE* 3.6 30.3 - - + -
217A ASP 3.2 7.6 - - - +
218A VAL* 4.3 8.3 - - + -
307A VAL 3.7 0.2 - - - -
308A MET* 2.7 41.6 + - + +
348A PHE* 5.2 0.4 - - + -
349A ILE* 3.9 21.1 - - + +
355A MET* 1.3 75.6 - - - +
357A VAL* 1.3 65.7 + - - +
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Residues in contact with VAL 357 (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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215A GLY 3.4 4.5 - - - +
216A PHE* 3.5 6.1 - - - -
217A ASP 3.0 20.6 + - - +
248A VAL* 3.8 13.9 - - + +
249A LEU* 3.8 30.3 - - + +
252A SER* 2.8 34.3 + - - +
305A ILE* 3.7 29.6 - - + -
306A CYS 3.5 6.1 - - - +
307A VAL* 4.0 18.6 - - + -
308A MET* 5.2 0.2 - - - -
355A MET* 4.9 0.7 - - + -
356A ALA* 1.3 79.9 - - - +
358A LEU* 1.3 63.4 + - - +
359A SER* 4.2 2.9 - - - +
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Residues in contact with LEU 358 (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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214A ASN* 5.3 7.0 - - + -
215A GLY 3.4 13.7 - - - +
216A PHE* 4.2 21.1 - - + -
304A ASP 3.9 1.0 - - - +
305A ILE* 3.6 1.6 - - - -
306A CYS* 2.8 53.1 + - + +
308A MET* 4.6 8.5 - - - -
357A VAL* 1.3 75.1 - - - +
359A SER* 1.3 66.2 + - - +
360A SER* 5.4 4.4 - - - -
1374A GPP 4.6 13.7 - - + -
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Residues in contact with SER 359 (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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214A ASN* 3.3 7.3 - - - +
215A GLY 2.9 28.5 + - - +
252A SER* 3.0 18.5 + - - -
253A LEU* 3.2 32.7 + - - +
256A ALA* 3.8 12.3 - - - -
304A ASP 3.5 4.3 - - - -
305A ILE* 3.7 18.8 - - - +
357A VAL* 4.2 2.1 - - - +
358A LEU* 1.3 77.3 - - - +
360A SER* 1.3 60.3 + - - +
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Residues in contact with SER 360 (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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212A THR* 5.1 3.5 + - - -
213A GLY 3.4 7.6 + - - -
214A ASN* 4.8 1.2 - - - +
302A ASN* 5.2 0.7 + - - -
303A ILE* 4.5 0.2 - - - +
304A ASP* 2.7 50.3 + - - +
358A LEU* 5.4 5.2 - - - -
359A SER* 1.3 75.1 - - - +
361A VAL* 1.3 68.4 + - - +
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Residues in contact with VAL 361 (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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212A THR* 3.2 2.4 + - - -
213A GLY* 3.0 30.8 + - - +
253A LEU* 3.9 22.9 - - + -
256A ALA* 3.8 24.7 - - + +
257A ILE* 4.3 8.3 - - + -
260A ALA* 5.2 1.6 - - + -
300A LEU* 3.1 32.5 - - + -
302A ASN* 3.4 9.4 - - - +
303A ILE* 4.1 5.8 - - + -
360A SER* 1.3 82.9 + - - +
362A ASN* 1.3 79.9 + - - +
363A LEU* 4.6 5.8 - - + +
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Residues in contact with ASN 362 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210A ILE* 3.6 25.0 - - + +
211A PHE 3.2 3.4 - - - +
212A THR* 2.9 29.1 + - - -
300A LEU* 3.8 2.9 - - - -
301A ILE* 2.8 36.7 + - + +
302A ASN* 3.3 23.7 + - - +
361A VAL* 1.3 80.3 - - - +
363A LEU* 1.3 60.5 + - - +
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Residues in contact with LEU 363 (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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210A ILE* 3.4 4.8 - - - -
211A PHE* 2.7 44.2 + - + +
257A ILE* 4.0 5.4 - - + +
260A ALA* 3.5 38.8 - - + -
261A ALA* 3.9 3.8 - - + +
290A TYR* 4.7 0.4 - - + -
293A VAL* 3.8 31.6 - - + -
298A PHE* 3.9 21.5 - - + -
299A GLU 3.4 25.6 - - - +
300A LEU* 3.6 23.8 - - + +
301A ILE* 4.4 2.0 - - - -
361A VAL* 4.8 0.9 - - + -
362A ASN* 1.3 73.4 - - - +
364A LYS* 1.3 59.4 + - - +
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Residues in contact with LYS 364 (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 6.5 0.2 - - - -
209A GLU 4.2 7.0 - - - +
210A ILE* 4.3 7.6 - - + -
298A PHE* 3.5 8.1 - - - -
299A GLU* 2.8 61.4 + - + +
300A LEU 5.4 2.2 - - - -
301A ILE* 3.7 35.1 - - + +
335A ARG* 6.1 3.6 - - - +
363A LEU* 1.3 74.0 - - - +
365A TYR* 1.3 70.1 + - - +
367A ASP* 4.1 24.7 + - - +
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Residues in contact with TYR 365 (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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27A ARG* 3.5 58.6 + - + -
30A ASN* 4.1 11.1 + - - -
206A PRO* 4.2 11.4 - - + +
207A SER* 3.5 40.7 + - - +
209A GLU* 3.5 25.3 + - + -
211A PHE* 3.4 24.2 - + - -
297A GLY 3.4 9.2 - - - +
298A PHE* 3.6 29.4 - + - -
364A LYS* 1.3 88.0 + - - +
366A PHE* 1.3 65.8 + - - +
367A ASP* 3.2 4.0 + - - -
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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