Contacts of the strand formed by residues 298 - 308 (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 PHE 298 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A ARG* 4.1 14.8 - - - -
59A TYR* 4.3 2.5 - - - -
211A PHE* 3.8 37.2 - + + -
260A ALA 4.8 2.7 - - - -
261A ALA* 4.2 14.6 - - + -
293A VAL* 3.2 26.2 + - + +
294A ARG* 3.7 24.8 + - - +
296A ILE* 3.8 33.2 - - + -
297A GLY* 1.3 79.5 - - - +
299A GLU* 1.3 65.6 + - - +
363A LEU* 3.9 18.6 - - + -
364A LYS 3.5 14.8 - - - -
365A TYR* 3.6 30.7 - + - -
366A PHE* 4.4 3.1 - - - +
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Residues in contact with GLU 299 (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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290A TYR* 3.9 9.4 - - - +
294A ARG* 5.8 4.7 - - - +
298A PHE* 1.3 76.3 - - - +
300A LEU* 1.3 66.1 + - - +
363A LEU* 3.4 5.3 - - - -
364A LYS* 2.8 63.4 + - + +
366A PHE* 3.3 38.5 - - + -
367A ASP* 3.5 14.9 + - - +
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Residues in contact with LEU 300 (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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257A ILE* 3.8 15.5 - - + -
290A TYR* 3.0 35.7 + - + +
299A GLU* 1.3 78.3 - - - +
301A ILE* 1.3 66.7 + - - +
302A ASN* 4.6 1.1 - - - +
303A ILE* 3.7 18.6 - - + -
329A LEU* 3.8 14.4 - - + -
331A LEU* 3.6 34.9 - - + +
335A ARG* 4.4 9.9 + - - -
361A VAL* 3.1 36.3 - - + -
362A ASN 4.4 0.2 - - - +
363A LEU* 3.6 13.5 - - + +
364A LYS* 5.2 3.2 - - - +
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Residues in contact with ILE 301 (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* 3.6 37.0 - - + -
299A GLU 3.5 0.2 + - - -
300A LEU* 1.3 72.4 - - - +
302A ASN* 1.3 70.0 + - + +
335A ARG* 2.5 48.0 + - - +
362A ASN* 2.8 26.6 + - + +
364A LYS* 3.7 37.7 - - + +
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Residues in contact with ASN 302 (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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300A LEU* 3.8 2.4 - - - -
301A ILE* 1.3 91.4 - - + +
303A ILE* 1.3 76.7 + - - +
304A ASP* 4.1 9.3 - - - +
331A LEU* 6.1 0.2 - - - -
335A ARG* 3.4 18.6 + - - +
360A SER 5.2 0.6 + - - -
361A VAL* 3.4 12.1 - - - +
362A ASN* 3.3 40.6 + - - +
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Residues in contact with ILE 303 (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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253A LEU* 3.8 22.2 - - + -
300A LEU* 3.7 28.3 - - + -
302A ASN* 1.3 83.3 + - - +
304A ASP* 1.3 63.6 + - - +
305A ILE* 3.4 34.3 - - + -
325A ILE* 4.0 3.6 - - + -
329A LEU* 3.7 16.4 - - + -
331A LEU* 4.3 0.4 - - + -
335A ARG 2.7 15.2 + - - +
336A ILE* 3.5 30.1 - - + -
337A ASN* 3.1 23.9 + - - +
360A SER 3.6 4.3 - - - +
361A VAL* 4.1 7.0 - - + -
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Residues in contact with ASP 304 (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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302A ASN* 4.1 10.0 - - - +
303A ILE* 1.3 75.7 - - - +
305A ILE* 1.3 61.3 + - - +
337A ASN* 2.9 36.3 + - + +
339A LYS* 2.7 26.6 + - - +
358A LEU 3.9 1.2 - - - +
359A SER* 3.5 1.2 - - - -
360A SER* 2.7 53.1 + - - +
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Residues in contact with ILE 305 (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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249A LEU* 3.9 16.8 - - + -
253A LEU* 4.2 5.2 - - + -
303A ILE* 3.4 26.7 - - + -
304A ASP* 1.3 77.6 + - - +
306A CYS* 1.3 64.7 + - - +
307A VAL* 3.9 16.4 - - + -
325A ILE* 3.8 25.8 - - + -
336A ILE* 5.0 0.2 - - + -
337A ASN 3.0 10.4 + - - +
338A VAL* 4.0 15.0 - - + -
339A LYS* 2.8 32.4 + - - -
357A VAL* 3.7 22.7 - - + -
358A LEU 3.6 3.6 - - - -
359A SER* 3.7 17.5 - - - +
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Residues in contact with CYS 306 (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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305A ILE* 1.3 78.7 - - - +
307A VAL* 1.3 62.5 + - - +
308A MET* 3.4 14.1 + - - +
339A LYS* 3.6 26.9 - - - +
340A ALA 5.1 0.4 - - - -
341A THR* 3.9 28.5 - - - -
358A LEU* 2.8 55.7 + - + +
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Residues in contact with VAL 307 (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 LEU* 4.4 5.2 - - + -
249A LEU* 4.4 9.0 - - + -
305A ILE* 3.9 9.4 - - + -
306A CYS* 1.3 72.2 - - - +
308A MET* 1.3 58.3 + - - +
309A ALA* 3.5 2.4 + - - +
314A LEU* 4.0 15.3 - - + -
321A MET* 5.3 1.3 - - + -
338A VAL* 3.6 21.3 - - + -
339A LYS 2.8 22.8 + - - +
340A ALA* 3.2 9.5 - - + +
341A THR 2.8 26.9 + - - +
355A MET* 3.1 35.4 - - + -
356A ALA 3.9 2.5 - - - -
357A VAL* 4.0 13.5 - - + -
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Residues in contact with MET 308 (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* 4.2 21.3 - - + -
306A CYS* 3.4 15.0 + - - +
307A VAL* 1.3 67.3 - - - +
309A ALA* 1.3 62.7 + - - +
341A THR* 3.2 26.7 - - + +
343A THR* 4.9 9.2 - - + -
349A ILE* 3.7 34.0 - - + +
355A MET* 3.5 2.8 - - - +
356A ALA* 2.7 44.8 + - + +
358A LEU* 4.6 9.0 - - - -
1374A GPP 3.5 31.2 - - + -
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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