Contacts of the strand formed by residues 298 - 305 (chain A) in PDB entry 1N1M
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 298 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A TYR* 4.1 2.4 + - - -
263A ASN* 6.1 0.7 - - - +
264A PRO 4.9 6.8 - - - +
265A THR* 6.0 0.5 - - - -
266A VAL* 4.8 17.2 + - + +
289A ALA 5.6 0.4 - - - -
293A MET* 3.3 32.6 + - + +
294A LEU* 4.0 29.5 - - + +
296A GLY 3.0 21.9 + - - -
297A ASP* 1.3 77.9 - - - +
299A TYR* 1.3 74.8 + - - +
315A TRP* 3.7 34.2 - + - -
316A LEU 3.3 10.1 - - - +
317A ARG* 4.2 0.4 - - - -
318A ARG* 3.9 4.0 - - - +
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Residues in contact with TYR 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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202A VAL* 6.3 0.2 - - + -
203A TYR* 3.1 28.5 - + + +
207A VAL* 5.0 7.6 - - + -
263A ASN* 3.1 33.2 + - + -
264A PRO* 5.8 1.8 - - + -
266A VAL* 4.9 0.7 - - - -
298A HIS* 1.3 81.6 - - - +
300A LEU* 1.3 63.4 + - - +
301A CYS* 3.7 7.6 - - - -
315A TRP* 3.4 15.0 - - - +
316A LEU* 2.7 45.3 + - + +
317A ARG 3.9 5.8 - - - -
318A ARG* 3.6 30.4 - - + +
320A GLN* 4.0 20.5 + - + -
665A VAL* 3.7 43.7 + - + +
668A GLU* 4.1 3.5 + - - -
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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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203A TYR* 3.1 11.3 + - + +
207A VAL* 3.5 7.3 - - - +
208A PHE* 2.9 37.8 - - + -
215A TRP* 4.4 4.9 - - + -
226A ALA* 3.8 28.9 - - + -
266A VAL* 4.2 16.0 - - + +
268A PHE* 3.9 17.5 - - + -
299A TYR* 1.3 71.2 - - - +
301A CYS* 1.3 59.0 + - - +
302A ASP 4.2 12.1 - - - +
303A VAL* 4.5 4.7 - - + -
313A LEU* 4.2 13.2 - - + -
314A GLN 4.1 5.4 - - - +
315A TRP* 3.8 40.1 - - + -
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Residues in contact with CYS 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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207A VAL* 4.0 15.0 - - + +
208A PHE* 3.5 20.9 - - - -
299A TYR* 3.8 7.6 - - - -
300A LEU* 1.3 73.9 - - - +
302A ASP* 1.3 61.3 + - + +
314A GLN* 2.8 15.8 + - + +
315A TRP 3.6 4.5 - - - -
316A LEU* 3.2 49.8 - - - -
358A ARG* 5.2 7.0 - - + -
359A PRO* 3.7 30.5 - - + -
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Residues in contact with ASP 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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208A PHE* 5.2 1.1 - - - -
300A LEU* 3.8 2.4 - - - +
301A CYS* 1.3 83.7 - - + +
303A VAL* 1.3 76.7 + - - +
304A THR* 2.8 26.1 + - - -
312A SER 4.6 1.4 - - - +
313A LEU* 3.3 6.6 - - - +
314A GLN* 3.0 43.0 + - + +
358A ARG* 6.5 0.9 - - - -
359A PRO 5.2 6.5 - - - +
360A SER 5.7 0.2 - - - -
361A GLU* 4.3 16.9 - - - +
362A PRO* 3.6 17.2 - - - +
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Residues in contact with VAL 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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208A PHE* 5.2 0.9 - - + -
215A TRP* 3.2 80.5 + - + +
268A PHE* 4.1 13.9 - - + -
300A LEU* 4.5 10.5 - - + -
302A ASP* 1.3 84.3 + - - +
304A THR* 1.3 65.1 + - - +
305A TRP* 5.0 2.6 - - + +
311A ILE* 4.7 6.7 - - + -
312A SER 3.4 5.6 - - - -
313A LEU* 4.1 13.2 - - + -
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Residues in contact with THR 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 ASP* 2.8 21.5 + - - -
303A VAL* 1.3 75.6 + - - +
305A TRP* 1.3 76.0 + - - +
306A ALA 3.5 0.9 + - - -
311A ILE* 3.5 3.3 - - - +
312A SER* 2.7 51.8 + - - -
361A GLU* 4.5 6.8 - - + +
362A PRO* 3.7 27.0 + - - +
364A PHE* 4.4 9.1 - - + +
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Residues in contact with TRP 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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215A TRP* 3.3 23.2 + - + +
216A TRP 3.3 22.9 + - - -
217A SER* 3.6 24.0 - - - -
218A PRO* 3.7 22.8 - - + +
222A PHE* 3.5 26.5 - + + -
224A ALA* 3.9 21.5 - - + +
270A VAL* 4.3 3.1 - - + -
303A VAL* 5.1 1.1 - - + -
304A THR* 1.3 83.7 - - - +
306A ALA* 1.3 63.6 + - - +
307A THR 3.5 9.6 - - - +
308A GLN 4.1 9.0 - - - -
310A ARG 3.4 18.8 - - - -
311A ILE* 4.1 17.1 - - + +
337A TRP* 3.5 35.2 - + - -
364A PHE* 4.9 1.6 - - - +
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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