Contacts of the strand formed by residues 322 - 330 (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 TYR 322 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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292A SER* 4.0 14.9 - - - -
293A MET* 4.1 5.1 - - + +
316A LEU* 3.7 1.8 - - - -
317A ARG* 3.2 66.0 + - - +
319A ILE 3.7 1.8 + - - -
320A GLN 3.7 0.4 - - - -
321A ASN* 1.3 84.8 - - + +
323A SER* 1.3 62.8 + - - +
324A VAL* 3.7 21.9 - - + +
346A ILE* 3.2 39.7 - - + +
347A GLU 3.8 2.7 - - - -
348A MET* 4.0 28.0 - - + -
1H NAG 5.7 4.5 - - + +
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Residues in contact with SER 323 (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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293A MET* 4.9 0.2 - - - -
314A GLN* 4.6 5.0 + - - -
315A TRP 2.9 19.3 - - - -
316A LEU* 3.7 17.7 - - - +
322A TYR* 1.3 74.6 - - - +
324A VAL* 1.3 68.3 + - - +
345A HIS 4.7 0.2 - - - -
346A ILE* 3.6 3.3 - - - +
347A GLU* 2.9 53.5 + - - +
354A VAL* 3.9 10.8 - - - +
359A PRO* 4.3 10.3 - - - +
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Residues in contact with VAL 324 (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 PRO* 3.8 24.5 - - + -
292A SER* 3.5 22.7 - - - +
293A MET* 4.5 6.9 - - + -
313A LEU 3.7 1.0 - - - +
314A GLN* 3.3 3.0 - - - -
315A TRP* 2.7 42.4 + - - +
322A TYR* 3.7 17.9 - - + +
323A SER* 1.3 80.8 - - - +
325A MET* 1.3 72.8 + - - +
344A GLN* 3.6 25.8 - - - +
345A HIS 3.4 6.7 - - - +
346A ILE* 4.2 11.2 - - + -
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Residues in contact with MET 325 (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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312A SER* 3.6 19.3 - - - -
313A LEU 3.3 7.2 - - - +
314A GLN* 3.6 28.0 - - + +
324A VAL* 1.3 75.6 - - - +
326A ASP* 1.3 62.6 + - - +
327A ILE* 3.2 41.3 - - + -
343A ARG 4.7 0.2 - - - +
344A GLN* 3.0 25.1 - - - +
345A HIS* 2.8 28.9 + - + +
362A PRO* 4.6 10.5 - - - -
364A PHE* 3.8 4.9 - - + -
371A PHE* 3.6 33.0 - - + -
373A LYS* 5.0 3.6 - - - +
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Residues in contact with ASP 326 (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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287A ILE* 6.1 0.7 - - + -
288A THR 4.6 5.4 - - - +
289A ALA* 4.9 1.4 - - - +
290A PRO* 2.9 37.1 - - + +
312A SER* 3.0 9.4 - - - -
313A LEU* 2.6 44.6 + - + +
315A TRP* 4.6 2.8 + - - +
324A VAL 4.1 0.4 + - - -
325A MET* 1.3 74.7 - - - +
327A ILE* 1.3 62.9 + - - +
328A CYS* 4.0 9.9 - - - -
339A CYS* 3.0 36.8 - - - +
340A LEU 4.9 1.4 - - - +
344A GLN* 4.3 14.3 - - - +
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Residues in contact with ILE 327 (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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310A ARG* 3.4 34.8 - - + +
311A ILE 3.6 4.7 - - - +
312A SER* 4.2 4.5 - - - -
325A MET* 3.2 35.9 - - + +
326A ASP* 1.3 74.6 + - - +
328A CYS* 1.3 61.2 + - - +
329A ASP* 3.9 2.1 - - - +
338A ASN 4.0 0.5 - - - +
339A CYS* 3.7 12.7 - - - -
340A LEU 4.2 1.1 + - - -
343A ARG* 3.6 52.8 + - + +
344A GLN* 5.1 0.8 - - - +
345A HIS* 4.1 7.0 - - + +
364A PHE* 4.5 2.9 - - + -
371A PHE* 4.2 1.8 - - + -
389A ILE* 3.9 29.4 - - + +
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Residues in contact with CYS 328 (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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287A ILE* 3.7 21.5 - - + -
309A GLU 3.8 0.3 - - - +
310A ARG* 3.3 5.2 - - - +
311A ILE* 2.8 49.5 + - + +
313A LEU* 5.2 4.5 - - - -
326A ASP* 4.2 12.3 - - - -
327A ILE* 1.3 73.4 - - - +
329A ASP* 1.3 65.7 + - - +
337A TRP* 4.1 7.4 - - + -
338A ASN 3.2 7.2 - - - +
339A CYS* 2.0 46.7 - - - -
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Residues in contact with ASP 329 (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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309A GLU* 3.4 5.6 - - - +
310A ARG* 2.6 47.0 + - - +
327A ILE* 3.9 7.8 - - - +
328A CYS* 1.3 78.7 - - - +
330A TYR* 1.3 67.8 + - - +
331A ASP* 3.5 1.6 + - - +
337A TRP* 3.5 3.5 - - - -
338A ASN* 2.8 35.4 + - + +
343A ARG* 4.0 10.0 + - - -
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Residues in contact with TYR 330 (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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222A PHE* 3.8 18.4 - + + -
272A ASN* 5.3 1.6 + - + -
309A GLU* 2.9 38.3 + - + +
329A ASP* 1.3 76.1 - - - +
331A ASP* 1.3 64.6 + - - +
332A GLU* 3.5 32.5 + - - -
335A GLY* 3.4 41.1 - - - -
336A ARG 3.7 5.2 - - - -
337A TRP* 3.5 42.3 - + + -
2E NAG 3.4 29.4 - - + +
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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