Contacts of the strand formed by residues 298 - 307 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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203B TYR* 4.1 2.6 + - - -
263B ASN* 6.1 0.3 - - - +
264B PRO 4.9 8.0 - - - +
265B THR* 6.0 0.5 - - - -
266B VAL* 4.6 18.0 + - + +
289B ALA 5.6 0.6 + - - -
293B MET* 3.1 33.1 + - + +
294B LEU* 4.3 24.5 - - + +
296B GLY 2.7 22.9 + - - -
297B ASP* 1.3 77.5 - - - +
299B TYR* 1.3 73.2 + - - +
315B TRP* 3.8 33.3 - + - -
316B LEU 3.1 15.5 - - - +
318B ARG* 3.9 3.8 - - - +
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Residues in contact with TYR 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202B VAL* 6.1 0.2 - - + -
203B TYR* 3.3 27.1 - + + +
207B VAL* 4.9 8.5 - - + -
263B ASN* 2.8 35.6 + - + -
264B PRO* 5.8 2.9 - - + -
266B VAL* 5.1 0.2 - - - -
298B HIS* 1.3 83.2 - - - +
300B LEU* 1.3 64.7 + - - +
301B CYS* 3.5 3.2 + - - -
315B TRP* 3.2 13.8 - - - -
316B LEU* 2.6 56.3 + - + +
317B ARG 3.9 5.4 - - - -
318B ARG* 3.2 30.2 - - + +
320B GLN* 4.1 17.2 + - - -
665B VAL* 3.7 38.6 + - + +
668B GLU* 4.1 2.6 + - - -
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Residues in contact with LEU 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203B TYR* 3.2 18.3 + - + +
207B VAL* 4.6 1.6 - - - +
208B PHE* 3.1 30.0 - - + -
215B TRP* 4.8 4.0 - - + -
226B ALA* 3.9 28.7 - - + -
266B VAL* 4.2 17.1 - - + +
268B PHE* 4.0 21.3 - - + -
299B TYR* 1.3 71.3 - - - +
301B CYS* 1.3 57.9 + - - +
302B ASP 4.4 7.6 - - - +
303B VAL* 4.8 2.9 - - + -
313B LEU* 4.4 15.7 - - + -
314B GLN 3.7 13.9 - - - +
315B TRP* 3.7 38.5 - - + -
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Residues in contact with CYS 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207B VAL* 4.5 9.5 - - - +
208B PHE* 3.4 24.1 - - - -
299B TYR* 3.9 4.3 - - - -
300B LEU* 1.3 72.8 - - - +
302B ASP* 1.3 63.6 + - + +
314B GLN* 2.8 18.7 + - + +
315B TRP* 3.5 15.7 - - - -
316B LEU* 3.3 36.8 - - - -
358B ARG* 5.1 8.3 - - + -
359B PRO* 3.7 29.4 - - + +
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Residues in contact with ASP 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208B PHE* 5.3 0.2 - - - -
300B LEU* 3.9 2.7 - - - +
301B CYS* 1.3 83.1 - - + +
303B VAL* 1.3 74.1 + - - +
304B THR* 2.9 34.2 + - - +
312B SER* 3.8 1.1 + - - +
313B LEU* 3.5 4.2 - - - +
314B GLN* 2.8 46.2 + - + +
358B ARG* 6.1 4.1 - - - -
359B PRO 5.6 2.9 - - - +
360B SER 5.4 0.7 - - - +
361B GLU* 3.8 22.0 - - - +
362B PRO* 3.8 14.0 - - - +
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Residues in contact with VAL 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208B PHE* 5.1 2.2 - - + -
215B TRP* 3.1 80.3 + - + +
268B PHE* 4.1 10.5 - - + -
300B LEU* 4.8 9.0 - - + -
302B ASP* 1.3 80.8 + - - +
304B THR* 1.3 68.8 + - - +
305B TRP* 5.1 0.9 - - - +
311B ILE* 3.9 23.8 - - + -
312B SER 3.4 7.0 - - - +
313B LEU* 4.6 4.5 - - + -
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Residues in contact with THR 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302B ASP* 2.9 29.1 + - - +
303B VAL* 1.3 77.2 - - - +
305B TRP* 1.3 67.3 + - - +
306B ALA 3.6 0.2 + - - -
311B ILE* 4.5 2.0 - - - -
312B SER* 3.0 43.7 + - - -
361B GLU* 4.6 8.1 - - + -
362B PRO* 3.3 27.4 - - + +
364B PHE* 3.8 7.0 - - - -
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Residues in contact with TRP 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215B TRP* 3.1 33.9 + - + +
216B TRP 3.3 14.4 + - - -
217B SER* 3.4 25.8 - - - -
218B PRO* 3.3 21.3 - - + +
222B PHE* 3.4 31.9 - + + -
224B ALA* 3.9 20.4 - - + -
270B VAL* 4.3 4.0 - - + -
303B VAL* 5.1 0.2 - - + -
304B THR* 1.3 77.7 - - - +
306B ALA* 1.3 60.2 - - - +
307B THR 3.7 13.9 - - - -
308B GLN 4.1 4.9 - - - -
310B ARG 3.8 13.0 - - - -
311B ILE* 3.9 19.1 - - + +
337B TRP* 3.7 30.3 - + - -
364B PHE* 4.7 6.3 - - - +
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Residues in contact with ALA 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218B PRO* 5.6 1.1 - - - -
304B THR 3.6 2.3 + - - +
305B TRP* 1.3 74.7 - - - +
307B THR* 1.3 66.7 + - + +
310B ARG* 2.8 35.8 + - - +
311B ILE* 4.9 1.1 - - - +
312B SER 5.3 0.7 - - - +
364B PHE* 3.6 46.2 - - + +
365B THR 4.7 0.9 - - - +
366B LEU 4.4 5.7 - - - +
368B GLY* 4.1 8.5 + - - -
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Residues in contact with THR 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B PRO* 3.4 20.3 - - - +
305B TRP* 3.7 12.6 - - - -
306B ALA* 1.3 84.2 - - + +
308B GLN* 1.3 65.8 + - - +
309B GLU* 3.2 10.6 + - - +
310B ARG* 3.2 32.6 + - + +
366B LEU 4.7 3.8 - - - +
367B ASP* 3.6 26.5 - - - +
368B GLY* 3.8 7.0 - - - -
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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