Contacts of the strand formed by residues 310 - 317 (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 ARG 310 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305B TRP* 3.7 4.2 - - - -
306B ALA* 2.8 37.0 + - - +
307B THR* 3.2 29.6 + - - +
308B GLN 3.8 0.8 - - - -
309B GLU* 1.3 77.2 - - - +
311B ILE* 1.3 60.6 + - - +
327B ILE* 3.2 29.3 - - - +
328B CYS 3.3 5.2 - - - +
329B ASP* 2.7 57.4 + - - +
337B TRP* 4.2 0.4 - - - -
343B ARG* 3.5 13.7 - - - +
367B ASP 3.7 6.5 + - - -
368B GLY 2.9 25.7 + - - -
369B ASN* 2.8 29.1 + - - -
389B ILE* 3.7 9.3 - - - +
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Residues in contact with ILE 311 (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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224B ALA* 4.1 3.4 - - + -
268B PHE* 3.3 33.4 - - + -
270B VAL* 4.9 1.1 - - + -
287B ILE* 4.2 13.2 - - + -
303B VAL* 3.9 11.9 - - + -
304B THR 3.9 12.8 - - - +
305B TRP* 3.9 30.5 - - + +
306B ALA* 4.4 0.9 - - - +
310B ARG* 1.3 75.4 - - - +
312B SER* 1.3 64.2 + - - +
313B LEU* 3.3 17.1 + - + -
326B ASP 3.9 0.2 - - - +
327B ILE* 3.5 3.1 - - - +
328B CYS* 2.8 45.7 + - + +
337B TRP* 3.9 19.7 - - + -
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Residues in contact with SER 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B ASP* 3.8 1.4 + - - +
303B VAL* 3.4 2.8 - - - -
304B THR* 3.0 46.3 + - - -
306B ALA* 5.0 0.4 - - - +
311B ILE* 1.3 72.8 - - - +
313B LEU* 1.3 68.1 + - - +
314B GLN* 5.7 0.9 - - - +
325B MET* 4.4 9.0 - - - +
326B ASP 3.1 11.0 - - - -
327B ILE* 4.3 9.6 - - - +
362B PRO* 4.0 7.4 - - - +
364B PHE* 3.6 27.4 - - - -
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Residues in contact with LEU 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B PHE* 3.6 34.1 - - + -
287B ILE* 3.9 22.4 - - + -
288B THR 5.5 0.2 - - - +
300B LEU* 4.4 10.1 - - + -
302B ASP 3.5 3.8 - - - +
303B VAL* 4.6 3.4 - - + -
311B ILE* 3.3 36.6 - - + +
312B SER* 1.3 83.7 - - - +
314B GLN* 1.3 62.0 + - - +
315B TRP* 3.7 30.4 - - + +
325B MET* 3.3 1.4 - - - -
326B ASP* 2.7 42.8 + - + +
328B CYS* 4.8 4.7 - - - -
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Residues in contact with GLN 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B LEU* 3.7 9.2 - - - +
301B CYS* 2.8 33.9 + - + -
302B ASP* 2.8 31.2 + - + +
312B SER* 5.7 0.9 - - - +
313B LEU* 1.3 73.7 - - - +
315B TRP* 1.3 57.2 + - - +
323B SER* 4.2 7.2 + - - +
324B VAL 3.4 2.2 - - - +
325B MET* 3.6 35.6 - - + +
347B GLU* 4.4 4.0 + - - +
359B PRO* 3.6 18.2 - - - +
360B SER 2.7 22.5 - - - +
362B PRO* 3.7 14.1 - - + +
373B LYS* 3.2 23.6 - - - +
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Residues in contact with TRP 315 (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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266B VAL* 3.9 21.3 - - + -
267B LYS* 5.6 0.2 - - - -
268B PHE* 4.6 14.1 - - + -
287B ILE 4.5 6.1 - - - -
288B THR* 4.0 9.1 + - - -
289B ALA 3.4 19.9 + - - -
290B PRO* 3.3 24.7 - - + +
293B MET* 3.2 22.7 - - + -
298B HIS* 3.8 20.9 - + - -
299B TYR 3.2 20.6 - - - -
300B LEU* 3.7 36.6 - - + -
301B CYS* 3.5 3.1 - - - -
313B LEU* 3.7 36.6 - - + +
314B GLN* 1.3 75.4 - - - +
316B LEU* 1.3 59.4 + - - +
323B SER* 2.7 25.8 + - - -
324B VAL 2.7 19.9 + - - +
326B ASP* 4.7 4.3 + - + +
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Residues in contact with LEU 316 (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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293B MET* 3.6 8.1 - - - -
298B HIS* 3.1 1.6 - - - +
299B TYR* 2.6 46.7 + - + +
301B CYS* 3.3 14.1 - - - -
315B TRP* 1.3 76.9 - - - +
317B ARG* 1.3 70.5 + - - +
320B GLN* 3.7 49.6 - - + +
322B TYR 3.4 24.5 - - - +
323B SER* 3.9 11.0 - - - +
354B VAL* 4.4 8.1 - - + +
358B ARG* 5.5 2.0 - - + -
359B PRO* 4.0 20.9 - - + -
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Residues in contact with ARG 317 (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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292B SER* 3.1 32.8 + - - +
293B MET* 3.5 19.9 - - - +
295B ILE* 4.8 10.9 - - + +
297B ASP 3.6 9.2 - - - +
299B TYR* 3.9 1.2 - - - -
316B LEU* 1.3 84.0 - - - +
318B ARG* 1.3 68.0 + - - +
319B ILE* 3.1 25.8 + - + +
320B GLN* 3.5 4.9 + - - +
321B ASN* 5.2 2.1 + - - -
322B TYR* 3.3 58.7 + - + +
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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