Contacts of the strand formed by residues 310 - 317 (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 ARG 310 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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305A TRP* 3.4 4.8 - - - -
306A ALA* 2.9 35.6 + - + +
307A THR* 3.1 24.2 + - - +
309A GLU* 1.3 80.2 - - - +
311A ILE* 1.3 60.7 + - - +
327A ILE* 3.4 24.1 - - + +
328A CYS 3.3 5.2 - - - +
329A ASP* 2.6 48.2 + - - +
343A ARG* 3.4 19.2 - - - +
364A PHE* 5.1 1.3 - - - -
367A ASP 4.3 5.9 + - - -
368A GLY* 2.9 24.8 + - - -
369A ASN* 3.3 25.5 - - - +
389A ILE* 4.0 8.2 - - - +
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Residues in contact with ILE 311 (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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224A ALA* 4.2 2.2 - - + -
268A PHE* 3.6 24.0 - - + -
270A VAL* 4.8 2.2 - - + -
287A ILE* 4.4 7.4 - - + -
303A VAL* 4.7 3.8 - - + -
304A THR 3.5 16.2 - - - +
305A TRP* 4.1 33.0 - - + +
306A ALA* 4.3 1.1 - - - +
310A ARG* 1.3 77.0 - - - +
312A SER* 1.3 63.0 + - - +
313A LEU* 3.5 25.3 + - + -
326A ASP 3.9 0.3 - - - +
327A ILE* 3.6 2.2 - - - +
328A CYS* 2.8 45.5 + - + +
337A TRP* 3.8 20.4 - - + -
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Residues in contact with SER 312 (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* 3.9 1.7 + - - +
303A VAL* 3.4 1.7 - - - -
304A THR* 2.7 45.1 + - - -
306A ALA 4.9 0.6 - - - +
311A ILE* 1.3 73.2 - - - +
313A LEU* 1.3 67.1 - - - +
325A MET* 3.6 13.4 - - - +
326A ASP 3.0 11.9 - - - -
327A ILE* 4.2 3.6 - - - -
362A PRO* 3.9 8.0 - - - +
364A PHE* 3.3 38.8 - - - -
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Residues in contact with LEU 313 (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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268A PHE* 3.5 35.0 - - + -
287A ILE* 4.3 18.4 - - + -
300A LEU* 4.2 11.7 - - + -
302A ASP 3.3 4.7 - - - +
303A VAL* 4.1 7.6 - - + -
311A ILE* 3.5 32.3 - - + -
312A SER* 1.3 85.0 - - - +
314A GLN* 1.3 60.8 + - - +
315A TRP* 3.6 34.2 - - + +
325A MET* 3.3 1.0 - - - -
326A ASP* 2.6 41.2 + - + -
328A CYS* 5.2 3.8 - - - -
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Residues in contact with GLN 314 (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 2.9 - - - +
301A CYS* 2.8 30.8 + - + +
302A ASP* 3.0 29.8 + - + +
312A SER 4.3 0.2 - - - -
313A LEU* 1.3 72.9 - - - +
315A TRP* 1.3 62.8 + - - +
323A SER* 4.6 4.2 + - - +
324A VAL 3.3 3.8 - - - +
325A MET* 3.6 28.3 - - + +
347A GLU* 3.9 4.4 + - - +
359A PRO* 3.2 28.6 - - + +
360A SER 2.9 19.5 - - - +
362A PRO* 3.7 14.4 - - + +
373A LYS* 2.6 31.1 + - - +
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Residues in contact with TRP 315 (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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266A VAL* 4.1 14.1 - - + -
267A LYS* 5.3 0.9 - - - -
268A PHE* 4.5 18.2 - - + -
287A ILE 4.6 4.7 - - - -
288A THR* 4.4 7.0 + - - -
289A ALA 3.4 20.2 + - - -
290A PRO* 3.3 24.9 - - + +
293A MET* 3.4 20.6 - - + -
298A HIS* 3.7 28.5 - + - -
299A TYR 3.4 19.7 - - - +
300A LEU* 3.8 34.8 - - + -
301A CYS* 3.6 1.8 - - - -
313A LEU* 3.6 36.8 + - + +
314A GLN* 1.3 78.1 - - - +
316A LEU* 1.3 61.8 + - - +
323A SER* 2.9 7.8 - - - -
324A VAL 2.7 38.0 + - - +
326A ASP* 4.6 4.4 + - - +
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Residues in contact with LEU 316 (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* 3.8 4.9 - - - -
298A HIS* 3.3 1.6 - - - -
299A TYR* 2.7 44.2 + - + -
301A CYS* 3.2 23.8 - - - -
315A TRP* 1.3 73.7 - - - +
317A ARG* 1.3 69.8 + - - +
320A GLN* 3.4 51.6 - - + +
322A TYR 3.5 22.2 - - - +
323A SER* 3.7 13.7 - - - -
354A VAL* 4.1 13.0 - - + +
358A ARG* 5.6 1.8 - - - -
359A PRO* 4.3 13.7 - - + -
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Residues in contact with ARG 317 (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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292A SER* 2.8 39.3 + - - +
293A MET* 3.2 21.6 - - + +
295A ILE* 3.3 24.2 - - + +
297A ASP 3.8 10.5 - - - +
298A HIS* 4.1 1.1 - - - +
299A TYR* 3.9 1.0 - - - -
316A LEU* 1.3 84.3 - - - +
318A ARG* 1.3 68.2 + - - +
319A ILE* 3.0 28.1 + - + +
320A GLN* 3.3 5.2 + - - +
322A TYR* 3.2 47.5 + - - +
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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