Contacts of the strand formed by residues 262 - 273 (chain A) in PDB entry 4NAM
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 VAL 262 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261A ILE* 1.3 84.2 - - - +
263A HIS* 1.3 71.9 + - - +
297A ARG* 5.6 0.2 - - - -
328A ASN* 3.1 29.8 + - - +
366A TYR* 4.2 15.0 - - + -
367A VAL 3.2 8.1 - - - +
368A ASN* 4.5 4.0 - - - -
374A ILE* 3.4 32.8 - - + -
379A PRO* 3.7 26.0 - - + -
405A LEU* 4.0 19.3 - - + -
452A THR* 3.9 4.6 - - + +
456A TYR* 3.6 14.2 + - + -
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Residues in contact with HIS 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A VAL* 1.3 78.1 - - - +
264A VAL* 1.3 87.0 + - - +
265A ASP* 4.7 4.4 - - - +
295A THR* 4.9 3.1 + - + +
296A SER* 4.8 1.4 - - - -
297A ARG* 3.3 51.9 + - + +
328A ASN* 5.0 3.6 - - + -
329A SER* 4.7 5.2 - - - +
330A SER* 3.7 19.3 - - - -
366A TYR* 3.5 3.6 - - - -
367A VAL* 2.8 68.6 + - + +
369A THR* 4.1 9.6 + - + +
450A LEU 5.9 0.4 - - - +
452A THR* 4.5 7.6 - - - +
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Residues in contact with VAL 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A HIS* 1.3 83.9 - - - +
265A ASP* 1.3 62.7 + - - +
295A THR* 3.4 8.3 - - - +
330A SER* 2.8 26.2 + - - -
364A ILE* 3.8 31.2 - - + -
365A ARG 3.5 8.3 - - - +
366A TYR* 3.8 26.5 - - + -
381A THR* 3.5 27.1 - - + +
394A ILE* 5.8 1.6 - - + -
450A LEU* 3.7 27.8 - - + +
452A THR* 3.9 7.6 + - + +
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Residues in contact with ASP 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A HIS* 4.2 5.1 + - - +
264A VAL* 1.3 73.2 - - - +
266A MET* 1.3 69.4 + - - +
267A GLU* 3.9 13.9 + - - +
295A THR* 3.2 26.7 + - - +
364A ILE* 3.1 4.7 - - - -
365A ARG* 2.8 39.0 + - + +
367A VAL* 3.8 20.0 - - + -
410A TYR* 4.3 14.2 + - - -
414A LYS* 4.7 6.9 + - - -
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Residues in contact with MET 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A VAL 4.0 0.6 - - - -
265A ASP* 1.3 77.4 - - - +
267A GLU* 1.3 57.8 + - - +
268A ASN 3.8 10.8 - - - +
269A ILE* 3.3 26.5 - - - -
293A THR* 2.8 27.7 + - - +
295A THR* 2.8 30.5 + - - +
332A VAL* 4.0 21.8 - - + -
360A LEU* 4.8 2.5 - - + -
362A ALA* 3.7 16.2 - - + -
363A ASN 3.5 7.4 - - - +
364A ILE* 4.1 13.9 - - + -
383A LEU* 4.3 24.2 - - + -
421A LEU* 4.3 9.9 - - + -
448A LEU* 4.6 6.7 - - + -
450A LEU* 4.4 13.4 - - + +
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Residues in contact with GLU 267 (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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265A ASP* 4.4 18.2 - - - +
266A MET* 1.3 72.4 - - - +
268A ASN* 1.3 75.0 + - - +
292A ASN* 3.9 5.2 - - - +
293A THR* 3.0 28.1 + - - +
363A ASN* 2.9 16.0 + - - +
365A ARG* 2.8 37.9 + - - +
414A LYS* 4.1 10.1 + - - +
418A PRO* 3.8 25.5 - - - +
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Residues in contact with ASN 268 (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 MET* 3.8 1.4 - - - +
267A GLU* 1.3 90.5 + - - +
269A ILE* 1.3 67.1 + - - +
291A LYS 3.4 14.6 - - - +
292A ASN* 3.8 14.5 + - - +
293A THR* 3.1 6.0 + - - +
362A ALA* 3.2 22.3 - - - +
363A ASN* 3.0 42.8 + - - +
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Residues in contact with ILE 269 (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 MET* 3.3 28.7 - - - -
268A ASN* 1.3 83.0 - - - +
270A ILE* 1.3 61.4 + - - +
271A LEU* 4.3 28.0 - - + -
289A ILE* 5.3 0.7 - - + +
290A SER* 3.4 4.2 - - - -
291A LYS* 2.9 46.4 + - + +
293A THR* 3.7 11.7 - - + -
334A ILE* 3.6 37.9 - - + -
360A LEU* 4.7 13.2 - - + -
361A ASN 3.3 8.7 - - - +
362A ALA* 3.9 4.7 - - + +
442A LEU* 5.3 0.2 - - + -
448A LEU* 5.2 2.2 - - + -
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Residues in contact with ILE 270 (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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269A ILE* 1.3 75.3 - - - +
271A LEU* 1.3 64.7 + - - +
272A SER* 4.2 6.1 + - - +
288A THR* 3.9 28.7 - - + +
289A ILE 3.3 5.8 - - - +
290A SER* 3.4 21.8 - - - +
359A ARG 3.9 0.3 - - - +
360A LEU* 3.4 2.4 - - - -
361A ASN* 2.8 62.7 + - + +
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Residues in contact with LEU 271 (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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269A ILE* 4.3 16.4 - - + -
270A ILE* 1.3 74.8 - - - +
272A SER* 1.3 60.6 - - - +
288A THR* 3.2 9.2 - - - -
289A ILE* 2.8 49.8 + - + +
346A FTR 3.3 44.4 - - + -
350A MET* 3.6 16.9 - - + +
358A ALA* 5.6 0.9 - - + -
359A ARG 3.3 3.4 - - - +
360A LEU* 3.7 35.0 - - + -
434A MET* 3.9 17.9 - - + -
439A PHE* 4.4 6.3 - - + -
442A LEU* 4.4 2.7 - - + -
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Residues in contact with SER 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A ILE* 4.7 8.0 + - - +
271A LEU* 1.3 72.8 - - - +
273A LYS* 1.3 63.9 + - - +
288A THR* 3.5 23.7 - - - +
350A MET* 3.4 6.7 - - - -
358A ALA* 3.2 3.8 - - - -
359A ARG* 2.9 64.6 + - - +
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Residues in contact with LYS 273 (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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272A SER* 1.3 74.7 - - - +
274A ASN* 1.3 74.7 + - - +
275A GLU* 3.5 6.6 + - - +
276A ASP* 5.1 4.3 - - - -
279A THR* 5.7 6.0 + - - -
287A ARG* 5.6 1.4 + - + -
288A THR* 5.6 0.4 - - - +
350A MET* 3.4 27.6 + - + +
351A GLY* 3.0 28.4 + - - +
352A LEU* 3.7 21.5 - - + -
356A ASP* 3.7 22.5 + - + -
357A THR 3.9 4.9 - - - +
359A ARG* 4.0 6.5 + - - -
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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