Contacts of the strand formed by residues 291 - 305 (chain A) in PDB entry 1NQG
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 ASP 291 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A VAL* 3.2 25.5 - - + +
272A SER* 3.7 1.5 + - - +
273A LYS* 3.5 0.7 - - - -
274A ASP* 2.8 43.1 + - + +
289A THR* 3.8 14.0 + - - +
290A LEU* 1.3 92.9 - - - +
292A GLU* 1.3 57.9 + - - +
325A GLY 4.5 1.9 - - - +
326A THR* 3.1 16.7 - - + -
327A GLY* 3.1 24.2 + - - -
328A TYR 5.1 0.3 + - - -
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Residues in contact with GLU 292 (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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90A VAL* 5.1 0.2 - - - -
271A HIS* 2.7 31.2 + - + +
272A SER 3.2 12.3 - - - +
273A LYS* 3.8 20.3 - - + +
290A LEU* 3.9 12.3 - - + +
291A ASP* 1.3 76.7 - - - +
293A MET* 1.3 64.6 + - - +
294A LYS* 3.8 13.0 - - + +
321A THR 4.2 0.3 - - - +
322A THR* 3.5 5.2 - - - -
323A THR* 3.3 42.4 + - + +
326A THR* 3.0 15.0 + - - +
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Residues in contact with MET 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A ASN 4.9 5.2 - - - +
89A GLY* 3.4 27.6 - - - +
90A VAL* 3.1 45.3 - - + +
270A SER 4.0 0.3 - - - +
271A HIS* 3.4 4.9 - - - -
272A SER* 3.0 39.8 + - - +
292A GLU* 1.3 73.2 - - - +
294A LYS* 1.3 76.0 + - - +
295A GLN* 4.2 5.8 - - + +
320A GLN* 4.2 19.7 - - + +
321A THR 3.8 7.9 - - - +
322A THR* 3.2 27.6 - - + -
335A GLN* 5.7 0.7 - - - +
398A LEU* 5.2 2.0 - - + -
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Residues in contact with LYS 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A TYR* 3.6 32.6 + - + +
270A SER 3.4 4.0 - - - -
271A HIS* 3.6 32.5 - - + -
292A GLU* 3.8 10.5 - - + +
293A MET* 1.3 82.5 - - - +
295A GLN* 1.3 60.4 - - - +
296A TYR* 4.0 21.3 + - - +
319A LYS 3.7 1.0 - - - +
320A GLN* 3.3 1.4 - - - -
321A THR* 2.9 46.4 + - - +
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Residues in contact with GLN 295 (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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83A VAL* 5.0 1.7 - - - +
84A ARG* 3.4 29.7 + - - +
85A LEU 5.0 4.2 + - - -
86A ASN* 4.4 13.6 - - + +
89A GLY* 5.0 5.5 - - - -
268A SER 3.8 0.9 - - - +
269A TYR* 3.4 7.6 - - - -
270A SER* 3.1 34.3 + - - +
293A MET* 4.2 6.1 - - + -
294A LYS* 1.3 74.1 - - - +
296A TYR* 1.3 65.7 + - - +
297A THR* 4.2 9.7 + - - +
318A GLN* 3.8 25.2 + - + +
319A LYS 3.0 4.0 - - - +
320A GLN* 2.9 43.0 + - + +
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Residues in contact with TYR 296 (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 SER 3.6 2.5 - - - -
269A TYR* 3.3 42.8 - + + -
294A LYS* 4.0 29.8 + - + +
295A GLN* 1.3 69.5 - - - +
297A THR* 1.3 62.7 + - - +
298A VAL* 6.1 0.2 - - + -
317A TRP* 3.7 12.9 - + + +
318A GLN* 3.4 6.8 - - - +
319A LYS* 2.4 94.4 + - + +
321A THR* 4.5 5.5 + - + -
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Residues in contact with THR 297 (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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83A VAL* 3.9 30.5 - - + +
266A ILE* 3.7 0.8 - - + +
267A THR* 3.2 3.3 - - - +
268A SER* 2.8 46.2 + - - +
295A GLN* 4.2 12.3 + - - +
296A TYR* 1.3 77.2 + - - +
298A VAL* 1.3 73.3 + - - +
299A GLN* 4.0 24.5 - - + +
316A ASP* 4.6 2.7 - - - +
317A TRP 3.5 10.3 - - - +
318A GLN* 4.2 13.2 + - + +
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Residues in contact with VAL 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A LEU* 4.7 10.3 - - + -
266A ILE 3.3 9.2 - - - +
267A THR* 3.6 15.3 - - + +
296A TYR* 6.1 0.2 - - + -
297A THR* 1.3 79.6 - - - +
299A GLN* 1.3 66.9 + - - +
315A VAL* 4.2 0.7 - - - +
316A ASP* 3.8 0.2 - - - -
317A TRP* 2.7 64.0 + - + +
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Residues in contact with GLN 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ARG* 3.5 29.6 + - - +
82A GLY 4.5 13.1 + - - +
83A VAL* 5.2 8.4 - - - +
84A ARG 6.0 0.2 - - - +
118A TYR* 5.9 0.2 - - - -
264A GLN* 3.9 12.5 + - - +
265A LEU* 3.2 7.1 - - - +
266A ILE* 3.1 47.4 + - + +
297A THR* 4.0 18.3 - - + +
298A VAL* 1.3 82.5 - - - +
300A TRP* 1.3 62.0 + - - +
301A ALA* 6.1 0.9 - - + -
315A VAL 3.1 10.8 - - - +
316A ASP* 3.3 28.3 + - - +
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Residues in contact with TRP 300 (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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263A SER* 3.5 16.5 + - - -
264A GLN 2.8 29.8 - - - -
265A LEU* 3.7 21.3 - - + +
298A VAL* 6.1 0.2 - - + -
299A GLN* 1.3 77.1 - - - +
301A ALA* 1.3 62.4 + - - +
302A ASN* 3.3 25.1 + - - -
314A GLY* 2.9 2.3 - - - -
315A VAL* 2.7 56.3 + - + +
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Residues in contact with ALA 301 (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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14A ARG* 4.4 2.0 - - - -
15A PHE* 3.3 13.1 - - + -
264A GLN* 2.9 57.2 + - + +
299A GLN* 6.1 1.3 - - + -
300A TRP* 1.3 76.6 - - - +
302A ASN* 1.3 67.2 + - - +
313A ALA 3.3 5.8 - - - +
314A GLY* 3.7 0.2 - - - -
341A TYR* 3.5 23.1 - - - +
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Residues in contact with ASN 302 (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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15A PHE* 3.8 5.2 - - - -
261A ILE* 5.7 1.8 - - + +
262A LYS 3.3 3.0 + - - +
263A SER* 2.1 44.5 + - - -
300A TRP* 3.3 32.5 - - - +
301A ALA* 1.3 76.7 + - - +
303A ASN* 1.3 63.6 + - - +
304A VAL* 5.8 3.1 - - + -
312A GLY* 3.4 1.3 - - - -
313A ALA* 2.7 35.5 + - + +
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Residues in contact with ASN 303 (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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13A ASN* 4.0 15.5 + - - +
15A PHE* 3.4 33.9 - - + +
260A LEU 4.1 0.2 - - - +
262A LYS* 2.4 59.4 + - + +
302A ASN* 1.3 74.4 - - - +
304A VAL* 1.3 67.9 + - - +
305A ILE* 4.6 0.7 + - - +
310A SER* 3.5 24.2 + - - -
311A ILE 3.1 24.6 + - - -
312A GLY* 3.6 6.5 - - - +
343A THR* 4.0 5.9 + - - -
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Residues in contact with VAL 304 (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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260A LEU* 3.3 5.4 - - + +
261A ILE* 3.7 29.2 - - + -
262A LYS 5.2 0.2 - - - +
302A ASN* 5.8 2.9 - - + -
303A ASN* 1.3 88.6 - - - +
305A ILE* 1.3 62.2 + - - +
306A VAL* 3.1 17.6 - - + +
310A SER* 3.2 1.6 - - - -
311A ILE* 3.0 41.3 + - + +
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Residues in contact with ILE 305 (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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259A GLU 3.1 27.8 - - - +
260A LEU* 2.7 46.8 + - + +
262A LYS* 3.2 31.0 - - - +
303A ASN* 5.3 0.4 - - - +
304A VAL* 1.3 69.5 - - - +
306A VAL* 1.3 64.9 + - - +
307A GLY 3.6 19.1 + - - +
309A GLY 3.6 9.2 - - - +
310A SER* 4.4 4.5 - - - +
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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