Contacts of the strand formed by residues 261 - 276 (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 ILE 261 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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256A TYR* 3.4 28.8 - - + +
258A GLY 2.9 25.0 + - - -
259A GLU 3.8 0.2 - - - -
260A LEU* 1.3 84.4 - - + +
262A LYS* 1.3 70.1 + - - +
263A SER* 4.8 4.3 - - - +
302A ASN* 5.7 1.1 - - - +
303A ASN 3.6 4.3 - - - +
304A VAL* 3.7 19.1 - - + -
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Residues in contact with LYS 262 (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* 3.7 29.6 - - + -
16A GLU* 4.8 19.8 + - - +
256A TYR 3.7 2.5 - - - +
257A ASN* 3.5 32.3 - - + +
258A GLY 4.0 6.7 - - - +
259A GLU 5.1 0.2 + - - -
260A LEU 4.6 4.5 - - - +
261A ILE* 1.3 79.0 - - - +
263A SER* 1.3 60.8 + - - +
302A ASN* 3.3 4.3 + - - +
303A ASN* 2.4 62.5 + - + +
305A ILE* 3.2 32.3 - - + +
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Residues in contact with SER 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A PHE* 3.9 5.0 - - - -
214A TRP* 6.0 2.0 - - - -
255A ARG* 3.6 4.4 - - - +
256A TYR* 3.0 45.5 + - - +
261A ILE* 5.1 3.1 - - - -
262A LYS* 1.3 73.7 - - - +
264A GLN* 1.3 64.1 + - - +
300A TRP* 3.5 12.6 + - - -
301A ALA 3.4 2.9 - - - -
302A ASN* 2.1 31.8 + - - +
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Residues in contact with GLN 264 (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* 3.8 40.4 + - - +
15A PHE* 3.9 15.3 - - + -
254A LEU 3.7 8.7 - - - +
255A ARG* 2.8 39.8 + - - +
263A SER* 1.3 76.7 + - - +
265A LEU* 1.3 62.2 + - - +
266A ILE* 3.9 17.3 - - + +
299A GLN* 3.9 12.0 + - - +
300A TRP* 2.8 25.3 - - - -
301A ALA* 2.9 32.3 + - + +
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Residues in contact with LEU 265 (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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253A GLY* 3.1 2.3 - - - -
254A LEU* 3.0 48.3 + - + +
264A GLN* 1.3 75.8 - - - +
266A ILE* 1.3 69.3 - - - +
267A THR* 6.0 1.8 - - - +
298A VAL* 4.7 12.8 - - + -
299A GLN 3.2 18.2 - - - +
300A TRP* 3.7 25.8 - - + +
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Residues in contact with ILE 266 (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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81A ASP 5.9 2.2 - - - +
83A VAL* 5.2 12.3 - - + -
217A PHE* 4.2 18.6 - - + -
219A ARG* 6.0 1.1 - - - +
251A ASP* 5.7 2.9 - - - +
252A ALA 3.8 4.5 - - - +
253A GLY* 4.4 0.4 - - - -
254A LEU 5.0 0.7 - - - +
255A ARG* 3.6 29.6 - - - +
264A GLN* 3.9 21.3 - - + +
265A LEU* 1.3 90.0 - - - +
267A THR* 1.3 81.0 + - - +
297A THR* 3.7 0.8 - - + +
298A VAL* 3.3 5.1 - - - +
299A GLN* 3.1 48.8 + - + +
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Residues in contact with THR 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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250A TRP 5.3 0.4 - - - +
251A ASP* 3.1 3.2 - - - +
252A ALA* 2.9 41.9 + - + +
265A LEU* 6.0 1.7 - - - +
266A ILE* 1.3 86.4 + - - +
268A SER* 1.3 76.7 + - - +
269A TYR* 5.1 1.6 - - + +
297A THR 3.2 3.8 - - - +
298A VAL* 3.6 21.0 - - + +
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Residues in contact with SER 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A VAL* 4.6 19.6 - - - +
249A SER* 4.9 0.2 - - - -
250A TRP 2.3 26.4 + - - -
251A ASP* 2.5 21.4 + - - -
266A ILE* 5.5 0.2 - - - -
267A THR* 1.3 84.6 - - - +
269A TYR* 1.3 66.0 + - - +
270A SER* 4.4 4.7 + - - -
295A GLN 3.8 0.3 - - - +
296A TYR* 3.6 3.3 - - - -
297A THR* 2.8 46.9 + - - +
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Residues in contact with TYR 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A GLN* 4.2 13.6 + - - -
249A SER 3.0 1.0 - - - -
250A TRP* 2.3 62.0 + + + +
267A THR* 5.1 1.5 - - + +
268A SER* 1.3 75.1 + - - +
270A SER* 1.3 71.5 + - - +
271A HIS* 3.4 30.7 + - + +
294A LYS* 3.6 26.6 + - + -
295A GLN 3.4 6.7 - - - +
296A TYR* 3.3 46.4 - + + -
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Residues in contact with SER 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A ASN* 3.8 30.0 - - - +
248A GLN 2.9 10.8 - - - -
249A SER* 3.0 24.5 + - - -
268A SER* 4.4 3.5 + - - -
269A TYR* 1.3 76.3 - - - +
271A HIS* 1.3 61.7 + - - +
272A SER 4.2 0.7 - - - -
293A MET 4.0 0.5 - - - +
294A LYS* 3.4 3.6 - - - -
295A GLN* 3.1 33.3 + - - +
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Residues in contact with HIS 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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246A TYR 4.4 0.5 - - - +
247A SER* 3.8 2.1 - - - -
248A GLN* 2.7 49.2 + - + +
269A TYR* 3.4 27.3 + - + +
270A SER* 1.3 74.8 - - - +
272A SER* 1.3 68.5 + - - +
273A LYS* 4.0 18.8 - - + +
292A GLU* 2.7 33.1 + - - +
293A MET 3.4 11.9 - - - -
294A LYS* 3.6 15.2 - - + -
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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
----------------------------------------------------------
86A ASN* 4.2 21.9 + - - +
87A LEU* 4.6 13.9 - - - +
90A VAL* 5.3 5.4 - - - +
245A LEU* 4.8 1.6 - - - -
246A TYR 3.4 10.3 - - - -
247A SER* 4.2 3.1 - - - -
270A SER 4.2 0.2 - - - -
271A HIS* 1.3 73.3 - - - +
273A LYS* 1.3 67.8 + - - +
274A ASP* 4.8 5.5 + - - +
291A ASP 4.8 1.4 + - - -
292A GLU* 3.2 24.6 - - - +
293A MET* 3.0 24.9 + - - +
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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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244A LYS 3.4 3.3 - - - +
245A LEU* 3.2 4.3 - - - +
246A TYR* 2.8 55.2 + - + +
271A HIS* 4.0 21.3 - - + +
272A SER* 1.3 79.4 - - - +
274A ASP* 1.3 59.9 + - - +
275A TYR* 3.3 32.4 + - + +
290A LEU* 4.1 9.2 - - + -
291A ASP 3.5 3.1 - - - -
292A GLU* 3.8 24.0 - - + +
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Residues in contact with ASP 274 (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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87A LEU* 6.6 0.2 - - + -
243A ARG* 3.2 42.6 + - - +
244A LYS 3.6 3.6 - - - +
245A LEU* 3.6 18.1 - - + +
272A SER* 5.1 4.9 - - - +
273A LYS* 1.3 73.3 - - - +
275A TYR* 1.3 61.6 + - - +
276A ASN* 4.4 4.3 - - - +
289A THR 3.5 3.6 - - - +
290A LEU* 3.4 2.6 - - - +
291A ASP* 2.8 51.4 + - + +
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Residues in contact with TYR 275 (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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243A ARG* 3.1 1.4 - - - +
244A LYS* 2.7 56.9 + - + +
246A TYR* 3.8 30.3 - + - -
273A LYS* 3.3 33.4 + - + +
274A ASP* 1.3 73.3 - - - +
276A ASN* 1.3 80.2 + - - +
277A TYR* 4.6 8.3 - + + -
288A ALA* 6.3 2.0 - - + -
289A THR 4.1 2.9 - - - -
290A LEU* 2.8 39.8 - - + +
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Residues in contact with ASN 276 (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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229A TYR* 3.1 29.9 + - - +
242A THR 3.5 10.1 - - - +
243A ARG* 3.1 22.3 + - - +
274A ASP* 4.1 6.5 + - - +
275A TYR* 1.3 93.5 - - - +
277A TYR* 1.3 65.5 + - - +
288A ALA* 3.1 25.0 - - - +
289A THR* 3.6 27.2 + - - +
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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