Contacts of the helix formed by residues 293 - 305 (chain A) in PDB entry 2NVT
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 GLU 293 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88A LYS* 3.9 38.8 + - - +
90A VAL* 5.2 2.4 - - - +
180A LYS* 4.2 5.2 - - - +
276A LEU* 3.1 26.5 - - - +
280A GLU* 4.7 0.5 - - - +
289A ILE* 3.2 24.3 - - + +
290A GLU* 2.7 42.3 + - - +
292A ALA* 1.3 78.1 - - - +
294A SER* 1.3 57.5 + - - +
296A LEU* 3.2 8.1 + - - +
297A GLN* 3.1 22.2 + - - +
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Residues in contact with SER 294 (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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179A LEU* 4.9 2.8 - - - +
180A LYS* 4.1 22.0 + - - +
290A GLU 3.4 11.5 + - - -
291A GLU* 4.4 6.4 - - - -
293A GLU* 1.3 73.9 - - - +
295A LEU* 1.3 51.3 + - - +
296A LEU 3.0 5.6 - - - -
297A GLN* 3.1 16.8 + - - +
298A PHE* 2.6 33.8 + - - +
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Residues in contact with LEU 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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272A ALA* 3.5 16.7 - - + +
291A GLU 3.6 24.0 - - - +
292A ALA* 3.8 8.4 + - - +
293A GLU 3.2 1.2 - - - -
294A SER* 1.3 76.7 + - - +
296A LEU* 1.3 55.8 + - - +
298A PHE* 3.3 24.6 - - + +
299A HIS* 3.9 28.6 - - + +
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Residues in contact with LEU 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A LEU* 3.9 18.8 - - + -
87A ALA* 5.5 1.3 - - + -
88A LYS 5.6 0.4 - - - +
90A VAL* 3.8 19.7 - - + -
269A ILE* 4.0 6.7 - - - +
272A ALA* 3.3 42.4 - - + +
273A ASN* 3.4 22.7 - - + +
276A LEU* 4.9 12.3 - - + -
292A ALA 3.6 8.9 + - - +
293A GLU 3.2 7.7 + - - +
294A SER 3.0 0.4 - - - -
295A LEU* 1.3 76.7 - - - +
297A GLN* 1.3 70.1 + - - +
298A PHE 3.7 2.2 - - - -
299A HIS* 4.1 2.9 - - - +
300A VAL* 3.3 25.7 + - + +
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Residues in contact with GLN 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A VAL* 3.2 25.9 - - + +
91A PHE* 2.9 57.4 + - - +
179A LEU* 3.3 33.6 - - + +
180A LYS* 5.9 4.9 - - + -
204A THR* 4.4 5.2 + - - -
293A GLU 3.1 8.8 + - - +
294A SER* 3.1 20.3 + - - +
296A LEU* 1.3 74.6 - - - +
298A PHE* 1.3 50.3 + - - +
300A VAL* 2.7 12.0 + - - +
301A ALA* 2.5 39.0 + - - +
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Residues in contact with PHE 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A LEU* 3.4 20.8 - - + +
294A SER 2.6 26.6 + - - +
295A LEU* 3.3 24.7 - - + +
296A LEU 3.8 1.3 - - - -
297A GLN* 1.3 77.6 - - - +
299A HIS* 1.3 75.1 + + - +
301A ALA* 3.8 8.3 - - + -
302A THR* 3.4 24.7 - - + +
308A ILE* 5.9 2.2 - - + -
311A GLN 6.0 2.0 - - - -
312A PRO 5.4 0.2 - - - -
313A GLN* 3.8 22.0 - - - -
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Residues in contact with HIS 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A LYS* 3.4 26.7 - - - +
268A ASP* 2.7 42.0 + - + +
269A ILE* 3.1 20.4 - - + +
272A ALA* 4.5 3.9 - - + +
295A LEU* 3.9 32.2 + - + +
296A LEU* 3.9 5.7 - - - +
297A GLN 3.1 0.9 - - - -
298A PHE* 1.3 88.5 + + - +
300A VAL* 1.3 53.1 + - - +
301A ALA 2.5 18.6 + - - -
302A THR* 2.7 15.6 + - - -
303A TYR 2.9 9.6 + - - -
313A GLN* 4.4 1.3 - - - -
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Residues in contact with VAL 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A LEU* 4.6 6.7 - - + -
90A VAL* 3.9 24.2 - - + -
91A PHE 4.9 2.0 - - - +
236A LEU* 5.2 3.4 - - + -
239A LEU* 3.7 24.9 - - + -
269A ILE* 3.2 32.9 - - + +
296A LEU* 3.3 22.4 + - + +
297A GLN* 2.7 12.6 + - - +
299A HIS* 1.3 71.9 - - - +
301A ALA* 1.3 63.7 + - - +
303A TYR* 3.6 10.7 - - - +
304A MET* 3.0 29.6 - - + +
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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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91A PHE 5.3 0.2 - - - -
93A VAL* 3.6 33.8 - - + +
179A LEU* 3.8 16.8 - - + -
297A GLN* 2.5 27.2 + - - +
298A PHE* 3.8 13.0 - - + +
299A HIS 2.5 2.2 + - - -
300A VAL* 1.3 73.0 - - - +
302A THR* 1.3 53.1 - - - +
303A TYR 3.1 0.2 - - - -
304A MET* 2.8 32.7 + - - +
305A ASP 3.4 5.9 + - - -
308A ILE* 5.1 0.9 - - + -
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Residues in contact with THR 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A VAL* 4.6 0.2 - - - +
265A LYS* 3.2 27.3 - - - +
298A PHE* 3.4 25.4 - - + -
299A HIS 2.7 10.9 + - - +
301A ALA* 1.3 73.6 - - - +
303A TYR* 1.3 59.3 + - - +
304A MET 3.2 0.4 - - - -
305A ASP 2.9 16.7 + - - +
306A ASN* 3.1 30.7 + - - +
308A ILE* 4.8 7.7 - - - +
311A GLN 5.6 0.3 + - - -
312A PRO 4.6 0.3 + - - -
313A GLN* 3.3 18.8 + - - +
324A SER* 3.3 15.4 - - - -
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Residues in contact with TYR 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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239A LEU* 4.5 15.3 - - + -
240A PRO 4.5 1.4 + - - -
242A PRO* 3.8 28.8 - - - +
262A LEU* 4.4 13.8 - - + +
265A LYS* 3.5 39.9 - - + +
266A LEU* 3.7 31.1 - - + +
269A ILE* 4.8 4.3 - - + -
299A HIS 2.9 8.1 + - - +
300A VAL* 3.6 18.6 - - - +
302A THR* 1.3 76.9 - - - +
304A MET* 1.3 83.1 + - + +
324A SER* 3.2 16.7 - - - -
325A ILE* 3.5 23.9 + - + +
1209B ALA* 4.1 19.4 + - - +
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Residues in contact with MET 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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92A HIS* 3.7 19.3 - - + +
93A VAL* 3.8 16.6 - - + -
236A LEU* 4.1 16.8 - - + -
239A LEU* 5.0 6.3 - - + -
300A VAL* 3.0 40.8 - - + +
301A ALA* 2.8 10.9 + - - +
303A TYR* 1.3 98.3 - - + +
305A ASP* 1.3 60.7 + - + +
324A SER* 3.8 1.6 - - - -
325A ILE* 4.5 1.1 - - - -
326A ARG* 2.9 29.8 + - - +
1410A PHE* 5.5 1.9 - - + -
1209B ALA 4.9 0.7 - - - +
1210B MET* 3.3 52.5 - - + +
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Residues in contact with ASP 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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93A VAL* 4.5 19.7 - - + +
301A ALA 3.4 2.5 + - - +
302A THR* 2.9 22.7 + - - -
304A MET* 1.3 82.3 - - - +
306A ASN* 1.3 58.7 + - - +
307A ASP* 3.0 41.3 + - - +
308A ILE* 4.0 11.9 - - - +
324A SER* 3.4 2.5 - - - -
326A ARG* 3.3 36.1 + - + +
1410A PHE* 5.8 5.8 - - + -
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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