Contacts of the helix formed by residues 252 - 269 (chain A) in PDB entry 1NVT
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 GLY 252 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227A MET* 6.0 0.2 - - - -
228A ASP 2.7 15.0 + - - -
229A LEU* 3.3 14.6 - - - -
230A ILE 2.9 23.6 + - - -
231A TYR* 4.1 5.1 - - - +
251A ASN* 1.3 71.1 - - - +
253A LEU* 1.3 65.0 + - - +
254A GLY 3.0 1.7 + - - -
255A MET* 3.2 9.2 + - - -
256A LEU* 3.3 3.3 + - - +
288A NAP 2.9 20.5 + - - -
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Residues in contact with LEU 253 (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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231A TYR* 4.2 6.8 - - + +
234A LEU* 4.6 5.8 - - + -
251A ASN* 3.1 28.7 + - - +
252A GLY* 1.3 76.7 - - - +
254A GLY* 1.3 62.9 + - - +
256A LEU* 3.6 10.0 + - + +
257A ILE* 3.1 53.6 + - + +
278A LYS* 3.8 37.7 - - + +
281A ILE* 4.1 26.0 - - + -
282A ILE* 4.4 14.8 - - + +
285A ILE* 5.1 10.1 - - + -
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Residues in contact with GLY 254 (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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118A ALA* 3.6 18.4 - - - -
250A ILE* 5.4 3.6 - - - +
251A ASN* 3.4 9.1 + - - -
252A GLY 3.0 1.8 + - - -
253A LEU* 1.3 79.3 - - - +
255A MET* 1.3 61.9 + - - +
257A ILE* 5.0 1.1 - - - -
258A TYR* 2.8 41.4 + - - +
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Residues in contact with MET 255 (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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111A ASP* 3.1 41.7 - - + +
114A GLY* 4.1 4.4 - - - -
115A ALA* 3.7 26.2 - - + +
118A ALA* 3.5 11.8 - - + +
139A ALA* 5.0 6.5 - - - +
142A ALA* 5.1 1.3 - - + -
143A VAL* 4.4 9.6 - - + -
227A MET* 5.8 0.6 - - - -
229A LEU* 3.3 37.9 - - + -
251A ASN 4.8 0.6 + - - -
252A GLY* 3.2 3.8 + - - +
254A GLY* 1.3 74.0 - - - +
256A LEU* 1.3 56.9 + - - +
259A GLN* 2.7 39.8 + - + +
288A NAP 3.0 42.2 - - + +
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Residues in contact with LEU 256 (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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25A PHE* 4.6 16.2 - - + -
26A SER* 5.6 6.3 - - - +
29A MET* 4.0 16.9 - - + +
231A TYR* 4.0 33.9 - - + +
252A GLY 3.3 12.5 + - - +
253A LEU* 3.8 12.6 - - + +
255A MET* 1.3 75.7 - - - +
257A ILE* 1.3 64.4 + - + +
259A GLN* 3.3 30.9 + - - +
260A GLY 3.4 1.2 + - - -
281A ILE* 4.2 24.7 - - + -
285A ILE* 6.2 0.9 - - + -
288A NAP 2.7 22.7 + - - +
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Residues in contact with ILE 257 (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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29A MET* 4.1 16.3 - - - +
253A LEU* 3.1 48.6 + - + +
254A GLY* 4.1 2.2 - - - +
256A LEU* 1.3 75.3 - - + +
258A TYR* 1.3 65.0 + - + +
260A GLY* 3.0 6.4 + - - -
261A ALA* 2.8 22.9 + - - +
274A ILE* 4.0 26.5 - - + +
277A MET* 3.9 27.8 - - + +
278A LYS* 3.6 31.4 - - + +
281A ILE* 5.2 1.6 - - + -
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Residues in contact with TYR 258 (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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114A GLY* 3.8 12.3 - - - +
117A MET* 3.2 33.4 - - + -
118A ALA* 3.8 20.6 - - - -
121A GLU* 3.5 33.9 + - + +
254A GLY* 2.8 35.0 + - - +
257A ILE* 1.3 78.3 - - + +
259A GLN* 1.3 67.3 + - - +
261A ALA* 3.0 12.5 + - + +
262A VAL* 3.1 19.4 + - - +
274A ILE* 3.9 45.5 - - + +
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Residues in contact with GLN 259 (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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26A SER* 5.2 6.1 + - - -
29A MET* 5.0 2.8 - - - +
30A HIS* 5.7 0.2 - - - -
69A ASN* 4.0 18.0 + - - +
96A ASN* 3.4 15.3 + - - +
97A THR* 4.5 0.7 + - - -
110A THR* 2.8 43.8 + - - +
111A ASP* 3.2 29.4 - - - +
114A GLY* 3.9 3.7 - - - -
255A MET* 2.7 29.0 + - + +
256A LEU* 3.3 20.7 + - - +
258A TYR* 1.3 72.6 - - - +
260A GLY* 1.3 74.7 + - - +
262A VAL 3.7 0.2 + - - -
263A ALA* 3.6 6.2 + - - +
288A NAP 5.0 2.0 + - - +
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Residues in contact with GLY 260 (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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29A MET* 3.9 16.4 - - - -
30A HIS* 3.7 14.3 + - - -
256A LEU 3.4 1.0 + - - -
257A ILE 3.0 7.8 + - - -
259A GLN* 1.3 94.5 - - - +
261A ALA* 1.3 58.1 + - - +
263A ALA* 2.9 6.6 + - - +
264A PHE* 2.8 29.3 + - - +
277A MET* 4.9 1.1 - - - -
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Residues in contact with ALA 261 (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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117A MET* 4.5 7.4 - - + -
257A ILE 2.8 15.6 + - - +
258A TYR* 3.0 15.5 + - - +
260A GLY* 1.3 72.1 - - - +
262A VAL* 1.3 60.9 + - - +
264A PHE* 3.4 4.2 - - - +
265A LYS* 3.2 17.8 + - - +
272A PRO* 3.7 21.9 - - + +
274A ILE* 3.9 25.4 - - + -
277A MET* 3.9 8.4 - - + -
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Residues in contact with VAL 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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110A THR* 3.7 25.6 - - + -
113A ILE* 4.2 29.8 - - + -
114A GLY 5.0 0.9 - - - +
117A MET* 3.4 26.0 - - + -
258A TYR 3.1 15.1 + - - +
259A GLN 4.5 0.7 - - - +
261A ALA* 1.3 72.8 - - - +
263A ALA* 1.3 66.6 + - - +
265A LYS* 3.2 9.8 + - + +
266A ILE* 3.0 33.2 + - + +
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Residues in contact with ALA 263 (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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69A ASN* 3.9 4.3 - - - +
97A THR* 3.5 31.4 - - + +
110A THR* 4.1 1.9 - - - +
259A GLN* 3.6 9.1 + - - +
260A GLY* 2.9 11.8 + - - +
262A VAL* 1.3 77.0 - - - +
264A PHE* 1.3 64.5 + - - +
266A ILE* 2.9 15.2 + - - +
267A TRP* 2.9 43.3 + - + -
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Residues in contact with PHE 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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30A HIS* 3.9 21.1 - + + -
33A ALA* 3.4 41.5 - - + -
34A PHE* 3.2 39.3 - + - -
37A LYS* 5.1 0.9 - - + -
39A LEU* 4.0 5.8 - - + -
260A GLY 2.8 12.7 + - - +
261A ALA* 3.4 10.8 - - - +
263A ALA* 1.3 76.2 - - - +
265A LYS* 1.3 57.5 + - - +
267A TRP* 3.2 11.3 + - - +
268A THR* 2.7 46.9 + - - +
270A VAL* 3.3 28.0 - - + -
272A PRO* 3.5 24.5 - - + -
277A MET* 5.2 1.8 - - + -
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Residues in contact with LYS 265 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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261A ALA 3.2 9.4 + - - +
262A VAL* 3.3 13.5 - - + +
263A ALA 3.2 0.2 - - - -
264A PHE* 1.3 79.1 - - - +
266A ILE* 1.3 61.5 + - + +
269A GLY* 2.6 49.7 + - - -
270A VAL 3.5 18.8 + - - +
271A GLU* 3.7 40.6 + - + +
272A PRO* 5.1 0.2 - - + -
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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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97A THR* 4.1 13.5 - - + -
99A LYS* 3.1 32.2 + - + +
108A TYR* 3.7 61.9 - - + +
110A THR* 4.3 10.8 - - + -
262A VAL* 3.0 20.8 + - + +
263A ALA* 2.9 8.8 + - - +
265A LYS* 1.3 79.7 - - + +
267A TRP* 1.3 58.6 + - + +
269A GLY* 4.5 1.0 + - - -
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Residues in contact with TRP 267 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A ILE* 3.7 38.4 - - + -
30A HIS* 3.3 29.4 - + - -
34A PHE* 4.9 4.0 - + - -
41A TYR* 4.1 8.1 + - - -
43A TYR* 3.7 11.4 - + - -
66A VAL* 4.3 9.8 - - + +
67A GLY* 4.1 10.1 - - - -
68A PHE 3.3 26.3 + - - +
69A ASN* 3.3 34.1 - - - -
97A THR* 4.1 5.3 - - + +
98A ILE 2.9 27.1 + - - -
99A LYS* 3.0 30.5 + - + +
263A ALA* 2.9 34.2 + - + -
264A PHE* 3.7 9.9 - - - +
266A ILE* 1.3 79.5 - - + +
268A THR* 1.3 63.5 + - + +
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Residues in contact with THR 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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34A PHE* 3.9 16.8 - - + -
39A LEU* 3.6 23.0 - - + +
41A TYR* 3.6 39.3 + - + -
264A PHE* 2.7 23.6 + - + +
267A TRP* 1.3 81.2 - - + +
269A GLY* 1.3 60.0 + - - +
270A VAL* 3.1 29.5 + - - +
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Residues in contact with GLY 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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265A LYS* 2.6 40.7 + - - -
266A ILE 4.5 1.3 + - - -
267A TRP 3.7 0.8 - - - -
268A THR* 1.3 73.5 - - - +
270A VAL* 1.3 61.2 + - - +
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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