Contacts of the helix formed by residues 256 - 273 (chain A) in PDB entry 1V2E
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 PRO 256 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A SER* 5.1 2.2 - - - +
229A TYR 3.9 6.7 - - - +
230A ARG* 3.7 15.0 - - + +
231A VAL* 4.5 1.8 - - + -
255A ALA* 1.4 85.8 - - + +
257A THR* 1.3 59.8 + - - +
258A PRO* 3.6 0.7 - - + -
259A LEU* 3.7 20.8 - - + -
260A GLN* 2.8 30.3 + - - +
228B GLY 3.0 12.1 - - - +
229B TYR 4.0 0.7 - - - +
230B ARG* 3.6 11.4 - - + -
256B PRO* 3.3 31.6 - - + -
259B LEU* 3.8 14.6 - - + -
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Residues in contact with THR 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A GLN* 3.2 27.8 - - + +
56A GLN 2.6 29.0 + - - +
57A TYR 3.8 1.9 - - - +
58A ALA* 3.7 13.0 + - + +
63A LEU* 4.0 27.1 - - + +
255A ALA 3.2 3.5 + - - -
256A PRO* 1.3 68.9 - - - +
258A PRO* 1.3 68.5 - - - +
260A GLN* 2.9 8.9 + - - +
261A ALA* 2.7 28.6 + - - +
228B GLY* 3.1 11.1 + - - -
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Residues in contact with PRO 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A VAL* 4.2 6.2 - - + +
50A ALA* 3.7 23.1 - - + +
51A LEU* 3.7 25.4 - - + -
54A GLN 3.2 19.9 - - - +
55A ASP* 4.4 1.6 - - - +
256A PRO 3.8 1.1 - - - -
257A THR* 1.3 91.1 - - - +
259A LEU* 1.3 70.5 + - + +
261A ALA* 3.4 2.7 + - + +
262A GLY* 3.0 22.7 + - - -
228B GLY 4.2 0.9 - - - +
229B TYR* 3.8 33.7 - - + -
259B LEU* 4.8 3.6 - - + -
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Residues in contact with LEU 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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47A VAL* 4.3 20.7 - - + +
51A LEU* 5.8 0.2 - - + -
229A TYR* 3.2 56.8 - - + +
231A VAL* 4.1 10.5 - - + -
256A PRO* 3.4 19.9 + - + +
257A THR 3.1 0.6 - - - -
258A PRO* 1.3 91.9 - - + +
260A GLN* 1.3 66.0 + - - +
262A GLY 4.4 0.2 - - - +
263A VAL* 3.0 32.3 + - - +
47B VAL* 6.3 0.2 - - + -
51B LEU* 5.7 0.4 - - + -
256B PRO* 4.0 13.2 - - + -
258B PRO* 4.7 7.6 - - + -
259B LEU* 4.1 17.9 - - + -
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Residues in contact with GLN 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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58A ALA* 3.8 17.2 - - - +
62A GLY* 3.4 9.5 - - - -
63A LEU* 2.7 40.4 + - + +
66A LEU* 3.6 29.6 - - + +
83A VAL* 4.1 5.8 - - + +
231A VAL* 4.6 5.4 - - + +
254A SER* 4.5 0.8 - - - -
255A ALA* 3.0 46.9 + - + +
256A PRO 2.8 21.1 + - - +
257A THR 2.9 5.1 + - - +
259A LEU* 1.3 75.0 - - - +
261A ALA* 1.3 62.1 + - - +
263A VAL* 4.7 1.6 - - - -
264A ALA* 3.0 24.3 + - - +
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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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46A ALA 4.9 0.4 - - - -
50A ALA* 3.6 19.7 - - + -
54A GLN* 3.7 27.1 - - - +
63A LEU* 4.0 8.2 - - + +
65A ALA* 6.1 0.7 - - - -
257A THR 2.7 15.2 + - - +
258A PRO* 3.5 6.3 - - + +
260A GLN* 1.3 78.1 - - - +
262A GLY* 1.3 63.5 + - - +
264A ALA* 3.1 20.9 - - - +
265A GLU* 3.4 12.0 + - - +
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Residues in contact with GLY 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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43A LEU* 3.9 6.3 - - - -
46A ALA* 3.6 35.0 + - - +
47A VAL* 4.0 7.4 - - - -
258A PRO 3.0 14.8 + - - -
259A LEU 3.9 1.1 - - - -
260A GLN 3.4 0.2 - - - -
261A ALA* 1.3 73.9 - - - +
263A VAL* 1.3 65.2 + - - +
264A ALA 3.3 0.2 + - - -
265A GLU 3.3 1.6 + - - -
266A ALA* 2.9 23.6 + - - +
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Residues in contact with VAL 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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43A LEU* 4.3 13.7 - - + -
66A LEU* 4.5 7.4 - - + -
220A ALA* 3.8 32.1 - - + -
224A LEU* 4.3 5.6 - - + -
229A TYR* 4.7 10.1 - - + -
231A VAL* 4.5 15.5 - - + -
233A TRP* 5.1 0.9 - - + -
259A LEU 3.0 23.7 + - - +
260A GLN 4.0 3.1 - - - +
262A GLY* 1.3 75.7 - - - +
264A ALA* 1.3 57.4 + - - +
266A ALA* 4.1 6.5 - - - -
267A LEU* 2.8 56.6 + - + +
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Residues in contact with ALA 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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65A ALA* 4.0 17.0 - - + +
66A LEU* 3.9 32.1 - - - +
69A ALA* 4.0 9.7 - - + +
260A GLN 3.0 15.2 + - - +
261A ALA* 3.1 13.7 - - - +
263A VAL* 1.3 78.9 - - - +
265A GLU* 1.3 63.6 + - + +
267A LEU 3.6 4.3 + - - -
268A LYS* 3.8 15.8 + - - +
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Residues in contact with GLU 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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46A ALA* 3.4 18.4 - - + +
49A ARG* 2.6 44.6 + - - +
261A ALA 3.9 11.2 - - - +
262A GLY 3.3 5.7 + - - +
263A VAL 3.3 0.4 - - - -
264A ALA* 1.3 76.3 - - + +
266A ALA* 1.3 64.8 + - - +
268A LYS* 3.2 8.1 + - - +
269A LEU* 3.0 36.2 + - + +
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Residues in contact with ALA 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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42A PHE* 3.6 29.1 - - + -
43A LEU* 3.9 23.6 - - + -
46A ALA* 4.7 0.2 - - - +
224A LEU* 4.0 12.7 - - + +
262A GLY 2.9 17.4 + - - +
263A VAL 3.6 3.8 - - - +
265A GLU* 1.3 78.6 - - - +
267A LEU* 1.3 57.4 + - - +
269A LEU* 4.4 1.8 - - - -
270A ALA* 2.9 32.6 + - - +
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Residues in contact with LEU 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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66A LEU* 3.8 12.1 - - + -
69A ALA* 4.7 10.1 - - + +
70A LEU* 3.4 32.5 - - + +
73A GLU* 3.6 10.1 - - - +
220A ALA* 5.6 0.4 - - - -
223A ARG* 3.9 16.4 - - + +
224A LEU* 4.0 16.4 - - + -
233A TRP* 4.5 9.6 - - + -
263A VAL* 2.8 38.9 + - + +
264A ALA 4.0 4.0 - - - +
265A GLU 3.3 0.4 + - - -
266A ALA* 1.3 73.9 - - - +
268A LYS* 1.3 62.5 + - - +
270A ALA* 3.7 4.4 - - - +
271A ARG* 3.3 27.4 + - - +
276A TYR* 3.7 19.7 + - - +
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Residues in contact with LYS 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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69A ALA* 4.2 23.1 + - + +
72A GLU* 3.0 52.5 + - - +
73A GLU* 4.7 11.5 - - - +
264A ALA 3.8 11.4 + - - +
265A GLU* 3.2 8.5 + - - +
267A LEU* 1.3 77.9 - - - +
269A LEU* 1.3 74.2 + - + +
271A ARG* 3.1 5.9 + - - +
272A ARG* 2.9 52.4 + - + +
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Residues in contact with LEU 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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42A PHE* 4.2 29.2 - - + +
49A ARG* 5.8 2.2 - - - +
265A GLU* 3.0 39.3 + - + +
266A ALA* 3.9 4.3 - - - +
268A LYS* 1.3 79.6 - - + +
270A ALA* 1.3 55.6 + - - +
272A ARG* 2.6 33.1 + - + +
273A GLU* 2.9 35.0 + - - +
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Residues in contact with ALA 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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42A PHE* 4.1 15.6 - - + -
224A LEU* 4.4 2.7 - - + -
266A ALA 2.9 20.2 + - - +
267A LEU 3.7 5.8 - - - +
269A LEU* 1.3 76.6 - - - +
271A ARG* 1.3 60.9 + - - +
273A GLU* 4.8 0.7 - - - +
274A GLY* 3.5 3.5 + - - -
275A PHE* 3.3 41.8 + - + +
276A TYR* 4.0 30.5 + - + +
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Residues in contact with ARG 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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73A GLU* 3.3 45.8 + - + +
196A GLU* 2.4 41.6 + - - +
202A ARG* 3.6 14.8 - - - +
205A ARG* 5.1 2.8 - - - +
223A ARG* 4.1 4.4 - - - +
267A LEU 3.3 14.7 + - - +
268A LYS* 3.1 6.8 + - - +
269A LEU 3.0 0.8 - - - -
270A ALA* 1.3 78.0 - - - +
272A ARG* 1.3 85.9 + - - +
274A GLY* 4.3 4.5 + - - -
276A TYR* 3.5 14.5 - - + -
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Residues in contact with ARG 272 (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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72A GLU* 4.3 5.3 + - - -
268A LYS* 2.9 58.9 + - + +
269A LEU* 2.6 21.2 + - + +
271A ARG* 1.3 99.3 - - - +
273A GLU* 1.3 61.8 + - + +
274A GLY 3.4 1.6 + - - -
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Residues in contact with GLU 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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42A PHE* 4.3 23.5 - - + +
269A LEU* 2.9 35.8 + - - +
270A ALA* 5.2 0.2 - - - -
272A ARG* 1.3 79.4 - - + +
274A GLY* 1.3 63.4 + - - +
275A PHE* 3.4 8.0 + - + +
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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