Contacts of the helix formed by residues 256 - 274 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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228A GLY 3.1 14.1 - - - +
229A TYR 4.2 0.2 - - - +
230A ARG* 3.7 10.2 - - + -
256A PRO* 3.3 28.7 - - + -
259A LEU* 4.0 11.9 - - + -
85B SER* 5.1 2.5 - - - +
229B TYR 3.8 8.5 - - - +
230B ARG* 3.7 15.0 - - + +
231B VAL* 4.4 2.9 - - + -
255B ALA* 1.3 86.3 - - + -
257B THR* 1.3 60.8 + - - +
258B PRO 3.5 0.7 - - - -
259B LEU* 3.3 20.7 + - + +
260B GLN* 2.9 29.5 + - - +
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Residues in contact with THR 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A GLY* 3.0 14.6 + - - -
54B GLN* 3.1 33.9 - - + +
56B GLN 2.4 30.4 + - - +
58B ALA* 3.6 17.7 + - + +
63B LEU* 3.8 15.6 - - + +
255B ALA 3.2 5.1 + - - -
256B PRO* 1.3 69.8 - - - +
258B PRO* 1.3 60.3 - - - +
260B GLN* 3.1 9.6 + - - +
261B ALA* 2.8 30.2 + - - +
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Residues in contact with PRO 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A GLY 4.0 7.0 - - - +
229A TYR* 3.9 26.2 - - + -
259A LEU* 4.7 8.7 - - + -
47B VAL* 4.3 7.1 - - + +
50B ALA* 3.9 20.7 - - + +
51B LEU* 4.0 22.4 - - + -
54B GLN 3.2 18.6 - - - +
55B ASP* 4.7 2.0 - - - +
256B PRO 3.7 2.0 - - - -
257B THR* 1.3 90.5 - - - +
259B LEU* 1.3 68.7 + - + +
261B ALA* 3.3 2.1 + - + +
262B GLY* 2.9 26.2 + - - -
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Residues in contact with LEU 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A LEU* 5.2 0.9 - - + -
256A PRO* 3.8 17.3 - - + -
258A PRO* 4.8 3.6 - - + -
259A LEU* 4.1 20.4 - - + -
47B VAL* 3.8 31.1 - - + +
229B TYR* 3.4 49.1 - - + +
231B VAL* 3.9 15.3 - - + -
256B PRO* 3.3 23.3 + - + +
257B THR 3.3 0.4 - - - -
258B PRO* 1.3 76.6 - - + +
260B GLN* 1.3 61.5 + - - +
262B GLY* 3.3 0.7 + - - -
263B VAL* 2.8 35.6 + - - +
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Residues in contact with GLN 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B ALA* 3.7 19.0 - - - +
62B GLY* 3.6 10.0 - - - -
63B LEU* 3.1 34.2 + - + +
66B LEU* 3.5 30.6 - - + +
83B VAL* 3.6 4.5 - - + +
231B VAL* 4.1 7.4 - - + +
254B SER* 4.6 0.6 - - - -
255B ALA* 2.9 49.4 + - + +
256B PRO 2.9 17.2 + - - +
257B THR 3.5 6.1 - - - +
259B LEU* 1.3 74.8 - - - +
261B ALA* 1.3 64.0 + - - +
263B VAL* 4.6 0.7 - - - -
264B ALA* 3.0 24.8 + - - +
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Residues in contact with ALA 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B ALA 5.3 0.4 - - - -
50B ALA* 3.9 14.1 - - + -
54B GLN* 3.6 26.0 - - - +
63B LEU* 3.7 13.4 - - + +
65B ALA* 6.2 1.1 - - - -
257B THR 2.8 16.5 + - - +
258B PRO* 3.5 5.6 - - + +
260B GLN* 1.3 78.8 - - - +
262B GLY* 1.3 61.2 + - - +
264B ALA* 3.2 16.8 + - - +
265B GLU* 3.4 13.1 + - - +
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Residues in contact with GLY 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B LEU* 3.6 8.7 - - - +
46B ALA* 3.8 33.8 + - - +
47B VAL* 4.1 7.0 - - - -
258B PRO 2.9 18.5 + - - -
259B LEU 3.7 2.0 - - - -
261B ALA* 1.3 72.7 - - - +
263B VAL* 1.3 58.6 + - - +
265B GLU 3.3 1.6 + - - -
266B ALA* 3.0 27.5 + - - +
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Residues in contact with VAL 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B LEU* 4.0 19.3 - - + +
66B LEU* 4.3 8.5 - - + -
220B ALA* 3.7 33.0 - - + -
224B LEU* 4.4 5.4 - - + -
229B TYR* 4.6 12.6 - - + -
231B VAL* 4.5 12.3 - - + -
233B TRP* 4.9 1.6 - - + -
259B LEU 2.8 26.8 + - - +
260B GLN* 3.9 4.9 - - - +
262B GLY* 1.3 69.4 - - - +
264B ALA* 1.3 58.2 + - - +
266B ALA* 4.0 0.7 - - - -
267B LEU* 2.7 56.0 + - + +
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Residues in contact with ALA 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B LEU* 6.1 0.2 - - + -
65B ALA* 4.0 15.7 - - + +
66B LEU* 3.8 35.7 - - - +
69B ALA* 3.8 15.9 - - - +
260B GLN 3.0 13.0 + - - +
261B ALA* 3.3 14.1 - - - +
262B GLY 3.2 0.2 - - - -
263B VAL* 1.3 79.0 - - - +
265B GLU* 1.3 63.0 + - + +
267B LEU 3.7 4.5 + - - -
268B LYS* 3.7 10.7 + - - +
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Residues in contact with GLU 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B ALA* 3.6 12.1 - - + +
49B ARG* 2.4 43.9 + - - +
261B ALA 3.4 10.5 + - - +
262B GLY 3.3 6.5 + - - +
264B ALA* 1.3 75.6 - - + +
266B ALA* 1.3 62.0 + - - +
268B LYS* 3.2 8.3 + - - +
269B LEU* 2.9 41.7 + - + +
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Residues in contact with ALA 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B PHE* 3.7 27.5 - - + +
43B LEU* 3.4 24.7 - - + -
46B ALA* 5.0 0.2 - - - +
224B LEU* 3.9 13.2 - - + -
262B GLY 3.0 17.8 + - - +
263B VAL 3.2 4.0 + - - +
265B GLU* 1.3 75.0 - - - +
267B LEU* 1.3 60.3 + - - +
269B LEU* 4.4 1.1 - - - -
270B ALA* 2.8 33.9 + - - +
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Residues in contact with LEU 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B LEU* 3.7 24.2 - - + -
69B ALA* 4.2 9.0 - - + -
70B LEU* 3.7 28.7 - - + +
73B GLU* 3.7 7.8 - - - +
220B ALA* 5.6 0.2 - - + -
223B ARG* 4.0 13.0 - - + +
224B LEU* 4.4 9.6 - - + -
233B TRP* 4.4 12.6 - - + -
263B VAL* 2.7 33.2 + - + +
264B ALA 4.0 3.1 - - - +
265B GLU 3.3 0.4 - - - -
266B ALA* 1.3 73.7 - - - +
268B LYS* 1.3 75.6 + - - +
270B ALA* 3.6 13.7 - - - +
271B ARG* 3.6 14.7 + - - +
276B TYR* 3.8 18.6 - - - +
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Residues in contact with LYS 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B ALA* 3.3 33.1 + - + -
72B GLU* 4.1 20.9 + - - +
73B GLU* 3.3 36.2 + - - +
264B ALA 3.7 11.2 + - - +
265B GLU* 3.2 9.0 + - - +
266B ALA 3.1 0.4 - - - -
267B LEU* 1.3 83.3 + - - +
269B LEU* 1.3 68.8 + - + +
270B ALA 3.1 0.5 + - - -
271B ARG* 3.3 4.5 + - - +
272B ARG* 2.9 50.6 + - - +
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Residues in contact with LEU 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B PHE* 3.9 24.9 - - + +
49B ARG* 5.3 5.4 - - - +
265B GLU* 2.9 43.6 + - + +
266B ALA* 3.9 4.5 - - - +
268B LYS* 1.3 77.8 - - + +
270B ALA* 1.3 58.0 + - - +
272B ARG* 3.3 9.7 + - + +
273B GLU* 2.8 57.9 + - + +
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Residues in contact with ALA 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B PHE* 4.1 10.2 - - + -
224B LEU* 4.6 1.8 - - + -
266B ALA 2.8 23.0 + - - +
267B LEU 3.6 6.3 - - - +
268B LYS 3.1 0.2 - - - -
269B LEU* 1.3 74.8 - - - +
271B ARG* 1.3 66.6 + - - +
274B GLY* 3.2 1.4 + - - -
275B PHE* 3.1 41.9 + - + -
276B TYR* 3.8 31.6 + - + +
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Residues in contact with ARG 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B GLU* 3.1 45.1 + - + +
196B GLU* 3.2 33.3 + - - -
202B ARG* 4.2 13.1 - - - +
205B ARG* 5.7 1.4 - - - +
223B ARG* 3.6 13.5 - - - +
267B LEU 3.7 13.0 - - - +
268B LYS* 3.3 5.3 + - - +
270B ALA* 1.3 78.6 - - - +
272B ARG* 1.3 94.4 + - - +
274B GLY* 3.1 10.4 + - - -
276B TYR* 3.7 16.0 - - - -
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Residues in contact with ARG 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B GLU* 5.1 3.2 + - - -
268B LYS* 2.9 66.8 + - - +
269B LEU* 3.3 16.1 + - + +
271B ARG* 1.3 101.1 - - - +
273B GLU* 1.3 60.8 + - + +
274B GLY* 3.0 5.7 + - - -
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Residues in contact with GLU 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B PHE* 3.8 26.7 - - + +
269B LEU* 2.8 50.8 + - + +
270B ALA 4.4 1.3 - - - +
272B ARG* 1.3 74.1 - - + +
274B GLY* 1.3 62.8 + - - +
275B PHE* 3.2 7.4 + - + +
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Residues in contact with GLY 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270B ALA 3.2 0.2 + - - -
271B ARG 3.1 11.2 + - - -
272B ARG 3.0 8.2 + - - -
273B GLU* 1.3 77.2 - - - +
275B PHE* 1.3 67.1 + - - +
276B TYR 3.5 2.2 - - - -
277B GLU* 3.0 30.0 - - - +
278B ALA* 3.3 7.1 + - - +
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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