Contacts of the helix formed by residues 244 - 265 (chain A) in PDB entry 1OV1
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 GLN 244 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141A LYS* 2.9 33.5 + - - +
241A ALA 5.5 1.6 + - - -
242A THR* 5.0 17.2 - - - +
243A THR* 1.3 84.8 - - - +
245A LYS* 1.3 60.4 + - - +
246A ALA* 3.0 4.9 - - + +
247A GLU* 3.0 22.1 + - + +
248A LYS* 2.8 23.0 + - - +
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Residues in contact with LYS 245 (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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67A LYS 3.1 26.3 + - - -
68A LEU* 4.6 2.4 - - - +
69A ARG* 5.4 2.2 - - - +
70A THR* 4.2 19.2 - - + +
243A THR* 3.3 12.8 + - + +
244A GLN* 1.3 74.6 - - - +
246A ALA* 1.3 66.6 + - + +
248A LYS* 3.4 10.0 + - - +
249A GLU* 2.8 59.9 + - + +
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Residues in contact with ALA 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A THR* 5.1 12.3 - - + -
72A LEU* 4.5 1.6 - - - +
138A VAL* 6.2 0.4 - - + -
147A ARG* 4.9 12.3 - - - +
244A GLN* 3.0 2.6 - - + -
245A LYS* 1.3 91.3 - - + +
247A GLU* 1.3 66.0 + - + +
249A GLU* 3.3 5.2 + - - +
250A VAL* 2.8 37.3 + - + +
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Residues in contact with GLU 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A VAL* 3.1 44.8 - - - +
139A VAL* 4.5 5.0 - - - +
141A LYS* 3.3 17.1 + - - +
147A ARG* 3.7 15.9 + - - -
226A LEU* 5.4 3.3 - - - +
244A GLN* 3.0 40.2 + - + +
246A ALA* 1.3 80.3 - - + +
248A LYS* 1.3 56.0 + - + +
250A VAL* 3.7 5.3 - - - +
251A THR* 2.7 36.9 + - - -
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Residues in contact with LYS 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A THR* 3.6 19.9 + - - -
243A THR* 3.1 33.6 + - + +
244A GLN 2.8 9.3 + - - +
245A LYS* 3.7 9.4 - - - +
247A GLU* 1.3 79.2 - - + +
249A GLU* 1.3 61.7 + - + +
251A THR* 3.6 7.0 + - - -
252A ARG* 3.4 19.6 + - - +
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Residues in contact with GLU 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A LEU* 3.3 31.7 - - - +
70A THR* 4.4 5.0 + - - +
72A LEU* 4.0 12.0 - - + +
245A LYS* 2.8 57.6 + - + +
246A ALA* 3.9 4.9 - - - +
248A LYS* 1.3 75.9 - - + +
250A VAL* 1.3 55.9 + - - +
251A THR 3.2 0.2 - - - -
252A ARG* 3.2 30.1 + - - +
253A MET* 2.8 35.3 + - - +
310A ASN* 5.1 0.2 + - - -
312A GLN* 4.2 17.2 + - - +
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Residues in contact with VAL 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A LEU* 3.4 23.3 - - + -
134A GLU* 4.1 10.8 - - - +
135A ARG* 3.7 23.1 - - + +
138A VAL* 3.4 41.1 - - + -
139A VAL* 5.2 1.6 - - + -
246A ALA* 2.8 25.0 + - + +
247A GLU* 3.7 10.1 - - - +
248A LYS 3.3 0.2 - - - -
249A GLU* 1.3 78.2 - - - +
251A THR* 1.3 60.5 + - - +
253A MET* 3.2 3.0 + - - +
254A VAL* 2.9 28.9 + - - +
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Residues in contact with THR 251 (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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135A ARG* 6.2 1.3 - - - +
247A GLU* 2.7 18.6 + - - +
248A LYS* 3.7 7.6 - - - -
250A VAL* 1.3 80.5 - - - +
252A ARG* 1.3 58.1 + - - +
254A VAL* 3.0 29.9 - - + +
255A ILE* 3.3 20.8 - - + +
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Residues in contact with ARG 252 (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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248A LYS 3.4 11.5 + - - +
249A GLU* 3.2 30.3 + - - +
250A VAL 3.2 0.2 - - - -
251A THR* 1.3 77.5 - - - +
253A MET* 1.3 64.8 + - - +
255A ILE* 3.2 25.6 + - + +
256A ILE* 3.3 25.1 + - + +
309A MET* 3.3 35.4 + - + +
310A ASN* 3.2 34.1 + - - +
311A LYS 5.1 0.2 - - - +
312A GLN* 2.9 30.8 + - - +
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Residues in contact with MET 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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72A LEU* 3.8 37.5 - - + +
75A ILE* 4.0 12.1 - - + -
76A LEU* 3.5 46.4 - - + -
128A LEU* 6.4 0.7 - - + -
131A LEU* 3.8 30.3 - - + -
249A GLU 2.8 17.4 + - - +
250A VAL* 3.4 9.6 - - - +
252A ARG* 1.3 75.0 - - - +
254A VAL* 1.3 60.6 + - - +
255A ILE 3.0 1.8 - - - -
256A ILE* 3.0 15.2 + - + +
257A MET* 2.9 26.5 + - - +
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Residues in contact with VAL 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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131A LEU* 5.4 1.6 - - + -
135A ARG* 3.6 47.8 - - + +
219A ILE* 4.6 7.6 - - + -
222A CYS* 6.2 0.2 - - - -
250A VAL 2.9 12.4 + - - +
251A THR* 3.0 30.1 - - + +
253A MET* 1.3 77.3 - - - +
255A ILE* 1.3 66.6 + - + +
257A MET* 3.4 33.2 + - + +
258A VAL* 3.3 23.2 + - - +
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Residues in contact with ILE 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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251A THR* 3.3 25.8 - - + +
252A ARG* 3.2 21.0 + - + +
253A MET 3.0 0.4 - - - -
254A VAL* 1.3 87.8 - - + +
256A ILE* 1.3 59.7 + - - +
258A VAL* 3.7 11.4 + - - +
259A ILE* 3.4 18.0 + - + +
309A MET* 4.4 23.8 - - + -
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Residues in contact with ILE 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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76A LEU* 4.3 36.6 - - + -
252A ARG* 3.3 26.9 - - + +
253A MET* 3.0 14.2 + - + +
255A ILE* 1.3 74.8 - - - +
257A MET* 1.3 60.8 + - - +
258A VAL 3.1 2.5 - - - -
259A ILE* 3.0 12.4 + - + +
260A ALA* 2.8 31.1 + - + +
302A ASN* 5.9 2.5 - - - +
305A ILE* 5.1 11.2 - - + +
306A TYR* 5.9 5.8 - - + -
309A MET* 3.6 36.3 - - + -
310A ASN* 6.2 2.5 - - + +
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Residues in contact with MET 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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128A LEU* 3.6 50.5 - - + +
131A LEU* 3.8 24.2 - - + -
132A ALA* 4.2 18.2 - - + -
135A ARG* 6.0 0.9 - - + -
218A VAL* 5.8 2.2 - - + -
219A ILE* 3.9 31.6 - - + -
222A CYS* 5.9 2.0 - - - -
253A MET* 2.9 13.7 + - - +
254A VAL* 3.5 32.1 - - + +
256A ILE* 1.3 78.8 - - - +
258A VAL* 1.3 56.0 + - - +
260A ALA* 3.8 1.5 - - - +
261A PHE* 2.9 35.3 + - + +
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Residues in contact with VAL 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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219A ILE* 3.9 33.7 - - + -
254A VAL 3.3 17.0 - - - +
255A ILE* 3.8 9.6 - - - +
256A ILE 3.1 0.6 - - - -
257A MET* 1.3 77.9 - - + +
259A ILE* 1.3 67.4 + - + +
261A PHE* 3.4 7.8 + - + +
262A LEU* 3.1 21.3 + - - +
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Residues in contact with ILE 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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255A ILE* 3.4 20.9 - - + +
256A ILE* 3.0 13.8 + - + +
258A VAL* 1.3 78.6 - - + +
260A ALA* 1.3 65.0 + - - +
262A LEU* 3.2 14.3 + - + +
263A ILE* 3.1 35.9 + - + +
305A ILE* 4.6 22.0 - - + -
309A MET* 3.8 30.3 - - + -
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Residues in contact with ALA 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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76A LEU* 6.0 4.0 - - + -
79A LEU* 4.9 15.9 - - + -
128A LEU* 3.7 27.6 - - + -
256A ILE* 2.8 20.5 + - + +
257A MET* 4.3 0.2 - - - -
259A ILE* 1.3 75.7 - - - +
261A PHE* 1.3 59.7 + - - +
263A ILE* 2.9 13.9 + - - +
264A CYS* 2.8 31.9 + - - +
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Residues in contact with PHE 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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125A LEU* 5.5 7.2 - - + -
128A LEU* 3.4 33.4 - - + +
129A VAL* 5.7 5.2 - - + -
211A HIS* 3.4 29.8 - + - +
214A ILE* 6.0 3.6 - - + -
215A PRO* 3.7 30.7 - - + -
218A VAL* 5.7 11.4 - - + -
219A ILE* 6.1 6.1 - - + -
257A MET* 2.9 25.1 + - + +
258A VAL* 3.4 10.5 - - + +
260A ALA* 1.3 76.1 - - - +
262A LEU* 1.3 57.8 + - - +
264A CYS* 3.2 5.2 + - + +
265A TRP* 2.9 54.2 + + - +
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Residues in contact with LEU 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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211A HIS* 3.9 26.2 + - + +
258A VAL 3.1 9.7 + - - +
259A ILE* 3.5 14.8 - - + +
260A ALA 3.1 0.6 - - - -
261A PHE* 1.3 78.8 - - - +
263A ILE* 1.3 60.7 + - + +
265A TRP 3.2 3.5 + - - +
266A LEU* 2.8 29.0 + - + +
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Residues in contact with ILE 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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79A LEU* 6.4 1.6 - - + -
259A ILE* 3.1 33.2 + - + +
260A ALA* 2.9 12.0 + - - +
262A LEU* 1.3 81.2 - - + +
264A CYS* 1.3 64.1 + - - +
266A LEU* 3.1 30.7 - - + +
267A PRO* 3.9 3.6 - - - +
295A ALA* 5.4 1.4 - - - +
298A SER* 3.4 40.3 + - - +
301A TYR* 5.4 7.9 - - + -
302A ASN* 5.9 4.5 - - - -
305A ILE* 5.3 8.7 - - + -
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Residues in contact with CYS 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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79A LEU* 5.9 0.2 - - - -
121A GLY* 3.4 29.5 - - - +
124A ALA* 3.7 22.7 - - - -
125A LEU* 3.7 26.1 - - + +
128A LEU* 4.2 5.6 - - + -
260A ALA* 2.8 15.5 + - - +
261A PHE* 3.5 12.6 - - + +
262A LEU 3.1 0.2 - - - -
263A ILE* 1.3 80.7 - - - +
265A TRP* 1.3 63.9 + - + +
266A LEU 3.2 3.2 + - - -
267A PRO* 3.6 10.9 - - - +
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Residues in contact with TRP 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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125A LEU* 3.6 31.4 - - + -
207A MET* 4.0 21.7 + - + +
210A VAL* 4.5 20.3 - - + +
211A HIS* 3.7 47.1 + + + +
214A ILE* 6.3 3.6 - - + -
261A PHE* 2.9 44.4 + + - +
262A LEU* 3.2 4.5 + - - +
264A CYS* 1.3 78.3 - - + +
266A LEU* 1.3 66.8 + - - +
267A PRO* 3.5 2.0 - - - -
268A TYR* 5.9 2.7 - - + -
269A ALA* 3.0 32.4 - - + +
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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