Contacts of the helix formed by residues 246 - 260 (chain A) in PDB entry 1O04
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 SER 246 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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243A PHE* 3.6 0.5 - - - -
245A GLY* 1.3 74.8 - - - -
247A THR* 1.3 65.1 + - - +
248A GLU* 3.8 10.0 + - - +
249A ILE* 3.3 18.5 + - - +
250A GLY 2.9 18.5 + - - -
269A LEU* 3.6 3.8 - - - +
6501A NAD 2.8 51.3 + - - -
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Residues in contact with THR 247 (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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245A GLY 3.8 1.4 + - - -
246A SER* 1.3 71.7 - - - +
248A GLU* 1.3 63.7 + - - +
250A GLY* 3.2 9.2 + - - -
251A ARG* 3.3 20.0 + - - +
269A LEU* 3.3 9.1 - - - +
270A GLY* 3.3 18.1 + - - +
425A TYR* 3.3 24.0 + - + +
470A MET* 2.9 43.4 + - + +
6501A NAD 4.6 0.4 + - - -
262B LEU* 3.9 15.6 - - + +
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Residues in contact with GLU 248 (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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246A SER* 3.2 11.4 + - - +
247A THR* 1.3 80.0 - - - +
249A ILE* 1.3 71.9 + - + +
251A ARG* 3.4 23.2 + - - +
252A VAL* 3.7 10.6 - - + +
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Residues in contact with ILE 249 (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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243A PHE* 3.5 22.9 - - + -
246A SER* 3.2 15.2 + - - +
248A GLU* 1.3 86.6 - - + +
250A GLY* 1.3 66.8 + - - +
251A ARG 3.1 0.7 - - - -
252A VAL* 3.0 14.3 + - + +
253A ILE* 3.0 22.6 + - + +
6501A NAD 3.4 73.4 - - + +
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Residues in contact with GLY 250 (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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243A PHE* 3.6 10.2 - - - -
246A SER 2.9 14.8 + - - -
247A THR 3.2 4.4 + - - -
249A ILE* 1.3 76.1 - - - +
251A ARG* 1.3 61.5 + - - +
253A ILE* 3.3 4.0 + - - +
254A GLN* 3.0 23.9 + - - +
267A LEU* 3.9 9.2 - - - +
269A LEU* 3.9 18.6 - - - -
262B LEU* 4.0 6.7 - - - -
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Residues in contact with ARG 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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247A THR* 3.3 18.1 + - - +
248A GLU* 3.6 13.6 - - - +
249A ILE 3.1 0.6 - - - -
250A GLY* 1.3 74.6 - - - +
252A VAL* 1.3 64.3 + - + +
254A GLN* 3.3 2.8 + - - +
255A VAL* 3.0 30.4 + - + +
470A MET* 3.6 31.2 - - - +
236B GLU* 5.1 4.0 + - - -
258B GLY 3.4 18.8 - - - +
259B SER* 3.5 15.7 + - - +
260B SER* 2.7 30.2 + - - +
262B LEU* 3.8 15.9 - - + +
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Residues in contact with VAL 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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230A ALA* 6.1 1.8 - - + -
248A GLU* 3.7 16.4 - - + +
249A ILE* 3.3 22.2 - - + +
251A ARG* 1.3 77.5 - - + +
253A ILE* 1.3 57.1 + - - +
255A VAL* 3.4 6.1 + - - +
256A ALA* 2.9 31.6 + - + +
6501A NAD 3.9 26.9 - - - +
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Residues in contact with ILE 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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165A ILE* 3.8 19.7 - - + -
233A ALA* 3.9 11.5 - - + +
241A VAL* 3.8 31.6 - - + -
243A PHE* 3.7 24.2 - - + -
249A ILE 3.0 18.5 + - - +
250A GLY 3.5 6.5 - - - +
252A VAL* 1.3 75.8 - - + +
254A GLN* 1.3 57.5 + - - +
256A ALA* 3.2 7.2 + - - +
257A ALA* 3.0 26.2 + - - +
265A VAL* 4.4 2.7 - - + -
267A LEU* 4.1 16.6 - - + -
6501A NAD 3.6 32.1 - - + +
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Residues in contact with GLN 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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250A GLY 3.0 14.3 + - - +
251A ARG 3.3 0.4 + - - +
253A ILE* 1.3 77.6 - - - +
255A VAL* 1.3 62.1 + - - +
257A ALA* 3.3 7.6 + - - +
258A GLY* 3.1 20.4 + - - -
265A VAL* 4.7 11.4 - - + -
267A LEU* 3.6 15.3 - - + +
254B GLN* 4.0 18.4 + - + +
257B ALA* 3.4 18.1 - - - +
258B GLY* 3.7 22.7 - - - +
262B LEU* 3.2 26.4 - - + +
263B LYS 3.3 22.8 + - - -
265B VAL* 3.8 10.5 - - - +
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Residues in contact with VAL 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 ARG* 3.0 21.9 + - + +
252A VAL* 3.8 6.1 - - - +
254A GLN* 1.3 76.2 - - - +
256A ALA* 1.3 57.4 + - - +
258A GLY* 3.3 1.6 + - - -
259A SER* 2.8 44.8 + - - +
255B VAL* 3.8 21.5 - - + +
258B GLY 3.8 0.9 - - - -
259B SER* 3.4 38.4 - - - +
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Residues in contact with ALA 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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230A ALA* 6.1 0.7 - - - -
233A ALA* 3.8 21.0 - - + +
234A SER* 3.5 24.0 + - - +
252A VAL* 2.9 20.7 + - + +
253A ILE 3.2 5.1 + - - +
255A VAL* 1.3 75.2 - - - +
257A ALA* 1.3 54.8 + - - +
259A SER* 3.4 5.6 + - - -
260A SER* 2.7 36.2 + - - -
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Residues in contact with ALA 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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233A ALA 3.9 2.0 + - - +
241A VAL* 4.9 0.7 - - + -
253A ILE 3.0 10.0 + - - +
254A GLN 3.6 4.5 - - - +
255A VAL 3.3 0.2 - - - -
256A ALA* 1.3 76.9 - - - +
258A GLY* 1.3 63.1 + - - +
260A SER* 3.4 9.4 + - - -
262A LEU 3.0 27.3 + - - -
263A LYS* 3.6 21.3 - - + -
265A VAL* 3.4 22.9 - - + -
254B GLN* 3.4 22.4 - - - +
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Residues in contact with GLY 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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254A GLN 3.1 11.2 + - - -
255A VAL 3.8 2.9 - - - -
257A ALA* 1.3 78.0 - - - +
259A SER* 1.3 59.6 + - - +
260A SER 3.5 0.9 + - - +
262A LEU* 4.0 2.3 - - - +
251B ARG* 3.4 31.2 - - - +
254B GLN* 3.7 32.2 - - - -
255B VAL* 3.8 11.7 - - - -
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Residues in contact with SER 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 VAL* 2.8 31.5 + - - +
256A ALA* 3.9 6.5 - - - -
257A ALA 3.3 0.2 - - - -
258A GLY* 1.3 76.2 - - - +
260A SER* 1.3 61.2 + - - +
251B ARG* 4.7 6.8 + - - +
255B VAL* 3.5 14.4 - - - +
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Residues in contact with SER 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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233A ALA 3.7 0.7 + - - -
234A SER* 3.3 28.3 - - - -
235A HIS 4.7 0.2 - - - -
236A GLU* 3.5 21.2 - - - +
256A ALA 2.7 20.8 + - - -
257A ALA 3.4 3.0 + - - -
258A GLY 3.3 1.3 - - - -
259A SER* 1.3 80.2 - - - +
261A ASN* 1.3 66.9 + - - -
262A LEU 3.6 1.9 + - - -
263A LYS* 3.1 20.1 + - - -
251B ARG* 2.8 27.0 + - - -
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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