Contacts of the helix formed by residues 248 - 264 (chain A) in PDB entry 5OQN
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 ASN 248 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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220A ALA* 3.5 23.1 - - + +
223A ARG* 3.8 1.3 - - - +
224A ARG* 2.9 19.2 - - - +
246A ASP* 2.6 33.7 + - - +
247A VAL* 1.3 73.4 - - + +
249A ILE* 1.3 68.9 + - - +
250A VAL* 3.9 6.9 + - - +
251A ASN* 2.7 30.2 + - - +
252A ARG* 3.3 14.3 + - - -
12C A 4.3 0.7 - - - +
13C C 3.1 37.5 + - - +
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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
----------------------------------------------------------
247A VAL 4.6 3.6 - - - +
248A ASN* 1.3 74.5 + - - +
250A VAL* 1.3 68.3 + - + +
252A ARG* 3.1 26.5 + - - +
253A ARG* 3.1 23.3 + - + +
288A GLU* 3.9 35.9 - - + +
290A SER* 4.7 11.7 - - - -
291A VAL* 3.9 13.5 - - + +
400B ARG* 5.9 2.9 - - + -
12C A 3.4 44.4 - - - +
13C C 4.1 4.3 - - - +
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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
----------------------------------------------------------
224A ARG* 3.3 36.3 - - - +
248A ASN* 3.3 6.0 - - - +
249A ILE* 1.3 79.4 - - + +
251A ASN* 1.3 63.6 + - - +
253A ARG* 3.0 39.0 + - - +
254A LEU* 3.1 39.1 + - + +
12C A 6.5 1.3 - - - +
13C C 6.4 0.4 - - - -
9D G 4.4 15.7 - - - +
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Residues in contact with ASN 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A ALA* 3.0 26.9 + - - +
223A ARG* 3.9 8.5 - - - +
224A ARG* 2.9 36.6 + - - +
227A MET* 3.4 27.0 - - + +
243A ARG 3.7 8.0 - - - +
246A ASP* 3.7 27.4 + - - +
248A ASN* 2.7 32.4 + - - +
249A ILE 3.3 0.8 - - - -
250A VAL* 1.3 76.3 - - - +
252A ARG* 1.3 58.4 + - - +
254A LEU* 4.3 2.5 - - - -
255A VAL* 3.8 11.6 + - - +
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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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243A ARG 3.4 4.5 - - - +
244A ALA 3.2 25.1 - - - +
245A ARG* 3.7 3.7 - - - +
246A ASP 2.6 42.4 + - - +
247A VAL 4.2 5.5 + - - -
248A ASN 3.3 3.4 + - - -
249A ILE* 3.1 43.4 + - - +
251A ASN* 1.3 75.2 - - - +
253A ARG* 1.3 60.2 + - - +
255A VAL* 3.0 19.7 - - - +
256A TYR* 3.3 15.9 - - - -
286A ASP* 2.0 45.8 + - - -
288A GLU* 4.4 5.3 - - - +
291A VAL* 3.6 18.3 - - + +
498B LEU* 3.4 18.9 - - - +
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Residues in contact with ARG 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A ILE* 3.1 12.8 + - - +
250A VAL* 3.0 41.1 + - - +
252A ARG* 1.3 78.1 - - - +
254A LEU* 1.3 66.4 + - + +
255A VAL 3.3 0.4 - - - -
256A TYR* 3.3 6.4 + - - +
257A SER* 3.0 29.1 + - - +
290A SER* 2.5 42.3 + - - +
291A VAL* 4.4 11.6 - - + +
294A ALA* 3.8 21.0 - - + +
9D G 4.0 18.6 + - - +
10D C 3.4 40.8 + - - +
11D T 3.8 5.3 + - - -
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Residues in contact with LEU 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A ARG* 4.6 14.8 - - + -
227A MET* 5.3 2.7 - - + -
228A LEU* 3.9 34.1 - - + -
250A VAL* 3.1 38.8 + - + +
251A ASN* 4.9 3.8 - - - +
252A ARG 3.6 0.2 - - - -
253A ARG* 1.3 79.6 - - - +
255A VAL* 1.3 61.4 + - - +
257A SER* 4.2 2.0 - - - -
258A ARG* 2.6 55.0 + - + +
259A ILE* 3.2 7.2 + - - +
9D G 3.8 7.0 - - - +
10D C 3.2 31.6 - - - +
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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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227A MET* 4.5 8.2 - - - -
240A ILE 4.3 16.6 - - - +
241A LEU* 4.5 21.1 - - + -
243A ARG 4.9 0.4 - - - -
244A ALA* 3.9 27.8 - - + +
251A ASN 3.8 11.7 + - - +
252A ARG 3.0 28.9 - - - +
254A LEU* 1.3 78.3 - - - +
256A TYR* 1.3 63.5 + - + +
259A ILE* 3.3 20.2 - - + +
260A LEU* 3.1 30.1 + - + +
279A LEU* 5.1 3.4 - - + -
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Residues in contact with TYR 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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244A ALA* 4.2 15.0 + - + +
252A ARG 3.3 25.1 - - - -
253A ARG* 3.3 5.3 + - - +
254A LEU 3.2 0.4 - - - -
255A VAL* 1.3 80.6 - - + +
257A SER* 1.3 67.4 + - - +
260A LEU* 3.3 42.2 - - + +
279A LEU* 2.7 42.9 + - + -
280A ILE* 4.8 1.6 - - + -
282A TRP* 3.7 7.4 - - - +
283A GLY* 2.9 27.1 + - - -
291A VAL* 3.9 17.3 - - + -
294A ALA 3.9 18.4 - - - +
295A CYS* 4.1 22.7 - - + -
298A LEU* 3.7 15.8 - - + +
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Residues in contact with SER 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A ARG* 3.0 22.5 + - - +
254A LEU* 4.2 5.6 - - - -
256A TYR* 1.3 75.9 - - - +
258A ARG* 1.3 66.4 + - - +
261A LYS* 3.0 42.8 - - - +
294A ALA* 3.5 21.3 + - - +
298A LEU* 5.5 0.7 - - - -
10D C 5.2 5.7 + - - -
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Residues in contact with ARG 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A LEU* 4.3 24.0 - - + +
254A LEU* 2.6 44.6 + - + +
257A SER* 1.3 81.3 - - - +
259A ILE* 1.3 58.7 + - + +
261A LYS* 3.9 2.1 - - - +
262A SER* 3.0 29.1 + - - -
9D G 5.7 1.8 - - - -
10D C 2.7 30.4 + - - -
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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
----------------------------------------------------------
227A MET* 3.7 32.5 - - + +
228A LEU* 4.3 15.3 - - + +
232A ASN* 4.9 8.3 - - - +
240A ILE* 3.3 35.7 - - + -
241A LEU* 5.0 7.2 - - + -
254A LEU 3.2 8.9 + - - +
255A VAL* 3.3 16.6 - - + +
258A ARG* 1.3 77.6 - - - +
260A LEU* 1.3 63.5 + - + +
262A SER* 2.5 26.4 + - - +
263A MET* 3.1 27.6 + - + +
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Residues in contact with LEU 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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241A LEU* 4.1 25.4 - - + -
255A VAL* 3.1 12.4 + - + +
256A TYR* 3.3 45.3 + - + +
258A ARG 3.5 0.2 - - - -
259A ILE* 1.3 74.8 - - + +
261A LYS* 1.3 61.4 + - - +
263A MET* 3.9 11.9 - - - +
264A GLY* 3.4 16.3 + - - -
267A CYS* 4.1 26.8 - - - -
271A ILE* 4.4 5.2 - - + -
276A PHE* 6.4 1.1 - - + -
279A LEU* 5.2 12.8 - - + -
280A ILE* 6.5 0.7 - - + -
298A LEU* 3.6 25.0 - - + +
303A TRP* 4.2 12.0 + - + -
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Residues in contact with LYS 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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257A SER* 3.0 31.7 + - - +
258A ARG* 3.9 2.5 - - - +
259A ILE 3.2 0.4 - - - -
260A LEU* 1.3 76.8 - - - +
262A SER* 1.3 63.8 + - - +
263A MET 3.2 1.0 + - - -
264A GLY* 3.4 11.5 + - - +
297A ARG* 3.8 24.0 - - - +
298A LEU* 3.9 10.8 - - + -
301A HIS* 5.8 0.4 - - - -
302A ASP* 3.1 35.8 + - + +
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Residues in contact with SER 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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232A ASN* 4.9 4.9 + - - -
258A ARG 3.0 13.7 + - - -
259A ILE* 2.5 26.7 + - - +
261A LYS* 1.3 77.0 - - - +
263A MET* 1.3 62.7 + - - +
264A GLY 3.8 0.2 + - - -
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Residues in contact with MET 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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232A ASN* 4.0 19.3 - - - +
237A ARG* 3.4 35.4 - - - +
241A LEU* 5.2 1.8 - - - -
259A ILE* 3.1 22.3 + - + +
260A LEU* 3.8 10.7 + - - +
261A LYS 3.2 0.2 - - - -
262A SER* 1.3 83.7 + - - +
264A GLY* 1.3 58.0 + - - +
265A ARG 3.1 0.9 + - - -
266A LYS* 2.8 64.2 + - + +
267A CYS* 3.8 13.5 - - - -
271A ILE* 3.9 24.5 - - + -
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Residues in contact with GLY 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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260A LEU 3.4 9.2 + - - -
261A LYS* 3.4 11.6 + - - -
263A MET* 1.3 74.1 - - - +
265A ARG* 1.3 62.5 + - - -
267A CYS* 3.4 17.2 - - - -
268A PHE* 4.1 1.6 - - - -
303A TRP* 3.6 20.2 + - - -
306A ALA* 5.3 6.5 - - - -
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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
------------------------------------------------------------
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