Contacts of the helix formed by residues 244 - 259 (chain A) in PDB entry 1X79
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 244 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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245A SER* 1.3 70.1 + - - +
246A GLU* 4.1 11.5 + - - +
247A ASP* 2.6 36.9 + - - +
248A LEU* 4.5 1.6 + - - +
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Residues in contact with SER 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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231A MET* 4.2 6.2 - - - +
234A SER 5.5 5.6 - - - -
235A HIS* 4.9 10.3 - - - -
244A SER* 1.3 81.8 + - - +
246A GLU* 1.3 55.2 + - - +
247A ASP 2.7 16.7 + - - -
248A LEU* 3.2 16.6 + - - +
249A MET* 3.3 12.1 + - - +
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Residues in contact with GLU 246 (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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235A HIS* 3.6 31.0 + - - +
244A SER 4.1 9.2 + - - +
245A SER* 1.3 77.5 - - - +
247A ASP* 1.3 60.2 + - - +
249A MET* 3.9 8.5 - - + -
250A LYS* 3.1 59.8 + - + +
298A VAL* 4.8 7.8 - - - +
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Residues in contact with ASP 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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244A SER* 2.6 41.4 + - - +
245A SER 2.7 5.9 + - - -
246A GLU* 1.3 79.5 - - - +
248A LEU* 1.3 65.9 + - - +
249A MET 3.0 2.2 + - - -
250A LYS* 4.3 9.3 + - - +
251A GLU* 3.5 18.1 + - - +
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Residues in contact with LEU 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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227A LEU* 6.1 1.6 - - + -
231A MET* 4.0 19.5 - - + +
244A SER 4.5 1.6 + - - +
245A SER* 3.2 7.6 + - - +
247A ASP* 1.3 78.8 - - - +
249A MET* 1.3 62.3 + - - +
251A GLU* 3.3 39.4 - - - +
252A LEU* 3.3 8.4 + - + +
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Residues in contact with MET 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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228A LEU* 4.1 13.0 - - + -
231A MET* 3.4 45.2 - - + +
232A VAL* 4.1 7.6 - - - -
235A HIS* 4.2 21.3 - - - +
245A SER 3.3 10.6 + - - +
246A GLU* 3.8 5.8 - - + +
247A ASP 3.0 1.8 - - - -
248A LEU* 1.3 74.6 - - - +
250A LYS* 1.3 61.4 + - + +
251A GLU 2.6 15.4 + - - -
252A LEU* 2.7 14.6 + - - +
253A TYR* 3.1 10.0 + - - +
294A TYR* 3.5 15.0 - - + +
298A VAL* 3.1 50.9 - - + -
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Residues in contact with LYS 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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246A GLU* 3.1 50.0 + - + +
247A ASP* 4.3 8.8 + - - +
249A MET* 1.3 81.7 - - + +
251A GLU* 1.3 59.6 + - - +
253A TYR* 3.7 1.1 - - - +
254A GLN* 2.8 35.7 + - - +
294A TYR* 3.0 29.8 - - + +
298A VAL* 4.9 2.9 - - + -
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Residues in contact with GLU 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 ASP 3.5 11.0 + - - +
248A LEU* 3.3 35.0 - - - +
249A MET 2.6 4.4 + - - -
250A LYS* 1.3 74.8 - - - +
252A LEU* 1.3 67.2 + - - +
254A GLN* 3.1 15.7 + - - +
255A ARG* 3.1 12.9 + - + +
258A ARG* 5.6 0.2 + - - -
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Residues in contact with LEU 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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224A ASN* 4.1 31.0 - - + +
227A LEU* 3.3 35.4 - - + -
228A LEU* 3.3 33.9 - - + +
231A MET* 4.0 3.8 - - - -
248A LEU 3.3 8.8 + - - +
249A MET 2.7 13.2 + - - +
251A GLU* 1.3 74.3 - - - +
253A TYR* 1.3 68.7 + - - +
255A ARG* 2.9 28.7 + - - +
256A CYS* 2.9 17.1 + - - +
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Residues in contact with TYR 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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228A LEU* 3.7 19.3 - - + +
249A MET 3.1 4.5 + - - +
250A LYS 3.7 5.4 - - - +
252A LEU* 1.3 78.9 - - - +
254A GLN* 1.3 76.7 - - - +
256A CYS* 3.2 3.4 + - - +
257A GLU* 2.9 53.0 + - + +
291A ILE* 3.5 31.8 - - + +
294A TYR* 3.5 70.4 - + + -
295A LYS* 3.4 27.1 + - + +
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Residues in contact with GLN 254 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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250A LYS* 2.8 25.9 + - - +
251A GLU* 3.1 12.5 + - - +
252A LEU 3.0 1.0 - - - -
253A TYR* 1.3 90.8 - - - +
255A ARG* 1.3 66.8 + - - +
257A GLU* 3.1 27.7 + - - +
258A ARG* 3.2 37.4 - - + +
294A TYR* 5.1 1.0 + - - -
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Residues in contact with ARG 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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220A GLU* 4.1 24.8 + - - +
224A ASN* 4.2 19.7 + - - -
251A GLU* 3.1 8.4 + - + +
252A LEU* 2.9 20.6 + - + +
254A GLN* 1.3 77.5 - - - +
256A CYS* 1.3 61.8 + - - +
258A ARG* 2.9 40.3 + - - +
259A MET* 3.2 13.7 + - + +
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Residues in contact with CYS 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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221A VAL* 5.7 2.7 - - - -
224A ASN* 4.2 29.4 - - - -
225A VAL* 5.0 3.6 - - - -
228A LEU* 4.3 17.5 - - + -
252A LEU* 2.9 20.1 + - - +
253A TYR* 3.5 11.9 - - - +
255A ARG* 1.3 79.9 - - - +
257A GLU* 1.3 61.3 + - - +
258A ARG 3.5 0.2 + - - -
259A MET* 3.5 21.8 + - - +
260A ARG* 4.0 0.7 + - - +
287A LEU* 3.8 35.0 - - + +
291A ILE* 4.0 7.4 - - + +
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Residues in contact with GLU 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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253A TYR* 2.9 49.8 + - + +
254A GLN* 3.1 25.4 + - - +
256A CYS* 1.3 78.2 - - - +
258A ARG* 1.3 63.3 + - + +
259A MET 3.1 0.7 - - - -
260A ARG* 3.3 23.1 + - - +
261A PRO* 3.8 2.9 - - - +
291A ILE* 4.4 13.7 - - + -
570B GLN* 4.0 16.1 + - - +
573B LYS* 3.4 26.3 + - - -
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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
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254A GLN* 3.2 35.5 + - + +
255A ARG* 2.9 22.5 + - - +
257A GLU* 1.3 77.4 - - + +
259A MET* 1.3 61.5 + - - +
260A ARG 3.3 0.7 - - - -
261A PRO* 3.1 20.9 - - - +
262A THR* 3.8 8.0 + - - -
570B GLN* 5.2 1.8 - - - +
575C MET* 5.4 10.1 - - + +
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Residues in contact with MET 259 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217A ALA* 3.6 28.0 - - + +
220A GLU* 3.7 28.0 - - + +
221A VAL* 3.5 29.6 - - + -
255A ARG* 3.2 14.9 + - + +
256A CYS* 3.6 19.7 - - - +
257A GLU 3.1 0.2 - - - -
258A ARG* 1.3 79.8 - - - +
260A ARG* 1.3 65.3 + - - +
261A PRO 3.4 0.2 - - - -
262A THR* 3.0 29.1 + - + -
263A LEU* 3.0 17.6 + - + +
287A LEU* 4.3 10.3 - - + -
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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