Contacts of the helix formed by residues 250 - 263 (chain A) in PDB entry 7ACN
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 CYS 250 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151A LEU* 4.6 4.7 - - - -
173A GLY 3.4 20.4 - - - +
174A LEU* 3.5 26.9 - - - -
249A SER* 1.3 71.1 - - - +
251A THR* 1.3 56.9 + - - +
253A MET* 3.1 19.6 + - + +
254A ALA* 3.0 24.4 + - - +
275A ARG* 3.8 14.8 + - - +
276A MET* 4.3 2.5 - - - -
279A TYR* 3.6 39.7 - - + -
504A GLU* 4.9 1.8 + - - -
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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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148A GLN* 4.4 7.0 - - - +
151A LEU* 3.9 20.2 - - + -
249A SER* 3.9 8.1 + - - -
250A CYS* 1.3 71.0 - - - +
252A GLY* 1.3 60.7 + - - +
254A ALA* 3.3 9.3 + - - +
255A THR* 2.9 31.3 + - - -
279A TYR* 3.9 19.7 - - + +
362A SER* 3.7 36.4 + - - -
364A GLU* 4.0 9.5 + - - +
365A ASP* 5.6 0.8 - - - +
504A GLU 4.8 4.6 + - - +
505A LEU* 5.8 2.4 - - + +
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Residues in contact with GLY 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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217A PRO* 3.4 29.1 - - - +
248A ILE* 3.6 7.0 - - - -
249A SER* 3.1 22.7 + - - -
251A THR* 1.3 77.2 + - - +
253A MET* 1.3 59.3 + - - +
255A THR* 3.3 8.2 + - - -
256A ILE* 3.3 18.9 + - - +
364A GLU* 4.5 2.6 + - - -
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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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173A GLY* 3.7 14.1 - - - +
245A VAL 4.6 3.1 - - - +
248A ILE* 3.8 19.1 - - + +
249A SER 2.9 11.4 + - - +
250A CYS* 3.5 32.8 - - - +
252A GLY* 1.3 75.7 - - - +
254A ALA* 1.3 63.1 + - - +
256A ILE* 3.3 3.5 + - - +
257A CYS* 3.0 27.4 + - - -
270A PHE* 3.5 48.6 - - + -
273A ASN* 3.7 23.6 - - - +
275A ARG* 4.0 8.3 - - + -
276A MET* 3.7 26.9 - - + -
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Residues in contact with ALA 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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151A LEU* 3.9 20.4 - - + -
170A ASN* 3.4 40.8 - - - +
173A GLY* 3.5 4.2 - - - +
250A CYS 3.0 12.8 + - - +
251A THR* 3.4 8.5 - - - +
252A GLY 3.2 0.2 - - - -
253A MET* 1.3 76.9 - - - +
255A THR* 1.4 55.8 + - - +
257A CYS* 3.4 1.6 + - - +
258A ASN* 2.8 31.5 + - - +
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Residues in contact with THR 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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170A ASN* 5.0 0.4 - - - -
217A PRO* 4.6 2.5 - - + -
218A LYS* 3.8 32.5 - - + +
221A ILE* 4.0 1.0 - - + +
251A THR 2.9 14.0 + - - -
252A GLY* 3.3 12.7 + - - -
254A ALA* 1.4 75.1 - - - +
256A ILE* 1.3 62.8 + - - +
258A ASN* 3.4 5.4 + - - +
259A MET* 3.3 22.3 + - - +
358A CYS 5.7 0.2 - - - -
359A THR* 2.8 39.8 + - + +
360A ASN* 3.9 13.5 + - - +
365A ASP* 4.5 4.7 + - - -
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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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217A PRO* 3.2 31.2 - - + +
220A VAL* 4.0 20.0 - - + -
221A ILE* 3.6 31.3 - - + +
240A TYR* 3.3 41.2 + - + +
248A ILE* 4.0 19.1 - - + -
252A GLY 3.3 14.6 + - - +
253A MET 3.3 5.4 + - - +
255A THR* 1.3 76.5 - - - +
257A CYS* 1.3 63.6 + - - +
258A ASN 3.4 0.2 + - - -
260A GLY* 3.6 4.9 + - - -
268A SER* 4.8 0.2 + - - -
270A PHE* 3.9 21.1 - - + -
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Residues in contact with CYS 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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169A PRO* 3.0 34.8 - - - +
172A GLY* 3.5 26.9 - - - -
173A GLY 4.2 2.7 - - - +
240A TYR* 4.9 0.4 - - - -
253A MET 3.0 21.0 + - - +
254A ALA 3.9 2.7 - - - +
256A ILE* 1.3 77.5 - - - +
258A ASN* 1.3 65.8 + - - +
260A GLY* 3.3 8.3 + - - -
268A SER* 3.7 33.9 + - - -
269A VAL 4.0 0.2 - - - -
270A PHE* 3.5 20.6 - - - -
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Residues in contact with ASN 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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167A HIS* 3.1 32.8 + - - +
169A PRO* 4.5 3.5 - - - +
170A ASN* 3.0 35.6 + - - +
254A ALA 2.8 19.3 + - - +
255A THR* 3.4 8.7 - - - +
256A ILE 3.3 0.4 - - - -
257A CYS* 1.3 79.3 - - - +
259A MET* 1.3 61.8 + - - +
260A GLY 3.0 3.8 + - - -
261A ALA* 3.2 10.6 + - - +
358A CYS* 3.3 35.0 + - - +
359A THR* 2.8 23.5 + - - -
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Residues in contact with MET 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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218A LYS* 3.8 27.4 - - - -
221A ILE* 3.5 36.0 - - + +
222A LEU* 4.2 20.2 - - + -
225A ALA* 5.1 8.5 - - + +
255A THR 3.3 5.9 + - - +
256A ILE 3.6 0.2 + - - -
257A CYS 3.4 0.2 - - - -
258A ASN* 1.3 80.9 - - - +
260A GLY* 1.3 55.0 + - - +
261A ALA 2.9 5.2 - - - -
262A GLU* 2.9 41.4 + - + +
263A ILE* 4.2 2.4 + - - +
328A PRO* 4.0 20.6 - - + +
359A THR* 4.4 3.8 - - + -
446A ASN* 3.5 32.3 - - + +
463A VAL* 4.4 2.2 - - + -
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Residues in contact with GLY 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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169A PRO* 6.0 1.1 - - - -
221A ILE* 3.9 12.8 - - - -
238A VAL* 5.8 0.2 - - - -
240A TYR* 5.9 0.2 - - - -
256A ILE 3.6 5.0 + - - -
257A CYS 3.3 10.0 + - - -
258A ASN 3.0 3.2 + - - -
259A MET* 1.3 75.9 - - - +
261A ALA* 1.3 61.1 + - - +
262A GLU 3.2 0.4 - - - -
263A ILE* 3.1 29.9 + - - +
265A ALA* 3.5 16.2 + - - +
267A THR* 6.3 0.7 - - - -
268A SER* 4.1 13.0 - - - -
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Residues in contact with ALA 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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166A SER* 3.6 22.9 - - - +
167A HIS* 3.6 19.5 - - - +
169A PRO* 5.4 5.4 - - + +
257A CYS 4.4 0.8 + - - -
258A ASN 3.2 16.3 + - - +
260A GLY* 1.3 78.8 - - - +
262A GLU* 1.3 62.8 + - - +
263A ILE 3.2 0.2 - - - -
264A GLY* 3.1 18.9 + - - +
265A ALA 4.9 7.0 - - - -
447A ARG* 4.1 7.9 + - - +
641A GLY* 5.6 1.7 - - - +
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Residues in contact with GLU 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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167A HIS* 2.8 24.8 + - - -
225A ALA* 5.5 4.9 - - + +
230A VAL* 3.2 29.6 - - - +
259A MET* 2.9 27.9 + - + +
261A ALA* 1.3 77.2 - - - +
263A ILE* 1.3 61.4 + - + +
264A GLY 3.5 0.4 - - - -
328A PRO* 3.6 32.0 - - + +
446A ASN* 3.4 18.3 - - - +
447A ARG* 2.8 47.5 + - + -
449A PHE* 5.7 1.3 - - + -
640A GLU* 5.1 1.9 - - - +
641A GLY* 5.6 0.2 - - - -
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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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221A ILE* 5.4 2.9 - - + -
224A VAL* 4.5 8.5 - - + -
225A ALA* 3.7 32.3 - - + +
228A LEU* 3.8 28.9 - - + -
229A THR 3.5 19.5 - - - +
230A VAL 3.1 16.5 - - - +
231A LYS 3.8 0.2 - - - -
232A GLY 3.7 0.5 + - - -
233A GLY* 2.7 38.0 + - - +
234A THR 3.6 1.0 + - - -
238A VAL* 4.1 23.3 - - + -
259A MET 5.1 2.9 - - - +
260A GLY* 3.1 21.3 + - - +
262A GLU* 1.3 80.6 - - - +
264A GLY* 1.3 55.2 + - - +
265A ALA 4.1 4.5 - - - +
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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
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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