Contacts of the helix formed by residues 250 - 265 (chain A) in PDB entry 1H7B
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 250 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200A GLY 4.4 3.8 + - - -
202A GLY 2.8 27.8 + - - -
203A THR* 3.7 7.8 + - - +
208A ARG* 2.5 43.3 + - - +
211A GLN* 4.4 2.3 - - - +
242A VAL* 2.8 40.8 + - - +
243A ASN* 4.1 11.1 - - - +
249A PRO* 1.3 76.4 - - - +
251A TYR* 1.3 63.5 + - - +
252A ASP 3.1 2.7 - - - -
253A ILE* 2.9 27.1 + - + +
254A LYS* 3.1 9.4 + - - +
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Residues in contact with TYR 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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242A VAL 3.8 1.6 + - - -
243A ASN 3.8 13.7 - - - -
244A LEU 3.6 11.0 - - - -
245A TYR 3.1 22.9 - - - +
246A LYS* 3.3 46.7 - - + +
248A ASP* 3.1 17.6 + - - +
249A PRO 3.3 1.0 + - - -
250A ASN* 1.3 78.1 - - - +
252A ASP* 1.3 63.8 + - - +
254A LYS* 3.2 8.1 + - + +
255A GLN* 3.0 50.5 + - + +
518A LYS* 3.4 10.2 + - - -
521A GLU* 2.9 29.6 + - - -
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Residues in contact with ASP 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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208A ARG* 3.1 41.5 + - - -
212A LYS* 3.7 18.3 + - - +
249A PRO 3.4 8.4 + - - +
250A ASN 3.7 0.2 - - - -
251A TYR* 1.3 79.8 - - - +
253A ILE* 1.3 65.8 + - - -
255A GLN* 3.3 12.8 + - + +
256A LEU* 3.2 19.8 + - - +
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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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208A ARG* 3.8 43.1 - - + +
211A GLN* 3.2 36.3 - - + +
212A LYS* 4.3 15.5 - - + +
215A LEU* 3.6 14.1 - - + -
236A MET* 3.4 27.4 - - + -
243A ASN* 5.2 0.7 - - - +
250A ASN* 2.9 18.6 + - + +
252A ASP* 1.3 78.0 + - - +
254A LYS* 1.3 56.3 + - - +
256A LEU* 2.9 9.8 + - + +
257A ALA* 2.7 33.0 + - - +
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Residues in contact with LYS 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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236A MET* 4.7 6.1 - - - -
238A VAL* 5.7 5.8 - - + -
243A ASN* 3.1 32.5 + - + +
244A LEU* 2.9 27.2 + - + +
250A ASN 3.1 7.3 + - - +
251A TYR* 3.3 16.2 - - + +
253A ILE* 1.3 77.3 - - - +
255A GLN* 1.3 57.2 + - - +
257A ALA* 3.3 9.2 + - - +
258A LEU* 2.9 34.1 + - + +
521A GLU* 2.9 33.9 + - - +
524A TRP* 4.4 23.3 - - + -
525A ASP* 2.7 28.5 + - - -
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Residues in contact with GLN 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 TYR* 3.0 53.9 + - + +
252A ASP* 3.3 12.6 - - + +
253A ILE 3.1 0.4 - - - -
254A LYS* 1.3 77.4 - - - +
256A LEU* 1.3 65.2 + - - +
258A LEU* 3.2 15.0 + - - +
259A GLU* 3.0 21.8 + - - +
517A LEU* 4.3 14.7 - - - +
518A LYS* 4.9 2.7 - - - +
521A GLU* 3.1 16.6 + - - +
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Residues in contact with LEU 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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212A LYS* 3.9 24.5 - - + +
215A LEU* 3.8 26.0 - - + -
216A LYS* 3.8 36.8 - - + +
219A ILE* 3.9 13.2 - - + -
252A ASP 3.2 9.2 + - - +
253A ILE* 2.9 9.4 + - - +
255A GLN* 1.3 77.6 - - - +
257A ALA* 1.3 59.8 + - - +
259A GLU* 3.2 25.1 + - - +
260A CYS* 2.9 29.9 + - - +
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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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215A LEU* 3.9 15.6 - - + +
236A MET* 3.7 31.6 - - + -
253A ILE 2.7 15.4 + - - +
254A LYS* 3.4 9.9 - - - +
256A LEU* 1.3 72.3 - - - +
258A LEU* 1.3 57.1 + - - +
260A CYS* 3.2 3.3 + - - +
261A ALA* 2.8 30.1 + - - +
267A PRO* 3.7 9.8 - - + +
524A TRP* 3.8 14.6 - - + -
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Residues in contact with LEU 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 LYS* 2.9 30.5 + - + +
255A GLN* 3.2 21.3 + - - +
257A ALA* 1.3 73.2 - - - +
259A GLU* 1.3 67.5 + - - +
261A ALA* 3.2 2.6 + - - +
262A SER* 2.9 24.3 + - - -
517A LEU* 4.2 16.8 - - + +
520A LEU* 3.6 19.6 - - + +
521A GLU* 3.6 52.9 - - + +
524A TRP* 3.6 33.7 - - + -
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Residues in contact with GLU 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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219A ILE* 3.6 28.4 - - - +
255A GLN 3.0 12.4 + - - +
256A LEU* 3.2 20.2 + - - +
258A LEU* 1.3 76.7 - - - +
260A CYS* 1.3 63.7 + - - +
262A SER* 2.3 28.2 + - - +
263A LYS* 2.8 45.8 + - - +
514A LYS 6.1 0.4 - - - +
517A LEU* 3.7 16.5 - - + +
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Residues in contact with CYS 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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215A LEU* 3.9 18.8 - - + -
218A ARG* 3.6 35.7 - - - -
219A ILE* 3.9 19.7 - - + +
234A LEU* 4.8 0.7 - - - -
256A LEU 2.9 13.6 + - - +
257A ALA 3.3 8.5 - - - +
259A GLU* 1.3 75.1 - - - +
261A ALA* 1.3 55.5 + - - +
263A LYS* 2.8 3.0 + - - +
264A ARG* 2.7 34.8 + - - +
266A TYR 3.3 16.3 - - - +
267A PRO* 3.9 9.4 - - + -
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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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257A ALA 2.8 19.0 + - - +
258A LEU 3.6 4.7 - - - +
260A CYS* 1.3 72.5 - - - +
262A SER* 1.3 59.3 + - - +
265A MET* 2.9 35.4 + - - +
266A TYR 3.1 15.1 + - - +
267A PRO 4.1 4.7 - - - +
520A LEU* 4.3 6.7 - - + -
524A TRP* 3.8 24.0 - - + +
536A VAL* 5.5 4.3 - - + +
538A MET* 4.3 9.6 - - - +
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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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258A LEU 2.9 12.4 + - - -
259A GLU* 2.3 34.7 + - - +
261A ALA* 1.3 76.0 - - - +
263A LYS* 1.3 63.9 + - - +
512A ASP* 5.1 0.3 - - - +
513A MET 4.0 10.2 + - - -
514A LYS* 3.2 40.3 + - - +
517A LEU* 4.6 4.7 - - - +
520A LEU* 4.3 8.5 - - - +
538A MET* 4.0 16.7 - - - +
539A PRO 4.9 8.3 - - - +
540A VAL* 5.3 1.4 - - - +
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Residues in contact with LYS 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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219A ILE* 4.2 18.3 - - + +
259A GLU* 2.8 48.2 + - - +
260A CYS* 2.8 5.0 + - - +
262A SER* 1.3 81.8 - - - +
264A ARG* 1.3 78.3 + - + +
265A MET 3.8 0.4 - - - -
514A LYS* 3.5 35.0 - - + -
540A VAL* 3.1 25.5 - - - +
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Residues in contact with ARG 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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218A ARG* 2.7 49.4 + - + +
219A ILE* 2.6 39.5 + - - -
220A LYS 3.6 1.6 + - - -
221A GLY* 3.1 18.7 - - - +
226A GLY 3.0 22.5 + - - -
227A ILE* 3.6 5.7 - - - +
228A THR* 3.0 55.6 + - + +
229A PRO* 4.6 1.6 - - - -
260A CYS* 2.7 18.4 + - - +
263A LYS* 1.3 86.0 + - + +
265A MET* 1.3 64.7 + - - +
266A TYR* 2.8 14.2 + - - +
540A VAL* 4.5 5.1 - - - +
542A LYS* 4.3 16.1 - - - +
573A ASN* 4.6 1.8 + - - -
582A LEU* 3.9 4.9 - - - +
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Residues in contact with MET 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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261A ALA* 2.9 21.7 + - - +
263A LYS 3.8 0.4 - - - -
264A ARG* 1.3 80.0 - - - +
266A TYR* 1.3 62.2 + - + +
267A PRO 3.7 9.2 - - - +
268A ASP* 4.3 5.7 - - - +
536A VAL* 3.5 17.4 + - - +
537A ASN* 3.8 6.7 - - - +
538A MET* 3.3 43.7 - - - +
540A VAL* 3.6 22.3 - - + +
575A ILE* 3.9 6.3 - - + +
576A ARG* 4.0 0.7 - - - -
577A ARG* 3.7 35.4 + - - +
582A LEU* 3.4 35.7 - - + -
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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