Contacts of the helix formed by residues 291 - 308 (chain A) in PDB entry 3H8E
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 MET 291 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A LEU* 6.5 0.4 - - + -
190A GLY* 6.1 2.0 - - - -
197A CYS* 4.4 14.4 - - - +
198A HIS 5.1 1.1 - - - +
199A PRO* 5.2 4.7 - - - -
202A LEU* 0.9 88.6 - - + -
267A LYS* 3.5 13.1 - - - +
268A GLY* 3.3 25.1 - - - +
269A ILE* 3.1 32.4 + - - +
292A CYS* 1.3 64.0 + - - +
293A GLY 3.2 2.7 - - - -
294A ALA* 3.2 12.1 + - + -
295A ALA* 2.8 24.6 + - + +
298A PHE* 4.7 4.7 - - + -
319A CYS* 3.6 15.0 - - - -
376A THR* 4.6 9.3 + - - +
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Residues in contact with CYS 292 (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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186A THR* 4.7 5.3 - - + +
190A GLY* 4.4 21.1 - - - -
291A MET* 1.3 76.0 - - - +
293A GLY* 1.4 59.4 + - - +
295A ALA* 3.6 9.4 - - - +
296A SER* 2.8 30.3 + - - -
376A THR* 4.1 9.4 + - + +
465A ILE* 3.9 3.6 - - - +
469A ALA* 3.7 40.8 - - + -
470A TRP* 4.6 11.4 - - - -
479A ALA* 4.6 9.0 - - - -
482A ARG 5.2 1.2 - - - +
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Residues in contact with GLY 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A GLY* 3.8 6.5 - - - -
267A LYS 3.6 5.3 + - - -
291A MET 3.2 1.2 - - - -
292A CYS* 1.4 73.3 - - - +
294A ALA* 1.3 65.1 + - - +
296A SER* 2.8 23.1 + - - -
297A VAL* 3.1 12.8 + - - +
374A ILE* 3.4 23.0 - - - +
375A ALA* 4.5 1.6 - - - -
376A THR* 4.7 4.8 + - - +
465A ILE* 3.8 12.4 - - - +
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Residues in contact with ALA 294 (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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266A GLY* 3.6 15.2 - - - +
267A LYS 2.9 17.2 + - - +
268A GLY* 3.7 14.6 - - - -
291A MET* 3.2 23.5 + - + +
293A GLY* 1.3 76.3 - - - +
295A ALA* 1.3 60.8 + - - +
297A VAL* 3.1 4.2 + - - +
298A PHE* 3.0 26.1 + - - -
317A LEU* 3.9 20.7 - - + +
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Residues in contact with ALA 295 (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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186A THR* 2.8 47.9 + - + +
189A LEU* 4.1 24.0 - - + -
190A GLY* 4.5 4.0 - - - +
291A MET* 2.8 22.7 + - + +
292A CYS* 3.6 12.3 - - - +
293A GLY 3.2 0.2 - - - -
294A ALA* 1.3 72.9 - - - +
296A SER* 1.4 53.9 + - - +
298A PHE* 3.3 5.0 + - - +
299A GLY 2.9 16.3 + - - -
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Residues in contact with SER 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A THR* 3.6 12.1 - - - +
292A CYS 2.8 18.7 + - - -
293A GLY 2.8 17.3 + - - -
295A ALA* 1.4 71.1 - - - +
297A VAL* 1.3 59.7 + - - +
300A THR* 2.9 34.2 + - - -
374A ILE* 3.5 19.6 - - - +
482A ARG 4.4 2.7 - - - -
483A PRO* 3.5 26.1 - - - +
484A VAL* 3.5 10.9 - - - +
487A LEU* 4.2 4.7 - - - +
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Residues in contact with VAL 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A LEU* 5.8 0.2 - - + -
264A LEU* 3.9 19.5 - - + +
266A GLY* 4.0 15.3 - - - +
293A GLY 3.1 13.8 + - - +
294A ALA 3.1 6.9 + - - +
296A SER* 1.3 74.3 - - - +
298A PHE* 1.3 67.2 + - - +
300A THR* 3.3 5.6 + - - -
301A LEU* 2.8 23.9 + - - +
315A CYS* 3.5 36.5 - - + -
317A LEU* 3.6 13.7 - - + -
374A ILE* 3.9 26.7 - - + -
487A LEU* 5.2 0.9 - - + -
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Residues in contact with PHE 298 (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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185A PHE* 2.4 48.0 - + + -
189A LEU* 3.5 14.6 - - + -
202A LEU* 3.6 44.6 - - + -
205A GLN* 4.1 6.5 - - + -
206A ALA* 3.8 27.6 - - + -
209A LEU* 4.2 14.8 - - + +
250A LEU* 4.1 11.4 - - + -
291A MET* 4.7 2.0 - - + -
294A ALA 3.0 17.1 + - - -
295A ALA* 3.4 6.3 - - - +
297A VAL* 1.3 78.1 - - - +
299A GLY* 1.3 56.3 + - - +
301A LEU* 3.4 6.7 + - + +
302A ARG* 2.9 29.1 + - - +
317A LEU* 3.2 31.4 - - + +
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Residues in contact with GLY 299 (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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182A GLY* 3.2 28.0 - - - -
185A PHE* 3.5 6.0 - - - -
186A THR* 3.3 19.1 - - - -
295A ALA 2.9 11.7 + - - -
296A SER 3.4 0.6 + - - -
297A VAL 3.2 0.2 - - - -
298A PHE* 1.3 74.7 - - - +
300A THR* 1.3 64.7 - - - +
302A ARG* 3.3 1.3 + - - -
303A ALA* 3.0 19.8 + - - +
484A VAL* 4.1 4.4 - - - +
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Residues in contact with THR 300 (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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264A LEU* 3.9 13.9 - - + -
296A SER 2.9 18.6 + - - -
297A VAL 3.8 3.1 - - - -
299A GLY* 1.3 72.5 - - - +
301A LEU* 1.3 67.4 + - - +
303A ALA* 3.1 4.2 + - - +
304A VAL* 2.9 27.2 + - + +
313A LEU* 5.2 0.2 - - + -
484A VAL* 3.8 11.3 - - - +
487A LEU* 3.4 35.4 - - + +
488A THR* 3.9 17.9 - - - +
491A LEU* 3.9 24.7 - - + -
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Residues in contact with LEU 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A LEU* 3.8 14.1 - - + -
216A LEU* 4.2 8.3 - - + -
250A LEU* 3.8 39.9 - - + -
252A TYR* 4.1 20.6 - - + -
264A LEU* 5.5 0.2 - - - +
297A VAL 2.8 17.2 + - - +
298A PHE* 3.6 6.5 - - - +
300A THR* 1.3 77.8 - - - +
302A ARG* 1.4 57.0 + - - +
304A VAL* 3.1 6.2 + - + +
305A LEU* 2.9 52.3 + - + +
313A LEU* 4.0 20.8 - - + +
315A CYS* 4.1 15.3 - - - -
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Residues in contact with ARG 302 (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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181A THR* 3.7 38.6 + - + +
182A GLY* 4.2 5.2 - - - -
185A PHE* 3.3 42.3 - - + +
209A LEU* 3.9 28.0 - - + +
213A HIS* 5.7 1.8 + - - -
298A PHE 2.9 17.5 + - - +
299A GLY* 3.3 6.9 + - - +
301A LEU* 1.4 76.9 - - - +
303A ALA* 1.3 56.0 + - - +
305A LEU* 3.4 12.2 + - - +
306A GLU* 3.0 27.5 + - + +
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Residues in contact with ALA 303 (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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178A ALA* 3.4 34.0 + - + +
179A ILE* 4.3 2.5 - - - +
182A GLY* 4.8 0.7 - - - -
299A GLY 3.0 12.7 + - - +
300A THR 3.1 8.5 + - - +
302A ARG* 1.3 75.2 - - - +
304A VAL* 1.3 62.4 + - - +
306A GLU* 3.2 3.3 + - - +
307A LEU* 3.0 31.0 + - - +
484A VAL* 5.0 0.7 - - + -
488A THR* 3.7 26.9 - - + +
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Residues in contact with VAL 304 (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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252A TYR* 3.6 34.9 + - + -
300A THR* 2.9 17.9 + - + +
301A LEU* 3.5 10.3 - - + +
303A ALA* 1.3 72.8 - - + +
305A LEU* 1.3 61.3 + - - +
307A LEU* 3.3 1.4 + - - -
308A GLN* 2.8 24.8 + - - -
309A LEU* 3.3 33.3 + - + -
311A VAL* 4.7 3.6 - - + -
313A LEU* 4.1 11.7 - - + -
488A THR* 5.2 3.6 - - + -
491A LEU* 3.7 30.5 - - + -
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Residues in contact with LEU 305 (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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209A LEU* 4.3 8.7 - - + -
213A HIS* 3.8 56.0 + - + +
215A ALA* 5.5 1.1 - - + -
216A LEU* 4.2 13.0 - - + -
252A TYR* 3.6 34.5 - - + -
301A LEU* 2.9 41.1 + - + +
302A ARG* 3.6 7.4 - - - +
303A ALA 3.3 0.2 - - - -
304A VAL* 1.3 74.8 - - - +
306A GLU* 1.3 65.1 + - - +
308A GLN* 3.2 21.2 + - - +
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Residues in contact with GLU 306 (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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174A LYS* 5.0 6.2 + - - +
177A SER* 4.2 10.3 - - - +
178A ALA* 2.9 37.9 + - + +
181A THR* 3.7 22.0 + - + +
302A ARG* 3.0 14.5 + - + +
303A ALA 3.2 7.6 + - - +
305A LEU* 1.3 76.4 - - - +
307A LEU* 1.3 62.9 + - + +
308A GLN* 3.5 5.4 + - - +
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Residues in contact with LEU 307 (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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174A LYS* 3.9 40.1 + - + +
175A HIS* 4.0 19.5 - - + +
178A ALA* 3.5 24.7 - - + -
303A ALA 3.0 17.1 + - - +
304A VAL 3.9 2.0 - - - +
306A GLU* 1.3 77.8 - - + +
308A GLN* 1.3 69.6 + - - +
309A LEU* 3.3 21.5 + - + +
488A THR* 4.4 15.0 - - + -
492A LEU* 3.9 26.7 - - + -
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Residues in contact with GLN 308 (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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252A TYR* 3.4 11.5 + - + +
304A VAL 2.8 11.6 + - - -
305A LEU 3.2 15.6 + - - +
306A GLU 4.4 4.7 - - - +
307A LEU* 1.3 79.5 - - - +
309A LEU* 1.4 65.6 + - - +
310A PRO* 3.5 4.0 - - - +
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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
------------------------------------------------------------
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