Contacts of the helix formed by residues 301 - 314 (chain A) in PDB entry 3HF8
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 301 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106A PRO* 5.9 1.1 - - - -
239A ARG* 3.6 0.4 - - - +
300A ALA* 1.3 79.2 - - - +
302A GLU* 1.3 59.4 + - - +
303A GLU* 3.6 8.6 + - - +
304A ALA* 3.0 25.4 + - - +
305A VAL* 2.9 27.9 + - - +
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Residues in contact with GLU 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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239A ARG* 3.5 24.5 + - - +
301A SER* 1.3 72.0 - - - +
303A GLU* 1.3 62.3 + - - +
305A VAL* 3.5 6.5 + - - +
306A GLN* 3.1 24.6 + - - +
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Residues in contact with GLU 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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301A SER* 3.6 7.6 + - - +
302A GLU* 1.3 79.7 - - - +
304A ALA* 1.3 60.9 + - - +
306A GLN* 3.5 7.8 + - - +
307A LYS* 3.2 58.6 + - + +
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Residues in contact with ALA 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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300A ALA* 3.9 17.5 - - + -
301A SER* 3.0 23.5 + - - +
303A GLU* 1.3 73.0 - - - +
305A VAL* 1.3 60.6 + - - +
307A LYS* 3.4 3.4 + - - +
308A LEU* 3.0 37.6 + - + +
393A ILE* 3.9 33.5 - - + +
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Residues in contact with VAL 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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238A PRO* 4.2 10.3 - - + -
239A ARG* 3.6 64.6 - - + +
242A LEU* 4.2 6.1 - - + +
297A SER* 4.0 18.6 - - - +
300A ALA* 4.0 3.8 - - + +
301A SER 2.9 20.1 + - - +
302A GLU* 3.8 8.1 - - - +
304A ALA* 1.3 73.5 - - - +
306A GLN* 1.3 55.1 + - - +
308A LEU* 3.3 7.7 + - - +
309A ALA* 2.8 32.9 + - - +
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Residues in contact with GLN 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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238A PRO* 6.0 0.9 - - - -
302A GLU 3.1 16.9 + - - +
303A GLU* 3.8 7.3 - - - +
304A ALA 3.4 0.2 - - - -
305A VAL* 1.3 77.7 - - - +
307A LYS* 1.3 66.6 + - - +
309A ALA* 3.7 6.4 - - + +
310A THR* 2.9 39.9 + - - +
360A CYS 4.6 7.1 - - - +
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Residues in contact with LYS 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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303A GLU* 3.2 47.3 + - + +
304A ALA* 3.8 4.7 - - - +
305A VAL 3.3 0.2 - - - -
306A GLN* 1.3 85.0 - - - +
308A LEU* 1.3 59.7 + - - +
310A THR* 3.5 1.2 + - - -
311A CYS* 3.0 34.3 + - - -
360A CYS* 3.6 32.8 - - + +
361A LYS* 3.8 25.4 - - - +
389A PHE* 4.2 12.9 - - + -
393A ILE* 4.2 27.6 - - + +
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Residues in contact with LEU 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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242A LEU* 4.2 11.7 - - + -
293A ILE* 4.0 15.7 - - + +
296A ALA* 3.7 14.4 - - + +
297A SER* 3.6 37.2 - - - +
304A ALA* 3.0 28.0 + - + +
305A VAL* 3.7 4.0 - - - +
307A LYS* 1.3 74.3 - - - +
309A ALA* 1.3 57.0 + - - +
311A CYS* 3.3 5.4 + - - +
312A TYR* 2.9 30.0 + - - +
386A MET* 3.7 18.2 - - + -
389A PHE* 5.2 1.1 - - + -
390A THR* 3.7 28.5 - - + -
393A ILE* 4.3 11.7 - - + -
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Residues in contact with ALA 309 (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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238A PRO* 3.8 29.4 - - + -
242A LEU* 3.9 12.7 - - + +
305A VAL 2.8 21.1 + - - +
306A GLN* 3.7 6.3 - - - +
308A LEU* 1.3 73.3 - - - +
310A THR* 1.3 57.6 + - - +
312A TYR* 3.5 9.7 + - + +
313A PHE* 2.9 27.9 + - - +
364A CYS* 5.4 0.9 - - - -
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Residues in contact with THR 310 (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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306A GLN* 2.9 24.9 + - - +
307A LYS 3.8 3.4 - - - -
309A ALA* 1.3 74.9 - - - +
311A CYS* 1.3 64.1 + - - +
313A PHE* 3.2 5.5 + - - +
314A PHE* 3.0 34.8 + - + +
359A THR 3.3 21.5 - - - +
360A CYS* 3.4 17.6 + - - +
362A GLN 3.3 26.2 + - - +
364A CYS* 3.9 10.6 - - - -
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Residues in contact with CYS 311 (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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289A PHE* 6.4 0.2 - - + -
293A ILE* 4.9 1.1 - - + -
307A LYS 3.0 20.5 + - - +
308A LEU 3.6 4.9 - - - +
310A THR* 1.3 76.0 - - - +
312A TYR* 1.3 55.7 + - - +
314A PHE* 3.4 2.1 + - - +
315A THR* 2.7 37.6 + - - +
354A PHE* 4.6 5.8 - - + -
356A PRO* 4.0 24.9 - - - -
359A THR* 4.6 8.1 - - - -
360A CYS* 4.1 14.4 - - - -
386A MET* 3.7 38.8 - - + -
389A PHE* 4.2 5.4 - - - -
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Residues in contact with TYR 312 (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 PHE* 3.2 25.3 - + - -
242A LEU* 4.1 13.5 - - + -
245A LEU* 3.8 29.2 - - + -
250A PHE* 3.5 15.1 - + - -
277A HIS* 3.5 2.9 - - - -
290A SER* 5.5 0.7 - - - -
293A ILE* 4.0 15.2 - - + +
308A LEU 2.9 16.9 + - - +
309A ALA* 3.5 11.2 - - + +
311A CYS* 1.3 76.5 - - - +
313A PHE* 1.3 62.9 + - + +
315A THR* 3.6 5.4 - - - -
316A VAL* 2.8 60.5 + - + -
317A GLU* 2.9 40.0 + - + -
401A ML0 3.8 11.0 - - - -
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Residues in contact with PHE 313 (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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309A ALA 2.9 17.3 + - - +
310A THR 3.2 6.5 + - - +
312A TYR* 1.3 80.3 - - + +
314A PHE* 1.3 69.3 - + - +
315A THR 3.4 0.2 + - - -
317A GLU* 3.2 10.2 - - + +
318A PHE* 2.9 57.0 + + - +
364A CYS* 3.5 25.6 - - + -
365A LEU 3.7 11.7 - - - -
370A GLN* 3.4 32.5 - - - -
401A ML0 3.4 59.0 - + - -
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Residues in contact with PHE 314 (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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310A THR* 3.0 28.9 + - + +
311A CYS 3.7 0.7 - - - +
312A TYR 3.3 0.2 - - - -
313A PHE* 1.3 85.0 - + - +
315A THR* 1.3 63.5 + - - +
318A PHE* 4.1 10.0 - - + +
319A GLY* 3.4 17.2 - - - -
359A THR* 3.6 25.8 - - + -
362A GLN* 3.7 34.5 - - + -
363A GLU 3.4 18.6 - - - -
364A CYS* 3.9 13.5 - - - -
370A GLN* 3.9 22.4 - - + -
372A VAL* 3.5 22.4 - - + -
373A TYR* 5.2 0.4 - - - -
374A PHE* 3.6 36.6 + + + +
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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