Contacts of the helix formed by residues 301 - 316 (chain A) in PDB entry 5I0H
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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299A THR 4.3 1.2 + - - -
300A ILE* 1.3 70.4 - - - +
302A ASP* 1.3 58.9 + - - +
303A GLN* 3.9 5.5 + - - +
304A GLU* 3.3 33.4 + - - +
305A SER* 3.0 29.0 + - - -
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Residues in contact with ASP 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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258A ARG* 3.0 41.4 + - - -
261A HIS* 4.7 2.3 - - - +
264A TYR* 3.6 31.3 - - - +
265A ALA* 3.4 14.0 + - - +
268A ALA* 3.9 10.3 - - + -
295A VAL 4.3 3.3 - - - +
296A GLU* 4.9 5.4 - - - +
297A ASP 5.4 0.5 + - - -
300A ILE* 3.4 17.6 + - - +
301A SER* 1.3 69.1 - - - +
303A GLN* 1.4 64.9 + - - +
305A SER* 3.3 6.3 + - - -
306A PHE* 3.0 18.2 + - - +
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Residues in contact with GLN 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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268A ALA* 3.7 36.9 + - + +
269A GLY* 4.4 9.1 + - - +
301A SER* 3.3 6.0 + - - +
302A ASP* 1.4 77.7 - - - +
304A GLU* 1.3 65.9 + - + +
306A PHE* 3.3 5.2 + - - +
307A ARG* 3.2 19.8 + - - +
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Residues in contact with GLU 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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301A SER* 3.3 26.5 + - - +
303A GLN* 1.3 80.3 - - + +
305A SER* 1.4 66.2 + - - +
307A ARG* 3.3 38.6 + - - +
308A GLU* 3.1 23.3 + - - +
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Residues in contact with SER 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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206A ALA* 6.2 1.6 - - - -
261A HIS* 6.0 5.2 - - - -
265A ALA* 4.4 9.9 - - - -
300A ILE* 4.2 12.7 - - - +
301A SER 3.0 15.6 + - - -
302A ASP* 3.3 11.0 + - - -
304A GLU* 1.4 72.1 - - - +
306A PHE* 1.3 60.8 + - - +
308A GLU* 3.2 14.0 + - - +
309A VAL* 2.9 36.9 + - - +
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Residues in contact with PHE 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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262A ILE* 4.8 12.6 - - + -
265A ALA* 3.3 38.8 - - + +
266A LEU* 3.7 22.2 - - + -
269A GLY* 3.6 30.3 - - - -
270A LEU* 3.9 25.6 - - + -
302A ASP 3.0 8.3 + - - +
303A GLN 3.3 9.2 + - - +
305A SER* 1.3 75.2 - - - +
307A ARG* 1.3 58.3 + - - +
309A VAL* 3.2 6.4 + - + +
310A ILE* 2.9 64.4 + - + +
323A VAL* 5.8 0.2 - - + -
327A SER* 4.5 5.6 - - - -
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Residues in contact with ARG 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 GLN 3.2 9.9 + - - +
304A GLU* 3.5 37.9 + - - +
305A SER 3.3 0.2 - - - -
306A PHE* 1.3 78.0 - - - +
308A GLU* 1.3 62.6 + - - +
310A ILE* 3.4 8.9 + - + +
311A THR* 3.1 33.7 + - - +
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Residues in contact with GLU 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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199A GLU* 4.6 2.4 - - - +
202A PRO* 3.7 30.3 - - + +
304A GLU 3.1 14.1 + - - +
305A SER* 3.4 15.3 + - - +
307A ARG* 1.3 74.7 - - - +
309A VAL* 1.4 58.3 + - + +
311A THR* 3.5 6.1 + - - -
312A ALA* 3.0 29.3 + - - +
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Residues in contact with VAL 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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202A PRO* 3.8 13.9 - - + +
203A ILE* 4.8 5.8 - - + -
206A ALA* 3.5 28.3 - - + -
207A PHE* 4.6 3.1 - - + -
262A ILE* 4.1 18.4 - - + -
265A ALA* 5.6 0.9 - - + -
305A SER* 2.9 25.0 + - - +
306A PHE* 3.2 9.4 + - + +
308A GLU* 1.4 74.2 - - - +
310A ILE* 1.4 55.9 + - + +
312A ALA* 3.2 6.8 + - - +
313A MET* 2.8 63.9 + - + +
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Residues in contact with ILE 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 PHE* 2.9 57.3 + - + +
307A ARG* 3.7 9.2 - - + +
308A GLU 3.4 0.2 - - - -
309A VAL* 1.4 77.7 - - + +
311A THR* 1.3 63.0 + - - +
313A MET* 3.4 10.1 + - - +
314A ASP* 3.1 23.0 + - + +
323A VAL* 3.6 33.1 - - + +
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Residues in contact with THR 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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199A GLU* 4.7 13.5 - - - +
307A ARG* 3.1 25.5 + - - +
308A GLU* 3.7 7.0 - - - -
310A ILE* 1.3 73.7 - - - +
312A ALA* 1.4 67.6 + - - +
314A ASP* 3.3 10.4 + - - +
315A VAL* 3.1 26.2 + - + +
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Residues in contact with ALA 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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199A GLU* 3.4 48.9 + - - +
202A PRO* 4.0 6.1 - - + -
203A ILE* 3.6 13.0 - - + +
308A GLU 3.0 17.8 + - - +
309A VAL* 3.5 4.9 - - - +
311A THR* 1.4 76.9 - - - +
313A MET* 1.4 56.2 + - - +
315A VAL* 3.2 4.7 + - - +
316A MET* 2.9 30.5 + - - +
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Residues in contact with MET 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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203A ILE* 3.9 20.0 - - + -
207A PHE* 3.5 36.6 - - + -
262A ILE* 5.5 0.2 - - + -
309A VAL* 2.8 38.7 + - + +
310A ILE* 3.8 7.6 - - - +
311A THR 3.3 0.2 - - - -
312A ALA* 1.4 70.4 - - - +
314A ASP* 1.3 60.2 + - - +
316A MET 3.2 5.9 + - - -
317A GLN 3.3 0.2 + - - -
318A PHE* 3.0 58.4 + - + -
323A VAL* 4.0 35.0 - - + -
326A VAL* 4.8 9.9 - - + -
413A VAL* 5.2 1.3 - - + -
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Residues in contact with ASP 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 ILE* 3.1 13.9 + - + +
311A THR* 3.4 13.5 - - - +
313A MET* 1.3 72.1 - - - +
315A VAL* 1.3 68.8 + - - +
317A GLN* 3.1 15.4 + - - +
318A PHE 4.4 9.3 - - - +
323A VAL* 5.5 0.8 - - - +
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Residues in contact with VAL 315 (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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195A ARG* 4.0 29.8 - - - +
196A ALA* 3.8 29.2 - - + +
199A GLU* 3.9 25.8 - - + +
311A THR* 3.1 19.1 + - + +
312A ALA 3.5 7.0 - - - +
314A ASP* 1.3 79.0 - - - +
316A MET* 1.3 57.6 + - - +
317A GLN* 3.1 5.5 + - - +
420A ARG* 3.0 28.4 + - - +
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Residues in contact with MET 316 (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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196A ALA* 3.2 30.7 - - - +
199A GLU* 3.6 15.9 - - + +
200A SER* 3.5 23.1 - - - +
203A ILE* 3.8 7.6 - - + -
312A ALA 2.9 13.0 + - - +
313A MET 3.2 6.4 + - - +
315A VAL* 1.3 74.0 - - - +
317A GLN* 1.3 68.0 + - - +
318A PHE* 3.4 26.4 - - + -
416A LYS* 4.3 6.4 - - - +
417A ILE* 3.9 31.9 - - + +
420A ARG* 3.6 33.4 - - + +
421A ILE* 4.6 0.7 - - - -
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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