Contacts of the helix formed by residues 300 - 313 (chain A) in PDB entry 1OJ7
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 LYS 300 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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204A VAL* 2.9 29.1 + - + +
205A THR 4.0 8.5 - - - +
263A ASP* 2.8 29.8 + - - -
292A LEU* 3.8 18.4 - - - -
293A TRP* 3.8 23.3 - - + +
296A LYS* 3.1 29.2 + - + +
297A ARG 3.8 1.6 - - - -
299A THR* 1.3 78.2 - - - +
301A ARG* 1.3 58.7 + - - +
302A ALA 3.3 2.6 + - - -
303A LYS* 3.3 3.5 + - - -
304A LEU* 2.8 42.0 + - + +
370A GLU* 2.7 38.6 + - - +
374A ILE* 6.4 0.4 - - - -
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Residues in contact with ARG 301 (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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297A ARG 3.2 17.0 + - - +
298A ASP* 3.3 28.1 + - - +
299A THR 3.4 1.2 + - - -
300A LYS* 1.3 77.0 - - - +
302A ALA* 1.3 71.5 + - - +
304A LEU* 3.7 1.4 - - - +
305A LEU* 3.0 44.3 + - + +
319A ASP* 3.7 25.5 + - + +
323A ILE* 3.9 19.2 - - + +
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Residues in contact with ALA 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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-2A LYS* 6.3 0.2 - - - +
207A PRO* 3.8 31.2 - - + -
299A THR 5.3 0.4 + - - -
300A LYS 3.4 0.6 - - - -
301A ARG* 1.3 92.1 - - - +
303A LYS* 1.3 60.0 + - + +
305A LEU* 3.4 10.3 + - - +
306A GLN* 3.0 26.2 + - - +
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Residues in contact with LYS 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-2A LYS* 4.7 3.6 - - - +
203A TYR* 2.6 53.5 + - - +
204A VAL* 3.9 7.2 - - - +
205A THR* 3.6 31.1 + - - +
206A LYS 4.2 5.0 + - - -
207A PRO* 4.0 28.0 - - + +
208A VAL 5.0 4.2 + - - +
214A ASP* 3.0 36.4 + - - +
300A LYS 3.3 3.9 + - - +
302A ALA* 1.3 74.8 - - + +
304A LEU* 1.3 60.0 + - - +
306A GLN* 3.8 16.7 - - - +
307A TYR* 2.9 30.8 + - - +
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Residues in contact with LEU 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A VAL* 3.7 22.2 - - + +
293A TRP* 3.8 40.2 - - + +
297A ARG* 3.8 25.6 - - - +
300A LYS* 2.8 33.3 + - + +
301A ARG 3.7 3.8 - - - +
303A LYS* 1.3 76.4 - - - +
305A LEU* 1.3 55.3 + - - +
307A TYR* 3.5 11.5 + - + +
308A ALA* 2.8 29.3 + - - +
323A ILE* 3.9 30.5 - - + -
326A ALA* 4.6 4.4 - - + +
327A ILE* 5.0 2.9 - - + -
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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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301A ARG* 3.0 35.6 + - + +
302A ALA* 3.7 7.6 - - - +
304A LEU* 1.3 73.4 - - - +
306A GLN* 1.3 65.5 + - - +
308A ALA* 3.4 4.8 + - - +
309A GLU* 3.1 23.2 + - - +
319A ASP* 3.6 43.7 - - - +
322A ARG* 3.7 54.6 + - + +
323A ILE* 4.0 8.3 - - + -
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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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-2A LYS* 3.4 23.9 + - - -
203A TYR* 3.8 3.7 + - - +
214A ASP* 3.1 25.2 + - - +
218A GLU* 2.8 26.2 + - - +
302A ALA 3.0 16.8 + - - +
303A LYS* 3.8 15.6 - - - +
305A LEU* 1.3 74.1 - - - +
307A TYR* 1.3 55.4 + - - +
309A GLU* 3.2 5.1 + - - -
310A ARG* 2.7 67.7 + - + +
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Residues in contact with TYR 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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196A PHE* 3.2 21.6 - + - -
200A VAL* 4.3 1.6 - - + -
203A TYR* 3.6 20.3 + + + -
204A VAL* 4.2 9.4 - - + -
221A LEU* 3.9 22.7 - - + -
293A TRP* 3.6 24.0 - + - -
303A LYS 2.9 18.0 + - - +
304A LEU* 3.5 12.6 - - + +
306A GLN* 1.3 75.6 - - - +
308A ALA* 1.3 63.3 + - - +
311A VAL* 2.9 48.7 + - + +
312A TRP* 3.0 28.2 + + - -
326A ALA* 4.1 13.2 - - + -
330A THR* 2.5 30.3 + - - +
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Residues in contact with ALA 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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304A LEU 2.8 20.8 + - - +
305A LEU* 3.6 9.4 - - - +
307A TYR* 1.3 73.8 - - - +
309A GLU* 1.3 58.8 + - - +
312A TRP* 3.2 10.3 + - - +
313A ASN 3.1 10.0 + - - -
314A ILE* 2.8 37.8 + - + +
322A ARG* 4.0 11.9 - - + +
326A ALA* 3.7 26.2 - - + -
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Residues in contact with GLU 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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305A LEU 3.1 15.9 + - - +
306A GLN* 3.8 5.0 - - - +
308A ALA* 1.3 77.0 - - - +
310A ARG* 1.3 68.8 + - + +
313A ASN* 3.0 25.9 + - - +
314A ILE 3.4 15.7 + - - +
315A THR* 3.5 24.4 - - + +
322A ARG* 4.2 12.5 + - - +
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Residues in contact with ARG 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A TYR* 4.5 0.2 - - - +
214A ASP* 4.8 2.4 - - - +
215A ARG* 3.3 47.8 - - - +
218A GLU* 2.9 54.0 + - + +
222A LEU* 3.9 19.9 - - - +
306A GLN* 2.7 46.5 + - + +
309A GLU* 1.3 80.4 - - + +
311A VAL* 1.3 60.1 + - - +
313A ASN 4.7 0.4 + - - -
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Residues in contact with VAL 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A TYR* 4.7 0.2 - - - +
218A GLU* 4.2 22.7 - - + +
221A LEU* 3.9 26.9 - - + -
222A LEU* 3.5 19.1 - - + +
225A ILE* 3.4 32.0 - - + +
307A TYR* 2.9 40.8 + - + +
310A ARG* 1.3 78.7 - - - +
312A TRP* 1.3 75.6 + - + +
313A ASN 3.7 0.7 - - - -
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Residues in contact with TRP 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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196A PHE* 4.7 2.0 - + - -
225A ILE* 3.5 41.5 - - + -
307A TYR* 3.0 46.1 + + - -
308A ALA* 3.2 13.3 + - - +
311A VAL* 1.3 88.5 - - + +
313A ASN* 1.3 71.7 + - - +
314A ILE* 3.3 20.4 + - + +
326A ALA* 4.6 3.1 - - - -
329A ALA* 3.8 43.7 - - + -
330A THR* 3.8 5.9 + - - -
333A PHE* 3.9 19.1 - + + -
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Residues in contact with ASN 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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308A ALA 3.1 0.2 + - - -
309A GLU* 3.0 20.3 + - - +
310A ARG 4.7 0.2 - - - -
311A VAL 3.7 1.2 - - - -
312A TRP* 1.3 80.9 - - - +
314A ILE* 1.3 60.2 + - - +
315A THR* 3.8 14.0 + - - +
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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
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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