Contacts of the helix formed by residues 289 - 303 (chain A) in PDB entry 2F8J
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 GLU 289 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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288A MET* 1.3 71.8 - - - +
290A LYS* 1.3 66.9 + - - +
291A GLU 3.0 4.1 + - - -
292A GLU* 3.1 11.9 + - - +
293A LYS* 2.9 19.2 + - - +
502A EDO 3.5 13.8 + - - -
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Residues in contact with LYS 290 (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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288A MET 3.7 3.5 + - - -
289A GLU* 1.3 69.1 - - - +
291A GLU* 1.3 71.4 + - + +
293A LYS* 3.3 16.2 + - - +
294A GLU* 3.1 31.0 + - + +
311A ARG 5.3 7.9 + - - +
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Residues in contact with GLU 291 (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 GLU 3.0 1.0 + - - -
290A LYS* 1.3 84.4 - - + +
292A GLU* 1.3 64.7 + - - +
294A GLU* 3.3 14.7 + - - +
295A ARG* 3.3 19.9 + - - +
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Residues in contact with GLU 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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274A TYR* 4.9 4.8 - - - -
288A MET* 3.2 26.2 - - - +
289A GLU* 3.1 11.6 + - - +
291A GLU* 1.3 75.0 - - - +
293A LYS* 1.3 65.8 + - - +
295A ARG* 3.5 4.6 + - - -
296A LEU 3.3 2.1 + - - -
334A PHE* 3.1 51.2 - - + -
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Residues in contact with LYS 293 (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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288A MET* 3.8 24.8 - - + +
289A GLU 2.9 13.4 + - - +
290A LYS* 3.4 19.1 - - - +
291A GLU 3.3 0.2 - - - -
292A GLU* 1.3 77.4 - - - +
294A GLU* 1.3 73.8 + - - +
296A LEU* 3.1 5.7 + - - +
297A LEU* 3.0 30.3 + - + +
309A SER* 3.2 21.6 + - - +
310A PHE 2.4 31.1 + - - +
311A ARG* 3.7 11.7 + - - +
313A GLY* 3.6 28.3 - - - +
314A VAL* 3.9 18.2 - - + -
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Residues in contact with GLU 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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290A LYS* 3.1 20.6 + - + +
291A GLU* 3.7 16.6 - - - +
292A GLU 3.3 0.2 - - - -
293A LYS* 1.3 86.5 + - - +
295A ARG* 1.3 63.1 + - - +
297A LEU* 3.2 24.4 + - - +
298A GLU* 3.1 22.0 + - - +
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Residues in contact with ARG 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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291A GLU 3.3 10.0 + - - +
292A GLU* 3.6 6.5 - - - +
294A GLU* 1.3 80.2 - - - +
296A LEU* 1.3 61.0 + - - +
298A GLU* 3.4 8.1 + - - +
299A HIS* 3.3 17.8 + - - +
334A PHE* 3.4 24.7 - - + -
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Residues in contact with LEU 296 (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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288A MET* 3.7 21.8 - - + -
292A GLU 3.3 1.8 + - - +
293A LYS 3.1 10.3 + - - +
295A ARG* 1.3 73.5 - - - +
297A LEU* 1.3 61.6 + - + +
299A HIS* 3.2 5.5 + - + +
300A LEU* 2.9 62.4 + - + +
314A VAL* 4.6 14.4 - - + -
316A ILE* 5.9 0.9 - - + -
330A GLU* 4.3 13.5 - - + +
331A LEU* 3.5 29.6 - - + -
334A PHE* 3.1 41.4 - - + -
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Residues in contact with LEU 297 (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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293A LYS* 3.0 21.4 + - + +
294A GLU* 3.2 30.5 + - - +
296A LEU* 1.3 78.7 - - + +
298A GLU* 1.3 51.1 + - - +
300A LEU* 3.2 9.3 + - + +
301A ARG* 2.7 37.1 + - - +
307A VAL* 4.0 29.6 - - + +
309A SER* 4.0 27.8 - - - +
314A VAL* 4.2 11.7 - - + -
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Residues in contact with GLU 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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294A GLU 3.1 12.6 + - - +
295A ARG* 3.8 9.6 - - - +
296A LEU 3.3 0.4 - - - -
297A LEU* 1.3 75.5 - - - +
299A HIS* 1.3 56.3 + - - +
301A ARG* 3.8 24.6 - - - +
302A THR* 2.8 38.5 + - - +
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Residues in contact with HIS 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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295A ARG 3.3 10.0 + - - +
296A LEU* 3.2 15.1 + - + +
298A GLU* 1.3 80.8 - - - +
300A LEU* 1.3 62.8 + - + +
302A THR* 3.4 10.6 + - + +
303A LYS* 3.1 28.9 + - + +
330A GLU* 2.8 48.2 + - + -
333A VAL* 4.7 9.6 - - + +
334A PHE* 5.1 7.4 - + + -
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Residues in contact with LEU 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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296A LEU* 2.9 49.5 + - + +
297A LEU* 3.7 8.3 - - + +
299A HIS* 1.3 75.1 - - + +
301A ARG* 1.3 65.3 + - - +
303A LYS* 3.0 13.3 + - + -
304A ASN 3.0 0.2 + - - -
305A VAL* 3.0 49.7 + - + +
307A VAL* 4.1 36.6 - - + +
316A ILE* 6.2 1.3 - - + -
327A ILE* 4.9 8.7 - - + -
330A GLU* 4.0 27.4 - - + +
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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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20A ASP* 5.1 5.9 - - - +
297A LEU 2.7 20.9 + - - +
298A GLU* 3.8 19.5 - - - +
300A LEU* 1.3 71.8 - - - +
302A THR* 1.3 78.2 + - - +
304A ASN* 3.1 13.9 + - - +
305A VAL 4.0 7.3 + - - +
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Residues in contact with THR 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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298A GLU* 2.8 23.7 + - - +
299A HIS* 3.4 11.4 - - + +
301A ARG* 1.3 93.2 + - - +
303A LYS* 1.3 62.1 - - + +
304A ASN* 3.8 1.0 + - - +
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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
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22A THR* 5.4 0.3 + - - -
299A HIS* 3.1 24.9 + - + +
300A LEU* 3.0 9.1 + - + +
302A THR* 1.3 81.5 - - + +
304A ASN* 1.3 71.0 + - - +
305A VAL* 3.4 14.0 - - + +
326A MET* 5.9 0.4 - - - -
330A GLU* 3.5 25.1 - - - +
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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