Contacts of the helix formed by residues 289 - 297 (chain A) in PDB entry 2J25
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 PRO 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 LEU* 1.4 81.6 - - + +
290A HIS* 1.3 68.8 - - + +
291A TRP 3.4 2.2 - - - -
292A ALA* 3.0 8.2 + - + +
293A LYS* 2.9 35.3 + - + +
322A ALA 3.9 14.8 - - - +
326A GLU* 4.2 14.6 - - + -
327A THR* 3.3 26.7 - - - +
330A LEU* 4.3 18.8 - - + -
331A PHE* 5.3 0.4 - - + -
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Residues in contact with HIS 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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253A PRO* 4.2 17.5 - - + +
254A GLU* 4.5 7.0 + - - -
287A LEU 3.7 7.0 - - - +
288A LEU 3.3 2.6 - - - -
289A PRO* 1.3 81.6 - - + +
291A TRP* 1.3 71.6 + + - +
293A LYS* 2.9 24.6 + - - +
294A VAL* 2.9 38.1 + - + +
441B LYS* 5.7 7.9 - - - -
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Residues in contact with TRP 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A PRO* 3.4 29.2 - - + -
237A SER* 4.7 7.3 - - - -
240A LEU* 5.7 0.6 - - + +
251A PHE 3.4 24.2 - - - -
252A THR* 4.3 0.2 - - - -
253A PRO* 3.5 41.6 - - + +
256A GLN* 2.9 48.0 - - + -
280A MET* 3.8 14.1 - - + -
281A LEU* 3.7 25.8 - - + -
287A LEU* 2.9 52.2 + - + +
288A LEU* 4.2 6.1 - - + -
290A HIS* 1.3 79.0 - + - +
292A ALA* 1.3 57.6 + - - +
294A VAL* 3.4 2.3 + - - +
295A VAL* 3.0 33.3 + - + +
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Residues in contact with ALA 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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280A MET* 3.9 7.3 - - + +
288A LEU* 4.0 5.3 - - + +
289A PRO* 3.0 10.8 + - + +
291A TRP* 1.3 76.0 - - - +
293A LYS* 1.3 67.2 + - - +
296A LEU* 2.8 52.1 + - + +
308A ILE* 3.8 17.0 - - + -
327A THR* 4.0 14.6 - - + -
331A PHE* 3.6 8.6 - - + -
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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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289A PRO* 2.9 33.4 + - + +
290A HIS* 2.9 17.4 + - - +
292A ALA* 1.3 78.7 - - - +
294A VAL* 1.3 57.5 + - + +
297A THR* 2.6 42.2 + - + +
326A GLU* 5.4 2.0 + - - -
330A LEU* 3.7 33.0 - - + -
331A PHE* 4.0 11.9 - - + -
321B LYS* 6.1 0.6 - - - +
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Residues in contact with VAL 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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253A PRO* 3.7 30.3 - - + +
254A GLU* 3.8 18.6 - - + +
257A ARG* 3.5 38.8 + - - +
290A HIS* 2.9 44.4 + - + +
291A TRP 3.7 1.8 - - - +
293A LYS* 1.3 75.5 - - + +
295A VAL* 1.3 64.1 + - - +
297A THR* 4.3 5.1 + - - -
298A ASP* 4.3 2.8 + - - +
1508A SO4 4.7 0.2 - - - +
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Residues in contact with VAL 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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253A PRO 3.9 20.9 - - - +
256A GLN* 4.2 10.5 - - + -
257A ARG* 4.0 15.5 - - - +
260A ILE* 4.5 7.9 - - + -
280A MET* 3.7 33.0 - - + -
291A TRP* 3.0 18.7 + - + +
294A VAL* 1.3 77.5 - - - +
296A LEU* 1.3 64.5 + - + +
298A ASP* 3.5 6.6 + - - +
301A ALA* 3.3 32.5 - - + +
302A ALA 4.0 0.3 + - - -
305A VAL* 4.2 17.0 - - + -
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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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280A MET* 4.1 9.2 - - - -
292A ALA* 2.8 41.8 + - + +
295A VAL* 1.3 75.3 - - - +
297A THR* 1.3 54.9 + - - +
298A ASP 3.0 10.0 + - - +
299A PRO* 4.5 1.2 - - - +
302A ALA* 3.3 32.9 - - + +
305A VAL* 4.1 26.2 - - + +
308A ILE* 3.9 16.6 - - + -
331A PHE* 3.4 39.4 - - + -
334A THR* 3.9 20.4 - - + +
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Residues in contact with THR 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* 2.6 31.9 + - + +
294A VAL* 4.3 4.2 + - - -
296A LEU* 1.3 74.3 - - - +
298A ASP* 1.3 57.6 + - - +
299A PRO* 3.4 9.5 - - - +
331A PHE* 3.9 20.0 - - + -
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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