Contacts of the helix formed by residues 287 - 299 (chain A) in PDB entry 3J2I
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 287 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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286A GLU* 1.3 78.9 - - - +
288A LYS* 1.3 72.2 + - + +
290A ARG* 3.1 61.7 + - - +
291A MET* 3.3 35.2 + - + +
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Residues in contact with LYS 288 (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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261A THR* 5.1 8.0 - - + +
265A PHE* 4.7 4.4 - - - +
283A PHE 4.7 3.2 + - - -
286A GLU 3.3 22.6 - - - +
287A LYS* 1.3 91.6 - - + +
289A ALA* 1.3 60.8 + - - +
291A MET* 3.5 19.5 - - + +
292A GLY* 3.5 16.6 + - - -
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Residues in contact with ALA 289 (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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265A PHE* 3.8 20.3 - - + -
280A LEU* 4.5 11.7 - - + +
283A PHE* 3.3 37.8 + - + +
286A GLU 3.6 9.8 + - - +
287A LYS 3.2 0.4 - - - -
288A LYS* 1.3 77.2 - - - +
290A ARG* 1.3 56.8 + - + +
291A MET 3.3 0.2 - - - -
292A GLY 3.2 1.2 + - - -
293A VAL* 2.8 40.0 + - - +
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Residues in contact with ARG 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A LEU* 4.7 10.8 - - + -
94A SER* 4.0 21.4 + - - -
243A ARG* 3.3 36.3 - - - +
280A LEU* 5.3 9.9 - - + -
286A GLU* 3.2 15.6 + - + +
287A LYS* 3.1 64.2 + - - +
289A ALA* 1.3 80.1 - - + +
291A MET* 1.3 58.3 + - - +
293A VAL* 3.7 7.4 - - - +
294A VAL* 3.1 27.1 + - - +
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Residues in contact with MET 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A THR* 4.0 32.3 - - - +
262A SER* 4.3 5.2 + - - -
287A LYS* 3.3 41.7 + - + +
288A LYS* 3.5 21.3 - - + +
290A ARG* 1.3 75.6 - - - +
292A GLY* 1.3 66.9 + - - +
294A VAL* 3.2 21.7 + - - +
295A GLU* 3.8 4.3 + - - +
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Residues in contact with GLY 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A THR 4.4 0.9 - - - -
262A SER* 4.1 17.4 + - - -
265A PHE* 3.6 27.1 - - - -
288A LYS 3.5 4.0 + - - -
289A ALA 3.2 5.0 + - - -
291A MET* 1.3 84.7 - - - +
293A VAL* 1.3 62.4 + - - +
294A VAL 3.4 0.5 + - - -
295A GLU 3.7 1.2 + - - -
296A CYS* 3.4 27.2 + - - -
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Residues in contact with VAL 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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247A TYR* 3.7 33.9 - - + +
265A PHE* 3.5 16.5 - - + -
280A LEU* 3.2 41.3 - - + -
289A ALA 2.8 18.2 + - - +
290A ARG* 3.7 8.3 - - - +
292A GLY* 1.3 76.8 - - - +
294A VAL* 1.3 61.9 + - + +
296A CYS* 3.3 0.7 + - - +
297A ALA* 2.9 31.5 + - + +
302A LEU* 4.5 8.0 - - + +
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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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290A ARG 3.1 20.0 - - - +
291A MET* 3.5 11.2 - - - +
292A GLY 3.2 1.4 - - - -
293A VAL* 1.3 80.0 - - + +
295A GLU* 1.3 64.9 + - - +
297A ALA* 4.1 2.6 - - - +
298A LYS* 3.1 27.5 + - + +
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Residues in contact with GLU 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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255A TYR* 3.9 5.9 - - - -
257A LEU* 3.6 17.5 - - + +
258A LYS* 2.8 36.3 + - - +
259A MET* 3.4 22.3 + - + +
262A SER* 2.9 33.4 + - - +
291A MET 3.8 2.3 + - - +
292A GLY 3.7 1.8 + - - -
293A VAL 3.4 0.2 - - - -
294A VAL* 1.3 80.6 - - - +
296A CYS* 1.3 62.9 + - - +
298A LYS* 3.5 4.2 + - - -
299A HIS* 3.2 43.4 + - + +
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Residues in contact with CYS 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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257A LEU* 3.7 32.8 - - - -
262A SER* 4.0 10.8 - - - -
265A PHE* 4.1 11.0 - - - -
266A PHE* 4.3 10.3 - - - -
292A GLY 3.4 18.7 + - - +
293A VAL 3.3 1.4 + - - -
295A GLU* 1.3 78.6 - - - +
297A ALA* 1.3 58.9 + - - +
299A HIS 3.4 1.6 + - - -
300A GLU 3.3 3.1 + - - -
301A LEU* 2.9 37.3 + - + +
302A LEU* 3.8 25.8 - - + -
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Residues in contact with ALA 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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247A TYR* 4.1 26.5 - - + +
293A VAL* 2.9 19.5 + - + +
294A VAL* 4.1 2.9 - - - +
296A CYS* 1.3 73.2 - - - +
298A LYS* 1.3 66.4 + - - +
300A GLU* 3.1 15.8 + - - +
302A LEU* 3.8 17.9 - - + +
304A PRO* 5.8 2.9 - - + -
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Residues in contact with LYS 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 VAL* 3.1 22.8 + - + +
295A GLU* 3.6 8.1 - - - +
297A ALA* 1.3 79.3 - - - +
299A HIS* 1.3 73.6 + - + +
300A GLU* 3.5 8.1 + - - +
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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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253A LYS* 4.8 2.4 - - - +
254A GLN 5.3 0.9 - - - +
255A TYR* 3.3 68.9 + + + +
257A LEU* 5.0 0.2 - - + -
258A LYS* 4.8 5.6 + - - -
295A GLU* 3.2 40.1 + - + +
296A CYS 3.4 1.3 + - - +
297A ALA 3.2 0.2 - - - -
298A LYS* 1.3 91.0 + - + +
300A GLU* 1.3 68.4 + - - +
301A LEU* 3.1 17.5 + - + +
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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