Contacts of the helix formed by residues 286 - 300 (chain A) in PDB entry 5TOL
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 286 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284A LEU 4.3 1.6 - - - -
285A PRO* 1.3 70.8 - - - +
287A LYS* 1.3 64.1 + - + +
289A PHE* 3.3 6.1 + - - +
290A GLU* 3.0 40.5 + - + +
374A GLN* 2.7 41.5 + - + +
375A SER 3.3 14.2 + - - +
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Residues in contact with LYS 287 (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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263A MET* 3.9 17.8 - - + +
267A GLU* 2.9 29.2 - - - +
270A TYR* 6.1 5.8 - - + -
285A PRO* 3.3 2.7 - - + +
286A LYS* 1.3 78.1 - - + +
288A VAL* 1.3 64.5 + - + +
290A GLU* 3.4 16.9 + - - +
291A ALA* 3.2 21.5 + - - +
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Residues in contact with VAL 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A VAL* 5.2 4.5 - - + -
261A LEU* 4.3 8.6 - - + +
263A MET* 3.8 16.8 - - + -
267A GLU* 3.4 29.8 - - + +
268A TYR* 3.6 36.8 - - + -
284A LEU* 4.1 25.1 - - + -
285A PRO* 3.1 15.4 + - + +
287A LYS* 1.3 72.7 - - + +
289A PHE* 1.3 67.0 + - - +
291A ALA* 3.2 2.3 + - - +
292A ALA* 2.9 22.7 + - + +
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Residues in contact with PHE 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A LEU* 4.0 20.1 - - + +
285A PRO 2.8 20.4 + - - +
286A LYS 3.6 5.2 - - - +
288A VAL* 1.3 72.5 - - - +
290A GLU* 1.3 69.0 + - + +
292A ALA* 3.4 1.4 + - + +
293A VAL* 3.0 49.4 + - + +
310A TRP* 3.3 24.0 - - + -
311A LEU* 4.3 14.6 - - + -
370A PHE* 4.3 0.9 - + - -
372A ILE* 3.4 35.9 - - + -
373A SER* 3.6 21.1 - - - -
374A GLN* 3.3 33.4 - - + -
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Residues in contact with GLU 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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286A LYS* 3.0 36.0 + - + +
287A LYS* 3.4 22.7 - - - +
288A VAL 3.3 0.2 - - - -
289A PHE* 1.3 84.6 - - + +
291A ALA* 1.3 61.6 + - - +
293A VAL* 4.1 3.4 - - - +
294A LYS* 3.2 24.4 + - - +
374A GLN* 5.6 0.7 - - - +
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Residues in contact with ALA 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A LEU* 4.2 14.5 - - + +
263A MET* 3.9 21.5 - - + -
287A LYS 3.2 10.0 + - - +
288A VAL 3.2 5.8 + - - +
290A GLU* 1.3 79.9 - - - +
292A ALA* 1.3 58.7 + - - +
294A LYS* 3.5 7.3 + - - +
295A SER* 3.0 28.9 + - - -
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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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254A VAL* 5.9 1.3 - - + -
256A ILE* 4.4 14.1 - - + +
261A LEU* 3.9 16.7 - - + +
284A LEU* 4.2 18.8 - - + -
288A VAL* 2.9 16.5 + - + +
289A PHE* 3.7 3.6 - - + +
291A ALA* 1.3 74.4 - - - +
293A VAL* 1.3 56.0 + - + +
295A SER* 3.1 5.5 + - - -
296A ILE* 2.7 46.5 + - + +
331A ILE* 6.2 0.7 - - + -
372A ILE* 5.9 1.3 - - + -
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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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289A PHE* 3.0 56.1 + - + +
290A GLU* 4.1 3.4 - - - +
292A ALA* 1.3 71.7 - - + +
294A LYS* 1.3 58.7 + - - +
296A ILE* 3.0 8.1 + - + +
297A LYS* 2.6 49.0 + - + +
310A TRP* 3.9 31.4 - - + -
370A PHE* 4.2 17.9 - - + -
372A ILE* 5.9 0.7 - - + -
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Residues in contact with LYS 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A GLU 3.2 17.3 + - - +
291A ALA* 3.6 7.2 - - - +
293A VAL* 1.3 78.2 - - - +
295A SER* 1.3 57.4 + - - +
297A LYS* 3.6 12.1 - - - +
298A ALA* 3.2 24.9 + - - +
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Residues in contact with SER 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A ILE* 3.4 28.8 + - - +
259A GLN* 5.2 5.0 + - - +
261A LEU* 4.4 10.2 - - - +
291A ALA 3.0 17.5 + - - -
292A ALA 3.6 3.1 - - - -
293A VAL 3.1 0.2 - - - -
294A LYS* 1.3 76.3 - - - +
296A ILE* 1.3 64.7 + - - +
298A ALA* 3.5 7.1 + - - +
299A ALA* 3.1 23.7 + - - +
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Residues in contact with ILE 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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256A ILE* 4.0 16.6 - - + -
292A ALA* 2.7 35.8 + - + +
293A VAL* 3.7 7.0 - - + +
295A SER* 1.3 68.2 - - - +
297A LYS* 1.3 59.5 + - - +
299A ALA* 3.4 2.3 + - - +
300A SER* 2.8 34.4 + - - +
310A TRP* 3.8 24.7 - - + -
328A PHE* 4.8 4.0 - - + -
329A PRO* 4.1 26.6 - - + +
331A ILE* 4.0 24.2 - - + -
353A TYR* 4.6 6.1 - - + +
370A PHE* 3.9 26.2 - - + -
372A ILE* 4.3 3.6 - - + -
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Residues in contact with LYS 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A VAL* 2.6 33.9 + - + +
294A LYS* 3.6 11.2 - - - +
296A ILE* 1.3 74.8 - - - +
298A ALA* 1.3 65.3 + - - +
300A SER* 3.2 16.4 + - - -
301A SER* 3.5 9.2 + - - -
305A PHE 5.6 1.3 - - - -
307A ASP* 3.8 18.5 + - - -
310A TRP* 3.4 49.1 - - + +
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Residues in contact with ALA 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 LYS 3.2 15.0 + - - +
295A SER* 3.7 8.1 - - - +
296A ILE 3.4 0.2 - - - -
297A LYS* 1.3 79.5 - - - +
299A ALA* 1.3 61.5 + - - +
300A SER 3.5 0.2 + - - -
301A SER* 3.5 17.9 + - - -
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Residues in contact with ALA 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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256A ILE* 5.0 1.8 - - + -
257A ASN* 4.6 14.6 - - + +
295A SER 3.1 18.0 + - - +
296A ILE 4.0 2.9 - - - +
298A ALA* 1.3 76.7 - - - +
300A SER* 1.3 57.8 + - - +
301A SER* 3.3 4.1 + - - -
302A THR* 5.2 1.7 + - - -
327A ILE 4.0 5.3 - - - +
329A PRO* 4.2 25.1 - - + -
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Residues in contact with SER 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A ILE 2.8 23.5 + - - -
297A LYS* 3.2 9.9 + - - -
299A ALA* 1.3 74.6 - - - +
301A SER* 1.3 52.9 + - - +
302A THR* 3.3 5.6 + - - -
303A GLU 2.8 30.7 + - - +
305A PHE* 4.4 6.2 - - - -
310A TRP* 4.1 13.3 - - - -
327A ILE* 3.1 25.9 - - - +
328A PHE* 4.1 21.5 - - - -
329A PRO* 4.7 1.1 - - - -
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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