Contacts of the helix formed by residues 287 - 300 (chain B) in PDB entry 5I94
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 VAL 287 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283B LEU* 3.9 18.5 - - + +
284B GLN 3.0 22.5 + - - +
286B CYS* 1.3 76.3 - - - +
288B LYS* 1.3 66.8 + - + +
289B PRO 3.5 0.2 - - - -
290B LEU* 2.9 33.8 + - + +
291B LYS* 3.0 33.5 + - + +
357B VAL* 5.9 1.1 - - + -
361B LEU* 5.0 11.2 - - + -
416B LEU* 3.7 39.5 - - + +
417B CYS* 4.4 4.5 - - - -
419B ILE* 5.1 2.0 - - + -
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Residues in contact with LYS 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B SER* 2.5 49.4 + - - +
287B VAL* 1.3 80.7 - - + +
289B PRO* 1.3 67.5 - - + +
291B LYS* 3.5 14.3 + - - +
292B TYR* 3.0 25.2 + - - +
331B PRO 4.2 9.0 - - - +
332B MET* 3.1 35.2 - - - +
333B VAL 3.9 2.2 - - - -
334B ASN* 3.5 16.9 + - - +
337B ALA* 3.5 28.7 - - + -
340B VAL* 5.4 0.2 - - - +
413B TYR* 3.4 21.6 + - - -
417B CYS* 5.1 4.0 - - - -
480B LYS* 4.1 6.3 - - - -
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Residues in contact with PRO 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B CYS 3.3 15.0 - - - +
288B LYS* 1.3 97.4 - - + +
290B LEU* 1.3 58.2 + - + +
291B LYS 3.4 0.2 - - - -
292B TYR* 3.8 2.4 - - + +
293B ALA* 3.0 28.9 + - - +
332B MET* 3.9 12.8 - - + -
433B LEU* 5.4 0.4 - - + -
455B THR* 3.5 26.7 - - + +
459B MET* 3.7 18.6 - - + -
480B LYS* 3.5 31.2 - - + -
488B LEU* 4.4 7.9 - - + -
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Residues in contact with LEU 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B LEU* 4.2 18.4 - - + -
286B CYS 3.8 18.6 - - - +
287B VAL* 2.9 17.8 + - + +
289B PRO* 1.3 81.1 - - + +
291B LYS* 1.3 58.2 + - - +
293B ALA* 3.5 6.7 + - + +
294B ILE* 3.1 30.3 + - - +
361B LEU* 4.1 18.2 - - + -
364B MET* 3.8 28.3 - - + +
429B MET* 4.3 22.9 - - + -
433B LEU* 4.3 23.1 - - + -
488B LEU* 4.7 11.9 - - + -
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Residues in contact with LYS 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B VAL* 3.0 24.3 + - + +
288B LYS* 3.6 19.2 - - - +
290B LEU* 1.3 75.0 - - - +
292B TYR* 1.3 68.6 + - - +
293B ALA 3.2 0.2 - - - -
294B ILE* 3.2 13.8 + - + +
295B ALA* 3.1 20.3 + - - +
337B ALA* 4.1 21.1 - - - +
340B VAL* 3.8 9.1 - - + +
341B THR* 3.2 24.0 + - - +
344B ILE* 3.6 21.4 - - + +
357B VAL* 5.7 3.6 - - + -
413B TYR* 3.5 26.3 + - - +
416B LEU* 3.7 37.0 - - + +
417B CYS* 5.1 0.8 - - - -
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Residues in contact with TYR 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473A PHE* 3.8 1.4 - - - -
288B LYS 3.0 19.3 + - - +
289B PRO* 3.8 4.3 - - + +
291B LYS* 1.3 79.8 - - - +
293B ALA* 1.3 59.9 + - - +
295B ALA* 3.3 3.2 + - + +
296B VAL* 3.1 37.4 + - + +
304B VAL* 4.0 13.2 - - + -
305B HIS* 2.7 31.3 + - - -
331B PRO* 3.4 37.0 - - + -
332B MET* 4.7 2.9 - - + -
340B VAL* 3.8 14.4 - - + -
451B ALA 4.8 0.2 - - - -
454B ASN* 3.3 22.7 + - + +
455B THR* 3.3 46.0 - - + -
458B LEU* 3.7 15.7 - - + +
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Residues in contact with ALA 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B PRO 3.0 20.3 + - - +
290B LEU* 3.5 9.4 - - + +
292B TYR* 1.3 78.2 - - - +
294B ILE* 1.3 56.3 + - - +
296B VAL* 3.5 1.1 + - - +
297B ASN* 2.9 30.1 + - - +
364B MET* 5.7 0.2 - - + -
433B LEU* 5.2 2.9 - - + -
447B LEU* 4.1 25.8 - - + -
451B ALA* 3.4 13.9 - - + +
455B THR* 3.4 19.3 - - + +
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Residues in contact with ILE 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290B LEU 3.1 18.8 - - - +
291B LYS* 3.2 14.5 + - - +
293B ALA* 1.3 74.1 - - - +
295B ALA* 1.3 56.5 + - - +
297B ASN* 3.1 5.1 + - - +
298B ASP* 2.7 50.7 + - - +
344B ILE* 4.2 11.9 - - + -
356B TYR* 4.0 9.9 - - + -
357B VAL* 4.3 23.8 - - + +
360B PHE* 3.8 52.0 - - + -
361B LEU* 4.8 2.9 - - + -
364B MET* 4.7 7.0 - - + -
447B LEU* 5.0 0.4 - - + -
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Residues in contact with ALA 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291B LYS 3.1 12.5 + - - +
292B TYR 3.5 9.2 - - - +
294B ILE* 1.3 76.4 - - - +
296B VAL* 1.3 53.5 + - - +
298B ASP* 3.0 2.0 + - - -
299B LEU* 2.6 51.5 + - + +
304B VAL* 3.7 20.4 - - + -
340B VAL* 4.3 14.6 - - + -
343B LEU* 4.7 6.1 - - + -
344B ILE* 4.5 12.9 - - + +
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Residues in contact with VAL 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B TYR* 3.1 48.2 + - + +
293B ALA* 4.1 4.0 - - - +
295B ALA* 1.3 79.1 - - - +
297B ASN* 1.3 58.6 + - - +
300B GLY* 2.9 27.1 + - - +
301B THR* 4.0 7.9 - - - +
304B VAL* 4.1 16.8 - - + -
305B HIS* 4.9 0.4 - - - +
448B SER* 4.6 0.2 + - - -
450B GLU* 3.9 17.5 - - - +
451B ALA* 3.6 25.4 - - - +
454B ASN* 3.7 18.8 - - - +
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Residues in contact with ASN 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B ALA 2.9 18.8 + - - +
294B ILE 3.1 3.8 + - - +
296B VAL* 1.3 80.0 - - - +
298B ASP* 1.3 86.3 + - - +
300B GLY 4.9 0.3 + - - -
360B PHE* 3.5 20.9 - - - -
445B ARG* 3.6 15.4 + - - +
446B VAL 4.1 1.9 + - - +
447B LEU* 3.8 11.4 - - + -
448B SER* 3.2 33.4 + - - -
451B ALA* 3.8 8.7 - - + +
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Residues in contact with ASP 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B ILE* 2.7 26.0 + - + +
295B ALA* 3.9 2.5 - - - +
297B ASN* 1.3 96.5 + - - +
299B LEU* 1.3 73.2 + - + +
300B GLY 3.9 0.2 - - - -
344B ILE* 5.0 4.1 - - - +
345B LYS* 5.0 5.4 + - - +
356B TYR* 2.3 42.2 + - - -
360B PHE* 4.1 1.0 - - - -
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Residues in contact with LEU 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295B ALA* 2.6 26.6 + - - +
298B ASP* 1.3 90.7 - - + +
300B GLY* 1.3 61.7 + - - +
303B TYR* 3.5 52.5 + - + +
304B VAL* 4.0 5.6 - - + -
343B LEU* 3.5 36.8 - - + +
344B ILE* 5.1 1.3 - - - -
346B GLN* 4.8 1.8 - - - +
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Residues in contact with GLY 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296B VAL* 2.9 22.0 + - - -
297B ASN 4.7 0.4 + - - -
298B ASP 3.9 0.6 - - - -
299B LEU* 1.3 83.8 - - - +
301B THR* 1.3 67.7 + - - +
302B GLU 3.4 3.3 + - - -
303B TYR 3.6 0.4 + - - -
304B VAL* 3.4 19.2 + - - +
450B GLU* 3.8 8.3 - - - -
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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