Contacts of the helix formed by residues 287 - 296 (chain B) in PDB entry 5ITZ
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 THR 287 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285B ALA 4.1 0.4 + - - -
286B LEU* 1.3 76.0 - - - +
288B VAL* 1.3 63.4 + - - +
289B PRO* 3.2 18.2 - - + +
290B GLU* 2.8 48.7 + - + +
291B LEU* 2.8 28.4 + - - +
327B GLU* 3.8 6.1 + - - -
373B MET* 4.1 2.7 - - - -
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Residues in contact with VAL 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B THR* 1.3 76.5 + - - +
289B PRO* 1.3 65.1 - - + +
291B LEU* 3.6 5.9 - - - +
292B THR* 2.7 37.4 + - - +
319B PHE* 5.1 2.5 - - + -
323B MET* 4.1 18.8 - - + -
324B SER 4.5 2.0 - - - +
327B GLU* 3.5 23.1 - - + +
328B VAL* 3.5 44.0 - - + +
331B GLN* 3.8 10.3 - - + -
373B MET* 4.0 17.7 - - + -
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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
----------------------------------------------------------
287B THR* 3.2 13.7 - - + +
288B VAL* 1.3 89.1 - - + +
290B GLU* 1.3 61.9 + - - +
292B THR* 3.2 1.7 + - - -
293B GLN* 2.9 27.1 + - - +
327B GLU* 3.2 24.2 - - + +
331B GLN* 3.6 34.6 - - + +
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Residues in contact with GLU 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B ARG* 4.3 17.5 + - - -
285B ALA 4.6 0.2 - - - +
286B LEU* 3.2 32.3 - - + +
287B THR* 2.8 41.3 + - + +
289B PRO* 1.3 78.3 - - - +
291B LEU* 1.3 65.0 + - - +
293B GLN* 3.2 3.9 + - - +
294B GLN* 2.9 33.1 + - - +
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Residues in contact with LEU 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B ALA* 3.5 38.5 - - + +
274B PRO* 4.2 0.9 - - + -
286B LEU* 4.0 16.8 - - + +
287B THR 2.8 20.3 + - - +
288B VAL* 3.6 7.2 - - - +
290B GLU* 1.3 73.4 - - - +
292B THR* 1.3 58.1 + - - +
294B GLN* 3.9 1.5 - - - +
295B MET* 2.9 32.7 + - - +
319B PHE* 3.8 16.8 - - + -
323B MET* 4.6 2.0 - - + -
373B MET* 3.7 25.6 - - + +
374B SER* 3.5 30.5 - - - +
375B ALA* 3.6 16.8 - - + +
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Residues in contact with THR 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B VAL* 2.7 26.0 + - - +
289B PRO* 3.7 3.1 - - - -
291B LEU* 1.3 76.6 - - - +
293B GLN* 1.3 65.2 + - - +
295B MET* 3.2 15.3 + - - +
296B PHE* 3.3 19.2 + - + -
319B PHE* 4.2 8.9 - - - -
331B GLN* 3.2 30.9 - - + +
332B MET* 3.6 28.7 - - - -
335B VAL* 4.0 21.5 - - + -
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Residues in contact with GLN 293 (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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289B PRO 2.9 16.6 + - - +
290B GLU* 3.8 4.9 - - - +
292B THR* 1.3 78.4 - - - +
294B GLN* 1.3 63.2 + - + +
296B PHE* 3.3 5.1 + - - +
297B ASP* 3.3 19.0 + - - +
335B VAL* 5.5 5.1 - - - +
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Residues in contact with GLN 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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273B ALA* 3.9 10.8 - - + +
274B PRO* 3.8 17.6 - - - +
275B LEU* 4.6 1.7 + - - +
286B LEU* 3.3 41.6 - - - +
290B GLU* 2.9 24.6 + - - +
293B GLN* 1.3 75.0 - - + +
295B MET* 1.3 62.0 + - - +
297B ASP* 3.0 19.8 + - + +
300B ASN* 3.0 34.5 + - - +
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Residues in contact with MET 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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271B GLY* 5.4 0.9 - - - -
272B PHE 5.2 2.2 - - - +
273B ALA* 4.2 7.1 - - + +
291B LEU 2.9 16.3 + - - +
292B THR* 3.6 6.7 - - - +
293B GLN 3.2 0.2 - - - -
294B GLN* 1.3 78.6 - - - +
296B PHE* 1.3 81.3 + - + +
297B ASP 4.5 0.3 - - - +
300B ASN* 4.7 4.8 - - - +
301B MET* 3.4 17.7 - - - +
317B ALA* 3.9 17.7 - - + -
319B PHE* 3.7 24.0 - - + -
332B MET* 4.0 4.0 - - - -
375B ALA* 3.5 30.1 - - + +
376B THR 3.8 17.7 - - - +
377B PHE* 3.5 30.1 - - + +
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Residues in contact with PHE 296 (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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292B THR* 3.3 19.0 + - + +
293B GLN* 3.3 6.7 + - - +
294B GLN 3.2 0.6 - - - -
295B MET* 1.3 89.1 - - + +
297B ASP* 1.3 62.2 + - - +
298B SER* 3.7 1.4 + - - -
301B MET* 3.8 10.0 - - - +
307B PRO* 4.8 4.5 - - - +
312B TYR* 4.4 16.0 + + - -
315B VAL* 4.5 7.2 - - + -
332B MET* 3.5 37.0 - - + -
335B VAL* 4.0 28.5 - - + -
336B GLN* 5.7 0.9 - - + -
343B PHE* 3.7 29.8 - + - -
351B VAL* 4.6 3.1 - - + -
377B PHE* 3.7 24.9 - + - -
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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