Contacts of the helix formed by residues 286 - 297 (chain A) in PDB entry 2Z7S
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 SER 286 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161A GLU* 2.8 36.9 + - - -
284A PHE 3.7 1.8 + - - -
285A LEU* 1.3 77.2 - - - +
287A THR* 1.3 64.3 + - - +
288A GLU* 3.5 17.4 + - - +
289A ALA 3.0 17.2 + - - -
290A GLN* 3.0 19.9 + - - +
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Residues in contact with THR 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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286A SER* 1.3 73.8 - - - +
288A GLU* 1.3 77.3 + - - +
290A GLN* 3.7 15.9 - - - +
291A SER* 2.9 30.1 + - - -
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Residues in contact with GLU 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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286A SER* 3.6 19.0 - - - +
287A THR* 1.3 94.8 + - - +
289A ALA* 1.3 61.7 + - - +
291A SER* 3.4 7.1 + - - -
292A LEU* 3.1 19.8 + - - +
318A HIS* 3.5 9.7 - - - -
319A VAL* 3.9 29.9 - - + +
320A PHE* 3.9 23.0 - - + +
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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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161A GLU* 3.6 15.0 - - - +
252A MET* 3.5 12.1 - - + +
256A LEU* 4.2 9.9 - - + -
285A LEU* 4.5 4.7 - - + -
286A SER* 3.0 22.6 + - - +
288A GLU* 1.3 76.5 - - - +
290A GLN* 1.3 62.8 + - - +
292A LEU 3.3 1.4 + - - -
293A LEU* 3.0 29.2 + - + +
320A PHE* 3.6 22.4 - - + -
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Residues in contact with GLN 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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281A MET* 3.1 43.0 - - + +
282A PRO 4.2 8.3 + - - -
283A GLN* 4.4 14.2 + - - +
285A LEU* 2.8 33.1 + - + -
286A SER 3.0 18.3 + - - +
287A THR* 3.7 15.4 - - - +
289A ALA* 1.3 76.3 - - - +
291A SER* 1.3 62.4 + - - +
293A LEU* 3.4 1.6 + - - -
294A ARG* 3.0 49.7 + - - +
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Residues in contact with SER 291 (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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287A THR 2.9 18.7 + - - -
288A GLU* 3.5 7.2 - - - -
290A GLN* 1.3 77.1 - - - +
292A LEU* 1.3 62.3 + - - +
294A ARG* 3.2 12.6 + - - +
295A ALA* 3.0 22.7 + - - +
318A HIS* 2.9 20.3 + - - -
319A VAL* 5.9 0.3 - - - +
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Residues in contact with LEU 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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252A MET* 3.5 20.2 - - + -
288A GLU 3.1 10.5 + - - +
289A ALA 3.6 7.6 - - - +
291A SER* 1.3 79.7 + - - +
293A LEU* 1.3 57.6 + - - +
295A ALA* 3.2 2.6 + - - +
296A LEU* 2.9 45.3 + - + +
305A LEU* 3.6 27.1 - - + -
315A ILE* 4.5 7.9 - - + -
318A HIS* 3.4 23.1 + - + -
320A PHE* 3.3 35.9 - - + -
321A TYR* 3.6 17.7 - - + +
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Residues in contact with LEU 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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249A GLY* 3.5 27.1 - - - +
252A MET* 3.6 24.5 - - + -
253A PHE* 3.9 16.8 - - + +
256A LEU* 4.6 8.7 - - + -
281A MET* 4.0 17.7 - - + -
285A LEU* 3.8 29.2 - - + -
289A ALA 3.0 22.3 + - - +
290A GLN 3.8 3.6 - - - +
291A SER 3.3 0.2 - - - -
292A LEU* 1.3 75.5 - - - +
294A ARG* 1.3 58.6 + - - +
296A LEU* 3.2 3.8 + - - +
297A PHE* 2.8 53.4 + - + -
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Residues in contact with ARG 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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279A LEU 5.2 4.9 + - - -
281A MET* 3.5 32.6 - - + +
290A GLN* 3.0 52.6 + - - +
291A SER* 3.5 11.1 - - - +
293A LEU* 1.3 75.8 - - - +
295A ALA* 1.3 61.9 + - - +
297A PHE* 3.5 12.7 + - - +
298A LYS* 3.3 29.0 + - - +
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Residues in contact with ALA 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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291A SER 3.0 12.4 + - - +
292A LEU* 3.2 10.1 + - - +
294A ARG* 1.3 78.2 - - - +
296A LEU* 1.3 60.8 + - - +
297A PHE 3.7 0.2 + - - -
298A LYS* 3.9 13.8 - - - +
303A ASN 4.4 0.5 - - - +
304A ARG* 3.7 6.4 - - - -
305A LEU* 3.0 52.9 + - + -
318A HIS* 4.9 4.5 - - + +
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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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245A TRP* 3.6 28.9 - - + +
246A TRP* 3.7 8.1 - - - -
248A TYR* 3.7 21.8 - - + -
249A GLY* 3.6 27.6 - - - -
252A MET* 4.4 6.1 - - - -
292A LEU* 2.9 41.9 + - + +
293A LEU* 3.2 4.2 + - - +
295A ALA* 1.3 76.6 - - - +
297A PHE* 1.3 59.8 + - + +
298A LYS 3.2 2.6 + - - -
304A ARG* 3.2 27.0 + - - +
305A LEU* 4.0 29.8 - - + +
315A ILE* 5.4 3.4 - - + -
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Residues in contact with PHE 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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246A TRP* 3.6 38.9 - + + -
249A GLY* 3.3 23.6 - - - -
250A VAL* 3.5 32.1 - - + -
253A PHE* 4.4 4.5 - - + -
261A PRO* 4.0 10.3 - - + -
262A PHE* 4.1 8.3 - + + -
277A ALA* 4.9 8.2 - - + +
279A LEU* 3.5 33.2 - - + -
293A LEU* 2.8 47.1 + - + +
294A ARG* 3.5 10.7 + - - +
295A ALA 3.4 0.4 - - - -
296A LEU* 1.3 76.5 - - - +
298A LYS* 1.3 61.0 + - - +
299A ARG* 3.8 2.1 + - - +
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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