Contacts of the strand formed by residues 266 - 275 (chain A) in PDB entry 4MT7
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 LEU 266 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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240A ASN* 4.2 10.5 + - - +
244A ILE* 4.7 10.9 - - + +
265A GLU* 1.3 80.3 - - - +
267A ILE* 1.3 76.0 + - - +
268A TYR* 3.6 12.8 - - - +
269A THR* 4.1 22.0 - - + -
288A PHE* 4.5 7.0 - - + -
289A LEU 3.2 22.7 - - - +
290A PHE* 3.6 31.1 - - + -
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Residues in contact with ILE 267 (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 GLU* 3.4 6.9 + - + +
266A LEU* 1.3 80.6 - - - +
268A TYR* 1.3 63.9 + - + +
289A LEU* 2.9 22.4 + - + +
290A PHE 3.7 26.2 - - - +
291A ASP* 3.7 7.0 - - - +
366A ALA* 3.5 31.6 - - + +
369A GLU* 4.3 14.1 - - + -
370A GLU* 3.5 33.2 - - + +
373A MET* 4.6 18.6 - - + -
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Residues in contact with TYR 268 (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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266A LEU* 3.6 6.7 - - - +
267A ILE* 1.3 83.6 - - - +
269A THR* 1.3 82.5 + - + +
270A GLY* 5.0 0.9 - - - -
289A LEU* 2.9 29.9 + - + +
359A GLU* 2.8 22.7 + - - -
362A ARG* 3.5 35.0 + - + -
363A TRP* 3.5 56.5 - + + -
366A ALA* 3.6 25.6 - - + -
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Residues in contact with THR 269 (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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266A LEU* 4.1 17.5 - - + -
268A TYR* 1.3 98.0 + - + +
270A GLY* 1.3 59.2 + - - +
286A VAL* 4.4 4.5 - - - +
287A PHE 3.0 16.9 + - - -
288A PHE* 3.7 30.7 - - + -
363A TRP* 3.8 4.5 - - - -
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Residues in contact with GLY 270 (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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268A TYR* 5.0 2.2 - - - -
269A THR* 1.3 78.2 + - - +
271A GLU* 1.3 67.3 + - - -
286A VAL* 4.6 2.9 - - - -
287A PHE* 2.9 32.2 + - - +
359A GLU* 6.0 0.9 - - - -
363A TRP* 3.3 20.4 - - - -
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Residues in contact with GLU 271 (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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270A GLY* 1.3 74.5 - - - -
272A MET* 1.3 65.7 + - - +
284A GLN* 5.6 5.4 - - - +
285A ARG 3.6 9.4 - - - +
286A VAL* 3.7 23.8 - - + +
299A LYS* 3.4 31.7 + - - +
304A ARG* 5.3 1.6 + - - -
354A ALA* 5.3 2.1 - - - -
355A LYS* 5.4 5.7 + - - +
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Residues in contact with MET 272 (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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270A GLY 3.8 0.2 + - - -
271A GLU* 1.3 80.2 - - - +
273A ALA* 1.3 63.2 + - - +
284A GLN* 4.6 6.2 + - - -
285A ARG 3.3 22.7 + - - +
287A PHE* 3.2 40.6 - - + -
294A MET* 5.8 1.1 - - - -
339A PHE* 4.2 20.2 - - + -
352A PHE* 3.8 22.7 - - + -
353A PHE 3.4 12.1 - - - +
354A ALA* 4.1 15.3 - - + +
355A LYS* 6.2 2.0 - - - -
359A GLU* 6.0 0.7 - - + -
363A TRP* 3.4 53.8 - - + +
367A PHE* 5.7 1.3 - - + -
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Residues in contact with ALA 273 (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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272A MET* 1.3 73.2 - - - +
274A TRP* 1.3 64.2 + - - +
282A ASN* 3.5 19.7 - - - +
283A GLN 3.5 7.0 - - - +
284A GLN* 4.6 9.7 + - - +
352A PHE* 3.7 1.2 - - - -
353A PHE* 2.9 51.8 + - + +
355A LYS* 4.4 19.5 - - - +
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Residues in contact with TRP 274 (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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273A ALA* 1.3 77.3 - - - +
275A ILE* 1.3 77.4 + - - +
276A TYR* 3.5 47.1 + + + -
281A ARG 3.8 1.6 - - - +
282A ASN* 3.7 1.9 + - - -
283A GLN* 3.1 63.1 + - + +
285A ARG* 3.8 20.2 - - + +
287A PHE* 3.8 19.5 - + + -
296A LEU* 4.0 25.0 - - + +
313A ILE* 4.8 7.0 - - + -
350A HIS* 4.0 17.7 - + + -
351A LEU 3.3 9.9 - - - +
352A PHE* 3.7 28.5 - + + -
353A PHE* 4.5 2.0 - - - -
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Residues in contact with ILE 275 (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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274A TRP* 1.3 82.1 - - - +
276A TYR* 1.3 64.4 + - - +
277A GLN 3.1 24.0 - - - +
279A TYR 5.2 0.2 - - - +
280A GLY* 4.0 22.7 - - - +
281A ARG 4.4 3.1 - - - +
282A ASN* 4.2 22.0 - - + +
331A PHE* 3.6 13.3 - - + -
333A VAL* 4.8 17.5 - - + -
350A HIS* 3.6 1.0 - - - -
351A LEU* 2.9 45.5 + - + +
353A PHE* 3.9 26.9 - - + -
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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