Contacts of the strand formed by residues 283 - 286 (chain B) in PDB entry 1M7X
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 HIS 283 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236B ALA* 3.2 23.8 + - + +
237B ASN* 2.8 34.7 + - - -
243B ILE* 4.0 19.5 - - + +
244B SER 3.2 3.3 + - - +
245B ILE* 3.8 19.1 - - + -
246B TYR* 3.1 23.1 + - - +
276B ALA* 5.6 0.2 - - - +
281B PHE* 3.8 8.6 - - - +
282B THR* 1.3 114.7 + - - +
284B LEU* 1.3 62.5 + - - +
285B GLU 4.2 0.2 - - - -
330B LEU* 5.2 2.9 - - - -
331B ASN* 3.5 20.5 - - + +
333B ILE* 3.7 25.6 - - + +
456B MET* 5.3 2.5 - - + -
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Residues in contact with LEU 284 (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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245B ILE* 4.6 0.4 - - - -
246B TYR* 3.7 24.9 - - + +
248B VAL* 4.1 10.8 - - + -
272B LEU* 4.4 12.1 - - + -
273B VAL* 4.5 9.0 - - + -
276B ALA* 4.1 22.2 - - + -
283B HIS* 1.3 74.8 - - - +
285B GLU* 1.3 60.6 + - - +
286B LEU* 4.3 12.1 - - + -
321B PHE* 3.9 30.1 - - + -
325B ALA* 4.7 6.1 - - + -
330B LEU* 4.5 19.3 - - + -
331B ASN 3.1 12.6 + - - +
332B VAL* 3.4 9.6 - - + +
333B ILE* 2.8 28.9 + - - +
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Residues in contact with GLU 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B ILE* 3.4 18.9 - - + +
246B TYR 3.0 7.7 + - - +
247B GLU* 3.4 17.6 - - + +
248B VAL* 2.7 34.7 + - - +
284B LEU* 1.3 74.1 - - - +
286B LEU* 1.3 61.3 + - - +
333B ILE* 3.3 36.3 - - + +
335B ASP* 3.4 20.8 - - - +
403B ARG* 3.3 13.7 - - - +
456B MET* 5.0 2.1 - - - +
481B TRP* 3.2 29.1 + - - -
565B LEU* 3.5 15.6 - - - +
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Residues in contact with LEU 286 (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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248B VAL* 3.4 8.1 - - + +
250B LEU* 3.7 29.4 - - + -
272B LEU* 5.0 0.2 - - + -
284B LEU* 4.3 18.4 - - + +
285B GLU* 1.3 80.3 - - - +
287B LEU* 1.3 71.5 + - - +
289B ILE* 4.2 19.5 - - + -
318B PHE* 4.4 12.6 - - + -
321B PHE* 3.9 22.0 - - + -
322B ILE* 4.7 0.4 - - + -
332B VAL* 4.1 17.9 - - + -
333B ILE 3.0 13.8 + - - +
334B LEU* 4.3 10.0 - - + +
335B ASP* 3.0 28.5 + - - +
399B ILE* 5.9 0.2 - - + -
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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