Contacts of the strand formed by residues 287 - 291 (chain B) in PDB entry 1W6T
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 ILE 287 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238B PHE* 4.7 1.8 - - - -
239B LEU* 3.3 17.0 - - + +
240B GLY* 4.8 0.2 - - - -
241B PHE* 3.4 37.2 - - + -
281B LEU* 3.4 34.5 - - + +
282B VAL* 3.8 16.4 - - + +
285B TYR* 2.8 23.5 + - + +
286B PRO* 1.3 73.4 - - - +
288B ILE* 1.3 62.7 + - - +
289B THR 3.7 20.4 - - - +
290B ILE* 3.9 18.4 - - + -
312B LYS 5.2 0.5 - - - +
313B VAL* 4.2 13.9 - - + +
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Residues in contact with ILE 288 (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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168B LEU* 3.9 24.9 - - + -
170B VAL* 4.9 0.9 - - + -
238B PHE* 3.6 34.3 - - + -
239B LEU 2.8 11.2 + - - +
286B PRO 3.8 0.6 + - - -
287B ILE* 1.3 73.7 - - - +
289B THR* 1.3 63.1 + - + +
312B LYS 4.8 3.6 - - - +
313B VAL* 3.8 6.5 - - - +
314B GLN* 2.9 25.3 + - - +
426B LEU* 3.2 34.5 - - + -
429B PHE* 4.2 21.8 - - + -
432B LEU* 4.1 17.0 - - + -
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Residues in contact with THR 289 (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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146B MET* 4.2 14.6 - - + +
166B MET* 5.2 2.0 - - + -
168B LEU* 3.9 25.8 - - + -
239B LEU 3.7 0.2 + - - -
240B GLY* 3.2 22.0 - - - -
241B PHE 2.9 24.9 + - - +
287B ILE* 3.7 3.3 - - - +
288B ILE* 1.3 83.6 - - - +
290B ILE* 1.3 70.0 + - - +
291B GLU* 4.2 0.7 + - - +
313B VAL* 4.3 0.2 - - - -
314B GLN* 2.9 34.3 + - - +
316B VAL* 3.4 13.5 - - - +
429B PHE* 4.7 0.7 - - - -
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Residues in contact with ILE 290 (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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241B PHE* 3.5 12.1 - - + -
243B CYS* 3.6 29.8 - - - -
278B LEU* 4.4 25.6 - - + +
282B VAL* 3.8 27.8 - - + -
287B ILE* 3.9 11.7 - - + -
289B THR* 1.3 83.0 + - - +
291B GLU* 1.3 61.1 + - - +
292B ASP 4.0 0.5 + - - -
293B GLY* 3.9 16.1 + - - -
302B TRP* 5.2 1.0 - - - -
309B LEU* 4.6 2.7 - - + -
313B VAL* 4.0 9.9 - - + -
314B GLN 2.8 10.6 + - - +
315B LEU* 3.3 19.9 - - + +
316B VAL 2.8 23.0 + - - +
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Residues in contact with GLU 291 (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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146B MET* 5.1 2.6 - - - +
166B MET* 4.7 4.7 - - + +
241B PHE 2.8 14.9 + - - +
242B ASP* 2.8 10.7 - - + +
243B CYS* 2.9 25.5 + - - +
289B THR* 4.2 0.6 + - - +
290B ILE* 1.3 72.3 - - - +
292B ASP* 1.3 69.3 + - - +
293B GLY 3.2 2.9 + - - -
316B VAL* 3.2 26.0 - - + +
318B ASP* 2.9 21.7 - - + +
341B LEU* 3.9 9.9 - - - +
394B LYS* 2.6 33.1 + - - +
435B MG 2.1 33.0 - - - -
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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