Contacts of the strand formed by residues 280 - 286 (chain B) in PDB entry 4OE4
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 PHE 280 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203B GLY* 4.7 0.2 - - - -
204B PHE* 3.4 29.8 - + + -
206B TYR* 3.6 16.6 - + + -
274B VAL* 4.4 5.4 - - + +
275B LEU* 3.5 32.3 - - + -
277B ASP 3.1 16.0 + - - +
278B LYS 3.3 2.7 - - - +
279B ASP* 1.3 76.4 - - - +
281B GLY* 1.3 59.4 + - - +
282B ALA 3.3 33.7 - - - -
283B LEU* 3.7 2.9 - - + -
299B ILE* 3.7 27.8 - - + -
308B TYR* 3.9 29.5 - + + +
310B ASP* 5.0 5.7 + - - +
312B PRO* 3.8 28.7 - - + +
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Residues in contact with GLY 281 (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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201B LEU* 4.0 10.9 - - - +
203B GLY* 4.0 18.8 - - - -
204B PHE 2.8 17.4 + - - -
279B ASP 3.2 1.6 + - - -
280B PHE* 1.3 74.1 - - - +
282B ALA* 1.3 61.1 + - - +
310B ASP* 5.8 5.4 - - - -
311B TYR 4.5 0.7 - - - +
312B PRO* 3.2 9.7 - - - +
313B ARG* 2.9 21.8 + - - +
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Residues in contact with ALA 282 (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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201B LEU* 3.5 22.2 - - + -
204B PHE 3.2 3.8 + - - -
205B VAL* 3.5 11.8 - - + -
206B TYR 2.8 31.5 + - - -
280B PHE* 3.3 14.5 - - - -
281B GLY* 1.3 81.6 - - - +
283B LEU* 1.3 56.4 + - - +
313B ARG* 3.1 19.1 - - + +
315B ILE* 4.3 9.0 - - + -
552B PHE* 4.4 4.3 - - + -
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Residues in contact with LEU 283 (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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206B TYR* 3.6 21.1 - - + +
208B VAL* 4.1 22.4 - - + -
275B LEU* 6.2 0.2 - - + -
280B PHE* 3.7 4.0 - - + -
282B ALA* 1.3 74.3 - - - +
284B HIS* 1.3 65.8 + - - +
285B PHE* 3.9 20.0 - - + -
292B PHE* 4.7 3.6 - - + -
295B LEU* 3.8 37.7 - - + -
296B TYR 5.1 0.2 - - - +
299B ILE* 3.8 26.9 - - + -
313B ARG 2.8 9.1 + - - +
314B ILE* 4.1 18.2 - - + -
315B ILE* 2.8 32.5 + - - +
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Residues in contact with HIS 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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205B VAL* 4.1 9.0 - - + -
206B TYR 2.8 13.9 + - - +
207B ALA* 3.4 3.8 - - - -
208B VAL 2.9 27.6 + - - +
219B ASN* 3.9 14.7 + - - -
220B LEU* 2.8 58.1 + - + +
223B ALA* 4.4 4.5 - - + -
224B PRO* 3.9 2.0 - - + +
282B ALA 4.0 0.2 - - - -
283B LEU* 1.3 73.7 - - - +
285B PHE* 1.3 60.0 + - - +
315B ILE* 3.4 32.6 - - + +
548B ILE* 4.6 7.1 - - + +
552B PHE* 3.4 36.1 - + + -
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Residues in contact with PHE 285 (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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208B VAL* 3.5 17.3 - - + +
220B LEU* 4.2 2.4 - - - +
283B LEU* 3.9 20.0 - - + -
284B HIS* 1.3 75.2 - - - +
286B THR* 1.3 71.0 + - - +
287B GLY* 3.3 41.1 - - - -
288B SER 3.6 11.0 - - - -
291B VAL* 3.6 18.2 - - + -
292B PHE* 3.7 24.9 - + + -
295B LEU* 3.4 25.4 - - + -
315B ILE 2.9 7.6 + - - +
316B GLY* 3.3 8.6 - - - -
317B GLU 2.9 26.0 + - - -
318B THR* 4.7 0.2 - - + -
1000B NAD 3.5 25.1 - - - -
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Residues in contact with THR 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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208B VAL 3.3 9.6 + - - +
210B PRO* 3.3 29.5 - - + +
212B ASN* 5.7 0.2 - - - +
216B ILE* 3.9 35.2 - - + +
219B ASN* 5.4 0.7 + - - -
220B LEU* 3.5 17.7 - - - +
285B PHE* 1.3 81.4 + - - +
287B GLY* 1.3 61.3 + - - +
317B GLU* 3.3 26.6 - - + +
351B CYS* 4.6 14.6 - - - -
1000B NAD 3.9 4.0 - - - +
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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