Contacts of the strand formed by residues 246 - 252 (chain B) in PDB entry 5FFO
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 246 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B TYR* 3.9 22.7 - - + +
115B PRO 3.6 2.8 + - - -
116B VAL* 3.9 23.5 - - + -
117B ASP 2.8 27.9 + - - +
245B SER* 1.3 75.2 - - - +
247B HIS* 1.3 60.9 + - - +
248B LEU* 3.1 23.4 + - + +
306B ASN* 6.0 2.7 - - - +
308B LEU* 5.7 8.3 - - + -
350B ALA 4.6 10.8 - - - +
351B TYR* 4.3 14.8 - - + -
353B GLU* 4.5 20.0 - - + +
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Residues in contact with HIS 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B ASP* 4.1 2.5 - - - -
236B LYS* 6.1 2.2 - - - -
241B TRP* 3.4 47.0 - + + +
242B ARG 2.8 29.4 + - - -
243B ASN 4.4 7.4 - - - -
245B SER* 3.1 33.9 + - - -
246B LEU* 1.3 67.8 - - - +
248B LEU* 1.3 61.6 + - - +
305B ASN 3.0 25.9 + - - -
306B ASN* 3.0 20.1 + - + +
307B VAL* 3.4 9.5 - - + +
308B LEU* 2.9 27.2 + - - +
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Residues in contact with LEU 248 (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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116B VAL* 4.2 17.7 - - + -
117B ASP 3.0 10.3 + - - +
118B LEU* 3.2 17.9 - - + +
119B TYR 2.8 25.1 + - - -
241B TRP* 4.0 4.3 - - - -
246B LEU* 3.6 26.5 - - + +
247B HIS* 1.3 75.0 - - - +
249B LEU* 1.3 60.3 + - - +
308B LEU* 3.7 37.5 - - + +
310B ILE* 5.1 11.9 - - + -
347B ILE* 3.7 28.9 - - + -
350B ALA* 5.6 9.2 - - + -
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Residues in contact with LEU 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B TYR* 3.5 22.4 - - + +
121B LEU* 3.8 39.5 - - + -
229B ILE* 4.3 15.3 - - + +
232B ALA* 4.0 20.6 - - + -
233B ALA* 4.5 3.8 - - + +
241B TRP* 4.4 8.7 - - + -
247B HIS 4.0 0.2 + - - -
248B LEU* 1.3 72.5 - - - +
250B VAL* 1.3 67.4 + - - +
307B VAL* 3.9 26.5 - - + -
308B LEU 3.1 8.1 + - - +
309B LEU* 3.3 23.9 - - + +
310B ILE* 3.1 23.3 + - - +
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Residues in contact with VAL 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B LEU* 3.6 25.4 - - + -
119B TYR 2.9 12.9 + - - +
120B TYR* 3.9 21.3 - - + -
121B LEU* 2.9 32.7 + - - +
138B LEU* 5.2 1.8 - - + -
142B LEU* 4.9 4.3 - - + -
248B LEU 4.1 0.4 - - - -
249B LEU* 1.3 71.4 - - - +
251B PHE* 1.3 60.1 + - - +
252B VAL* 3.8 22.9 - - + -
310B ILE* 3.8 25.1 - - + +
312B ALA* 4.6 8.3 - - + -
343B ILE* 5.1 7.6 - - + -
347B ILE* 4.4 10.8 - - + -
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Residues in contact with PHE 251 (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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121B LEU* 3.7 23.3 - - + -
160B PHE* 3.5 25.6 - + - -
225B GLY* 3.7 30.3 - - - -
226B PHE* 5.5 0.7 - + - -
229B ILE* 3.8 11.9 - - + -
249B LEU 3.4 0.2 + - - -
250B VAL* 1.3 72.1 - - - +
252B VAL* 1.3 59.6 + - - +
253B SER* 3.3 28.9 - - - -
257B SER* 4.6 3.8 - - - -
309B LEU* 4.1 15.5 - - + -
310B ILE 2.8 17.5 + - - +
311B PHE* 3.7 20.2 - + + -
312B ALA* 2.7 33.8 + - - +
313B VAL* 4.9 2.0 - - + -
321B TYR* 3.6 23.8 - + - -
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Residues in contact with VAL 252 (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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120B TYR* 4.3 17.0 - - + +
121B LEU 3.1 13.1 + - - +
122B MET* 3.9 5.5 - - + -
123B ASP* 3.0 26.5 + - - +
128B MET* 4.2 14.4 - - + -
135B ILE* 3.5 27.1 - - + -
138B LEU* 4.7 3.1 - - + -
160B PHE* 4.0 2.8 - - - -
250B VAL* 3.8 16.2 - - + -
251B PHE* 1.3 77.8 - - - +
253B SER* 1.3 65.5 + - - +
312B ALA* 3.3 26.5 - - + +
336B LEU* 4.1 8.1 - - + -
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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
------------------------------------------------------------
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