Contacts of the strand formed by residues 267 - 273 (chain B) in PDB entry 1AHF
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 VAL 267 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B PHE* 3.9 18.2 - - + -
104B GLN* 5.8 0.7 - - + -
105B THR 4.1 0.4 - - - -
107B GLY* 3.7 5.9 - - - +
255B SER* 3.8 4.7 + - - -
256B TYR* 2.8 40.5 + - + -
257B SER* 3.8 6.6 + - - -
262B LEU* 4.0 23.1 + - + +
265B GLU* 4.0 4.9 - - + +
266B ARG* 1.3 78.1 - - - +
268B GLY* 1.3 59.7 + - - +
302B GLY* 3.7 30.1 - - - +
303B ALA* 3.8 28.0 - - + +
306B VAL* 4.0 4.9 - - + -
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Residues in contact with GLY 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B PHE* 3.6 13.0 - - - -
104B GLN* 3.6 0.7 - - - +
105B THR* 2.8 31.4 + - - -
107B GLY 3.6 11.0 - - - +
254B SER 3.2 14.6 - - - -
255B SER* 4.0 2.5 - - - -
256B TYR* 4.2 5.4 - - - -
267B VAL* 1.3 76.5 - - - +
269B ALA* 1.3 64.4 + - - +
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Residues in contact with ALA 269 (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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79B PHE* 3.9 12.3 - - + -
83B THR* 4.2 7.6 - - + -
102B THR* 3.6 20.6 - - + -
103B ALA 3.2 11.7 - - - +
105B THR* 3.5 3.6 + - - -
111B ALA* 3.5 7.0 - - - +
252B VAL 3.3 2.6 - - - +
253B ALA* 3.4 2.9 - - - -
254B SER* 2.8 49.2 + - - +
256B TYR* 5.0 0.9 - - + -
268B GLY* 1.3 77.4 - - - +
270B CYS* 1.3 60.3 - - - +
271B THR* 4.0 1.1 - - - +
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Residues in contact with CYS 270 (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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101B ARG 3.8 1.6 - - - +
102B THR* 3.3 1.4 - - - -
103B ALA* 2.8 39.4 + - + +
105B THR* 3.9 14.7 - - + +
111B ALA* 3.4 25.8 - - - +
114B VAL* 4.7 2.2 - - + -
115B ALA* 4.0 16.8 - - - -
251B ILE* 4.0 13.7 - - - -
252B VAL 3.3 3.8 - - - -
253B ALA* 5.3 0.2 - - - -
269B ALA* 1.3 72.6 - - - +
271B THR* 1.3 64.8 + - - +
272B LEU 4.0 0.3 + - - -
287B MET* 3.8 30.0 - - - +
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Residues in contact with THR 271 (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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83B THR* 4.4 1.2 - - - +
84B GLN* 4.5 0.7 - - + -
87B LEU* 3.8 14.5 - - + +
88B PHE* 3.9 32.3 - - + -
100B ALA* 4.3 6.5 - - + -
101B ARG 3.6 4.0 - - - +
102B THR* 2.8 34.1 + - - +
250B LEU 3.9 0.5 - - - +
251B ILE* 3.3 8.5 - - - +
252B VAL* 2.7 52.6 + - + +
254B SER* 5.3 0.7 + - - -
269B ALA* 4.7 1.0 - - - +
270B CYS* 1.3 75.0 + - - +
272B LEU* 1.3 67.3 + - - +
273B VAL* 4.6 2.0 - - + +
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Residues in contact with LEU 272 (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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6A PHE* 3.7 16.2 - - + -
100B ALA* 3.3 6.2 - - - +
101B ARG 3.0 30.8 + - - +
118B PHE* 3.7 23.8 - - + -
250B LEU 3.8 0.2 - - - -
251B ILE* 3.6 27.4 - - + -
270B CYS 4.0 0.2 + - - -
271B THR* 1.3 72.1 - - - +
273B VAL* 1.3 64.4 + - - +
280B VAL* 3.5 10.7 - - + +
283B ALA* 3.7 28.0 - - + -
284B PHE* 3.7 15.0 - - + +
287B MET* 3.0 33.9 - - + -
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Residues in contact with VAL 273 (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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6A PHE* 4.3 4.4 - - - -
88B PHE* 4.2 18.8 - - + -
94B LEU* 4.0 18.4 - - + -
99B ARG* 3.3 28.5 - - - +
100B ALA* 4.4 2.0 - - + -
244B ALA* 6.0 0.4 - - - +
247B HIS 5.3 0.9 - - - +
248B LYS 3.6 12.6 - - - +
249B GLU* 2.8 34.1 - - - +
250B LEU* 2.8 49.5 + - + +
271B THR* 4.6 5.2 - - + +
272B LEU* 1.3 79.3 - - - +
274B ALA* 1.4 53.3 + - - +
280B VAL* 4.2 0.4 - - - -
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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