Contacts of the strand formed by residues 285 - 289 (chain B) in PDB entry 3FZ7
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 GLY 285 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B ASN* 3.1 11.6 + - - -
123B THR* 2.6 46.4 + - - -
125B GLY 3.7 13.2 - - - +
272B ALA 3.6 10.5 - - - -
273B SER* 4.3 0.4 - - - -
274B GLY 3.9 1.3 - - - -
284B CYS* 1.3 73.9 - - - +
286B TRP* 1.3 65.2 + - - -
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Residues in contact with TRP 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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97B ASP* 3.6 13.0 - - - -
100B CYS* 3.2 32.8 - - + -
101B VAL* 4.1 13.0 - - + -
104B VAL* 4.2 31.6 - - + +
108B TRP* 4.6 5.0 - - + -
121B THR 3.5 7.0 - - - -
122B ASN* 3.5 46.7 - - + -
123B THR* 3.6 0.8 + - - -
129B ALA* 3.6 5.3 - - - +
249B PHE* 3.8 23.5 - + - -
271B SER* 3.2 6.8 - - - -
272B ALA 3.0 30.8 + - - +
274B GLY* 4.1 8.7 - - - -
284B CYS* 3.6 12.6 - - - -
285B GLY* 1.3 76.4 - - - -
287B VAL* 1.3 63.3 + - - +
288B ILE* 5.3 2.2 - - + -
324B VAL* 4.2 5.2 - - + -
327B GLN* 3.0 44.1 + - + +
331B PHE* 5.0 0.2 - + - -
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Residues in contact with VAL 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B GLY* 3.1 3.5 - - - -
121B THR* 2.8 63.1 + - + -
123B THR* 4.3 1.3 - - + -
129B ALA* 3.8 27.6 - - + +
132B LEU* 3.8 12.3 - - + -
133B GLY 4.6 0.9 - - - +
241B HIS* 4.2 13.2 - - + -
269B SER* 4.6 0.9 - - - -
270B ILE 3.4 11.2 - - - +
271B SER* 4.3 0.4 - - - -
286B TRP* 1.3 76.1 - - - +
288B ILE* 1.3 70.8 + - - +
289B TRP* 3.7 31.4 - - + -
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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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101B VAL* 3.6 41.5 - - + +
104B VAL* 3.9 13.9 - - + -
105B ALA* 3.7 23.8 - - + +
108B TRP* 3.6 23.1 - - + -
110B ALA* 4.6 1.8 - - + -
118B ALA* 5.0 1.6 - - + -
119B VAL 3.6 7.6 - - - +
120B GLY* 4.3 0.7 - - - -
121B THR 4.6 1.3 - - - +
262B PHE* 3.4 21.6 - - + -
269B SER* 3.1 5.4 - - - -
270B ILE 2.8 32.0 + - - -
286B TRP* 5.3 3.4 - - + -
287B VAL* 1.3 84.6 - - - +
289B TRP* 1.3 75.8 + - - +
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Residues in contact with TRP 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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110B ALA* 5.0 2.1 - - - +
119B VAL* 2.9 38.9 + - + +
120B GLY* 3.7 28.3 - - - -
121B THR* 4.4 3.8 - - + -
132B LEU* 3.8 18.2 - - + -
133B GLY* 4.2 0.8 - - - -
136B ALA* 3.4 18.2 - - - +
140B ARG* 4.2 2.4 - - - +
262B PHE* 3.9 3.7 - - - -
268B LYS 3.4 6.7 - - - +
269B SER* 3.5 22.4 + - - -
287B VAL* 3.7 31.4 - - + -
288B ILE* 1.3 85.7 - - - +
290B ARG* 1.3 64.2 + - - +
291B ASP 3.3 3.5 + - - +
294B ALA* 3.1 30.3 + - + -
295B LEU* 3.9 15.7 - - + +
313B PHE* 3.6 39.5 - + + -
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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