Contacts of the strand formed by residues 285 - 289 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122F ASN* 3.1 11.6 + - - -
123F THR* 2.7 45.9 + - - -
125F GLY* 3.7 9.6 - - - +
272F ALA 3.6 10.3 - - - -
273F SER* 4.2 0.2 - - - -
274F GLY 3.9 2.0 - - - -
284F CYS* 1.3 75.6 - - - +
286F TRP* 1.3 64.0 + - - -
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Residues in contact with TRP 286 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97F ASP* 3.7 13.5 - - - -
100F CYS* 3.4 28.9 - - + -
101F VAL* 3.9 14.1 - - + -
104F VAL* 4.3 30.0 - - + +
108F TRP* 4.6 6.5 - - + -
121F THR 3.8 4.3 - - - -
122F ASN* 3.3 51.4 - - + -
123F THR* 3.6 1.2 + - - -
129F ALA* 3.6 7.5 - - - +
249F PHE* 3.7 25.5 - + - -
271F SER* 3.1 3.5 - - - -
272F ALA 2.8 35.8 + - - +
274F GLY 4.1 5.2 - - - -
284F CYS* 3.6 8.1 - - - -
285F GLY* 1.3 75.5 - - - -
287F VAL* 1.3 59.8 + - - +
288F ILE* 5.3 3.1 - - + -
324F VAL* 4.1 4.0 - - + -
327F GLN* 2.9 43.5 + - + -
331F PHE* 5.2 0.2 - + - -
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Residues in contact with VAL 287 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120F GLY* 3.1 3.3 - - - -
121F THR* 2.9 55.9 + - + +
123F THR* 4.1 0.9 - - + -
129F ALA* 3.7 35.9 - - + +
132F LEU* 4.0 4.5 - - + -
133F GLY* 4.6 0.4 - - - -
241F HIS* 4.2 13.7 - - + -
269F SER* 4.6 0.9 - - - -
270F ILE 3.3 13.0 - - - +
271F SER* 4.2 0.9 - - - -
286F TRP* 1.3 74.3 - - - +
288F ILE* 1.3 73.5 + - - +
289F TRP* 3.8 30.7 - - + -
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Residues in contact with ILE 288 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101F VAL* 3.8 40.2 - - + +
104F VAL* 3.9 12.3 - - + -
105F ALA* 3.9 22.0 - - + +
108F TRP* 3.5 31.9 - - + -
110F ALA* 4.5 1.8 - - + -
118F ALA* 5.2 1.3 - - + -
119F VAL 3.6 8.7 - - - +
120F GLY* 4.2 0.2 - - - -
121F THR 4.9 0.7 - - - +
262F PHE* 3.4 21.3 - - + -
269F SER* 3.1 6.1 - - - -
270F ILE 2.9 30.0 + - - -
286F TRP* 5.3 3.8 - - + -
287F VAL* 1.3 87.0 - - - +
289F TRP* 1.3 72.6 + - - +
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Residues in contact with TRP 289 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110F ALA* 4.9 2.3 - - - +
119F VAL* 2.8 40.2 + - + +
120F GLY* 3.8 17.7 - - - -
121F THR* 4.3 8.3 - - + -
132F LEU* 3.8 23.6 - - + -
133F GLY* 4.7 0.8 - - - -
136F ALA* 3.4 17.2 - - - +
140F ARG* 4.2 1.8 - - - +
262F PHE* 3.9 2.9 - - - -
268F LYS 3.4 4.9 - - - -
269F SER* 3.4 21.4 + - - -
287F VAL* 3.8 37.5 - - + -
288F ILE* 1.3 83.1 - - - +
290F ARG* 1.3 67.5 + - - +
291F ASP* 3.0 3.8 + - - +
294F ALA* 3.4 29.2 - - + -
295F LEU* 3.9 28.0 - - + -
313F PHE* 3.6 27.4 - + + -
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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