Contacts of the strand formed by residues 285 - 289 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122E ASN* 3.1 12.1 + - - -
123E THR* 2.9 42.7 + - - -
125E GLY* 3.6 11.0 - - - +
272E ALA 3.6 10.1 - - - -
273E SER* 4.3 0.4 - - - -
274E GLY 3.9 1.8 - - - -
284E CYS* 1.3 73.9 - - - +
286E TRP* 1.3 67.3 + - - -
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Residues in contact with TRP 286 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97E ASP* 3.9 10.5 - - - -
100E CYS* 3.2 29.2 - - + -
101E VAL* 3.9 16.4 - - + -
104E VAL* 4.1 31.0 - - + -
108E TRP* 4.6 5.1 - - + -
121E THR 3.5 8.1 - - - -
122E ASN* 3.5 50.0 - - + -
123E THR* 3.6 1.2 + - - -
129E ALA* 3.7 3.9 - - - +
249E PHE* 3.9 22.2 - + - -
270E ILE 4.5 0.2 - - - -
271E SER* 3.2 25.6 - - - -
272E ALA 3.1 14.1 + - - +
274E GLY 4.1 9.0 - - - -
284E CYS* 3.5 8.9 - - - -
285E GLY* 1.3 77.9 - - - -
287E VAL* 1.3 60.7 + - - +
288E ILE* 5.4 2.0 - - + -
324E VAL* 4.2 4.5 - - + -
327E GLN* 3.0 44.5 + - + -
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Residues in contact with VAL 287 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120E GLY* 3.1 3.5 - - - -
121E THR* 3.0 48.9 + - + +
123E THR* 4.1 0.9 - - + -
129E ALA* 3.8 26.9 - - + +
132E LEU* 4.0 11.4 - - + -
133E GLY 4.7 0.4 - - - +
241E HIS* 4.2 14.6 - - + -
269E SER* 4.6 0.4 - - - -
270E ILE 3.2 11.9 - - - +
271E SER* 4.2 0.2 - - - -
286E TRP* 1.3 76.8 - - - +
288E ILE* 1.3 69.3 + - - +
289E TRP* 3.7 40.3 - - + -
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Residues in contact with ILE 288 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101E VAL* 3.4 42.4 - - + +
104E VAL* 3.8 13.2 - - + -
105E ALA* 3.7 24.0 - - + +
108E TRP* 3.7 23.6 - - + -
110E ALA* 4.5 1.3 - - + -
118E ALA* 5.1 1.3 - - + -
119E VAL 3.4 7.0 - - - +
120E GLY* 4.3 1.6 - - - -
121E THR 5.0 0.4 - - - +
262E PHE* 3.2 22.2 - - + -
269E SER* 3.1 6.5 - - - -
270E ILE 2.8 33.1 + - - -
286E TRP* 5.5 2.7 - - + -
287E VAL* 1.3 81.9 - - - +
289E TRP* 1.3 77.1 + - - +
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Residues in contact with TRP 289 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110E ALA* 4.8 1.9 - - - +
118E ALA* 5.9 0.2 - - - +
119E VAL* 2.8 37.0 + - + +
120E GLY* 3.9 19.3 - - - -
121E THR* 4.5 5.8 - - + -
132E LEU* 3.7 30.7 - - + -
133E GLY* 4.1 0.8 - - - -
136E ALA* 3.5 18.0 - - - +
140E ARG* 4.3 1.3 - - - -
262E PHE* 3.9 2.8 - - - -
268E LYS 3.5 6.3 - - - -
269E SER* 3.5 23.3 + - - -
287E VAL* 3.7 37.9 - - + -
288E ILE* 1.3 89.4 - - - +
290E ARG* 1.3 65.9 + - - +
291E ASP 3.4 2.2 + - - +
294E ALA* 3.4 27.1 - - + -
295E LEU* 4.0 15.5 - - + +
313E PHE* 3.7 28.5 - + + -
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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