Contacts of the strand formed by residues 92 - 97 (chain D) in PDB entry 6CU0
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 PHE 92 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140A VAL* 3.7 39.3 - - + -
203A LEU* 4.1 15.3 - - + -
240A VAL* 3.7 22.9 - - + -
241A THR* 4.5 9.6 - - - -
90D GLY* 4.1 15.0 - - - -
91D MET* 1.3 82.1 - - - +
93D ALA* 1.3 66.0 + - - +
119D SER* 4.2 15.3 - - - -
120D LEU 3.9 0.2 - - - -
121D THR* 2.9 60.3 + - + -
124D LEU* 3.5 10.2 - - - +
237D LEU 3.3 15.0 - - - +
238D PHE* 3.6 14.1 - - + +
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Residues in contact with ALA 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A LEU* 3.3 7.4 - - - +
92D PHE* 1.3 76.9 - - - +
94D GLN* 1.3 63.7 + - - +
95D LEU* 5.1 1.1 - - + -
119D SER 3.2 7.4 - - - -
120D LEU* 3.7 25.4 - - + -
124D LEU* 3.9 5.8 - - + -
133D LEU* 4.4 14.8 - - + -
236D GLY* 4.3 0.7 - - - -
237D LEU* 2.9 46.2 + - + +
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Residues in contact with GLN 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A ARG* 3.5 23.0 - - - +
203A LEU* 2.7 56.7 + - + +
204A LEU* 5.5 0.2 - - - +
93D ALA* 1.3 77.0 - - - +
95D LEU* 1.3 66.5 + - - +
117D GLY* 3.2 20.1 + - - +
118D VAL* 3.3 6.8 - - - -
119D SER* 2.7 41.9 + - - +
144D PHE* 3.6 7.1 - - - -
234D VAL* 3.6 24.0 - - + +
235D LEU 3.3 6.7 - - - +
236D GLY* 4.4 0.9 - - - -
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Residues in contact with LEU 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93D ALA* 5.4 0.4 - - + -
94D GLN* 1.3 80.9 - - - +
96D VAL* 1.3 63.9 + - - +
109D TRP* 3.5 37.9 - - + -
110D TYR 3.8 15.9 - - - +
111D SER* 4.3 9.4 - - - -
118D VAL* 4.6 1.1 - - + -
120D LEU* 4.1 29.6 - - + -
126D TYR* 4.2 13.7 - - + -
133D LEU* 4.0 29.8 - - + -
234D VAL* 3.4 10.7 - - - +
235D LEU* 2.7 41.4 + - + +
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Residues in contact with VAL 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A ARG* 5.1 1.3 - - - +
94D GLN* 5.5 0.7 - - + +
95D LEU* 1.3 79.3 - - - +
97D ALA* 1.3 71.8 + - - +
109D TRP* 3.4 3.4 - - - -
110D TYR* 2.9 46.5 + - + -
116D ALA 4.5 4.7 - - - +
117D GLY* 4.1 20.6 - - - +
118D VAL* 3.7 23.3 - - + -
231D GLY* 3.7 33.7 - - - +
233D THR 3.8 4.5 - - - +
234D VAL* 4.5 10.3 - - + -
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Residues in contact with ALA 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96D VAL* 1.3 80.8 - - - +
98D GLN* 1.3 61.9 + - - +
99D ASN* 4.0 17.6 - - + +
107D LEU* 4.7 2.9 - - + -
108D SER 3.5 10.1 - - - +
109D TRP* 3.2 20.7 - - + -
110D TYR* 3.9 3.5 - - - -
228D LEU* 5.3 2.0 - - + -
230D GLN* 5.9 0.5 - - - -
231D GLY 5.0 5.2 + - - -
233D THR* 3.0 40.7 + - + +
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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