Contacts of the strand formed by residues 116 - 121 (chain D) in PDB entry 2IZZ
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 ARG 116 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86D ILE* 6.2 0.2 - - - +
88D ASP 3.1 29.1 + - - -
89D ARG* 3.3 22.8 + - - +
90D HIS 3.5 12.7 + - - +
91D ILE* 3.5 20.5 - - + +
92D VAL* 2.8 35.2 + - - +
114D ALA 3.3 8.3 + - - +
115D PRO* 1.3 69.7 - - - +
117D VAL* 1.3 54.7 + - - +
140D HIS 3.4 21.8 - - - +
141D ALA* 4.3 7.9 - - + +
142D GLN* 3.9 24.1 + - - +
145D ASP* 3.0 42.7 + - - +
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Residues in contact with VAL 117 (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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92D VAL* 3.4 11.0 - - + +
101D ILE* 4.0 20.8 - - + +
104D ILE* 3.9 37.9 - - + -
105D GLU* 3.9 30.1 + - + +
108D LEU* 4.4 5.4 - - + -
115D PRO* 3.5 17.5 + - + +
116D ARG* 1.3 76.8 - - - +
118D ILE* 1.3 70.6 + - - +
138D GLY* 2.7 32.6 + - - -
141D ALA* 4.1 5.9 - - - +
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Residues in contact with ILE 118 (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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91D ILE* 3.8 22.2 - - + -
92D VAL 2.8 11.9 + - - +
93D VAL* 3.2 8.7 - - + -
94D SER* 2.8 27.2 + - - -
116D ARG 4.3 0.2 - - - -
117D VAL* 1.3 83.1 - - - +
119D ARG* 1.3 71.0 + - - +
135D TYR* 3.9 18.6 - - + -
136D ALA 3.5 10.8 - - - +
137D THR* 4.4 15.0 - - + -
141D ALA* 4.6 4.9 - - + -
145D ASP* 3.6 31.2 - - + +
146D GLY 4.5 1.8 - - - +
149D MET* 3.8 28.3 - - + -
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Residues in contact with ARG 119 (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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94D SER* 3.5 13.2 - - - +
96D ALA 4.6 6.4 + - - +
98D GLY* 3.5 22.1 + - - +
99D VAL 3.4 26.9 + - - +
100D THR* 4.0 9.1 - - - +
101D ILE* 3.6 21.5 - - + +
104D ILE* 5.9 0.4 - - + -
117D VAL* 5.6 0.4 - - + -
118D ILE* 1.3 74.7 - - - +
120D CYS* 1.3 66.3 + - - +
135D TYR* 3.1 6.6 - - - +
136D ALA 2.9 31.9 + - - +
164D GLU* 2.9 38.0 + - - +
167D ILE* 3.6 40.2 - - + +
168D ASP* 2.8 31.3 + - - +
171D THR* 5.2 0.2 + - - -
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Residues in contact with CYS 120 (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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15D LEU* 6.2 0.4 - - - -
67D PHE* 5.3 1.6 - - - -
93D VAL* 3.8 8.1 - - + -
94D SER 2.9 19.4 + - - +
95D CYS* 3.7 30.5 - - - +
96D ALA 4.8 1.0 - - - +
119D ARG* 1.3 83.9 + - - +
121D MET* 1.3 70.6 + - - +
122D THR* 4.3 7.6 - - - -
133D THR* 3.8 18.4 - - - -
134D VAL 3.3 5.6 - - - -
149D MET* 3.6 30.3 - - + -
153D LEU* 4.9 3.6 - - - -
167D ILE* 4.8 2.7 - - - +
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Residues in contact with MET 121 (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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1276C EDO 4.3 1.8 - - - +
95D CYS* 3.8 20.6 - - - +
96D ALA 4.6 0.9 - - - +
97D ALA* 4.0 15.7 - - - +
98D GLY 5.4 0.2 - - - +
119D ARG* 6.4 0.2 - - - +
120D CYS* 1.3 76.2 - - - +
122D THR* 1.3 81.1 + - - +
132D ALA 3.7 1.4 - - - +
133D THR* 3.3 3.3 - - - +
134D VAL* 2.9 42.4 + - + +
167D ILE* 3.8 20.2 - - + -
170D VAL* 4.1 8.4 - - + +
171D THR* 3.5 46.2 - - + +
174D SER* 5.4 0.2 - - - +
175D GLY* 4.1 12.6 - - - -
350D NAD 3.7 15.7 - - + -
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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