Contacts of the strand formed by residues 87 - 95 (chain D) in PDB entry 2ZNZ
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 MET 87 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85D TYR 4.6 3.6 - - - +
86D SER* 1.3 80.6 + - - +
88D LEU* 1.3 79.1 + - - +
89D ALA 4.9 0.7 - - - +
129D ILE* 5.6 0.9 - - + +
130D ARG* 3.4 9.4 + - - +
131D THR* 3.0 52.2 + - - +
133D ASN* 4.0 9.4 - - - +
134D SER* 3.8 34.8 - - - +
137D LEU* 3.8 26.9 - - + -
157D ILE* 4.0 24.7 - - + -
158D VAL 5.8 0.2 - - - +
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Residues in contact with LEU 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C TYR* 3.5 33.4 - - + -
86D SER 4.1 1.2 + - - -
87D MET* 1.3 83.4 - - - +
89D ALA* 1.3 64.7 + - - +
90D PHE* 5.4 0.4 - - + -
128D LYS* 3.6 29.6 - - + -
129D ILE 3.5 17.3 - - - +
130D ARG* 3.9 31.6 - - + +
158D VAL* 3.0 48.1 + - + +
161D THR* 4.2 5.4 - - - +
164D GLU* 4.1 4.9 - - - +
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Residues in contact with ALA 89 (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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87D MET* 4.7 0.9 - - - +
88D LEU* 1.3 79.0 - - - +
90D PHE* 1.3 63.7 + - - +
91D ILE 4.0 0.2 - - - -
128D LYS* 3.6 5.5 - - - +
129D ILE* 3.0 46.8 + - + +
137D LEU* 4.3 13.0 - - + -
155D THR* 3.8 22.7 - - + -
156D MET 3.4 12.6 - - - +
157D ILE* 4.2 5.4 - - + -
158D VAL* 4.3 1.6 - - - +
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Residues in contact with PHE 90 (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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90C PHE* 3.8 22.7 - + - -
115C GLU* 4.4 2.0 - - - -
117C TYR* 3.5 40.8 - + - -
119C THR* 4.6 1.3 - - + -
126C VAL* 4.1 24.7 - - + -
88D LEU* 5.4 0.9 - - + -
89D ALA* 1.3 72.6 - - - +
91D ILE* 1.3 64.5 + - - +
92D LEU* 3.9 2.9 + - + -
115D GLU* 4.8 0.4 - - - -
126D VAL* 3.8 24.0 - - + -
127D VAL 3.1 8.7 - - - +
128D LYS* 3.6 33.2 - - + -
154D HIS 3.8 0.9 - - - +
155D THR* 3.6 0.7 - - - -
156D MET* 2.8 53.0 + - + +
158D VAL* 3.9 18.6 - - + -
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Residues in contact with ILE 91 (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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90D PHE* 1.3 73.3 - - - +
92D LEU* 1.3 66.0 + - - +
93D VAL* 3.8 7.9 + - + +
125D MET 3.7 0.9 - - - +
126D VAL* 3.6 1.7 - - - -
127D VAL* 2.7 47.6 + - + +
129D ILE* 3.5 36.1 - - + -
137D LEU* 4.6 1.8 - - + -
141D LEU* 3.8 11.9 - - + +
144D ILE* 3.6 28.0 - - + -
153D THR* 3.7 36.1 - - + -
154D HIS 3.7 2.2 - - - +
155D THR* 3.8 21.8 - - + +
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Residues in contact with LEU 92 (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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92C LEU* 5.7 4.7 - - + -
156C MET* 4.1 18.4 - - + -
90D PHE* 5.2 3.6 - - + -
91D ILE* 1.3 73.7 - - - +
93D VAL* 1.3 59.5 + - - +
123D TYR* 3.6 38.8 - - + -
125D MET 3.3 3.4 - - - +
126D VAL* 3.7 32.3 - - + -
153D THR* 3.2 6.6 - - - -
154D HIS* 2.8 52.8 + - + +
156D MET* 4.2 27.1 - - + -
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Residues in contact with VAL 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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91D ILE* 3.8 22.7 - - + +
92D LEU* 1.3 77.4 - - - +
94D LYS* 1.3 70.6 + - - +
95D VAL* 3.7 9.8 + - + +
103D VAL* 4.7 4.5 - - + -
107D LEU* 4.6 5.4 - - + -
123D TYR* 3.9 4.2 - - - +
124D ASP* 2.9 25.5 + - - +
125D MET* 2.9 23.3 + - + +
127D VAL* 4.1 20.2 - - + -
144D ILE* 4.7 6.5 - - + -
150D VAL* 3.9 26.5 - - + -
152D GLY 3.6 7.2 - - - +
153D THR* 4.6 4.7 - - + -
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Residues in contact with LYS 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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93D VAL* 1.3 72.7 - - - +
95D VAL* 1.3 56.3 + - - +
122D ASP* 3.1 49.5 + - - +
123D TYR* 3.7 29.6 + - + -
124D ASP* 3.7 6.5 - - - +
150D VAL* 3.5 5.0 - - - -
151D GLU* 2.7 50.3 + - + +
152D GLY* 2.8 26.0 + - - +
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Residues in contact with VAL 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 VAL* 4.0 13.9 - - + +
94D LYS* 1.3 77.2 - - - +
96D LYS* 1.3 73.4 + - - +
97D ALA* 3.2 4.7 + - - -
99D LYS* 3.8 1.3 - - + -
100D TYR* 3.5 44.5 + - + +
103D VAL* 3.7 22.7 - - + -
124D ASP* 2.9 21.7 + - + +
125D MET* 4.0 29.4 - - + -
149D GLY 3.2 10.5 - - - +
151D GLU* 4.0 8.8 - - - +
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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