Contacts of the strand formed by residues 150 - 164 (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 VAL 150 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93D VAL* 3.9 21.5 - - + -
94D LYS 3.5 3.1 - - - -
96D LYS* 4.1 7.6 + - - -
103D VAL* 3.7 28.0 - - + -
144D ILE* 3.4 31.4 - - + +
145D GLY* 3.9 20.6 - - - +
147D ILE* 3.3 20.6 + - + +
149D GLY* 1.3 77.5 + - - +
151D GLU* 1.3 62.3 + - - +
152D GLY* 3.7 17.7 - - - +
153D THR* 4.6 0.9 - - + -
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Residues in contact with GLU 151 (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 LYS* 2.7 37.3 + - + +
95D VAL 4.0 5.3 - - - +
96D LYS* 3.3 57.1 + - + +
97D ALA 4.3 1.7 + - - -
150D VAL* 1.3 73.5 - - - +
152D GLY* 1.3 54.7 + - - +
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Residues in contact with GLY 152 (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* 3.6 2.3 - - - +
94D LYS* 2.8 32.6 + - - +
123D TYR* 4.8 3.4 - - - -
145D GLY* 6.4 0.2 - - - -
150D VAL* 3.5 6.7 - - - +
151D GLU* 1.3 82.4 - - - +
153D THR* 1.3 69.3 + - - +
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Residues in contact with THR 153 (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* 3.7 20.2 - - + -
92D LEU 3.2 6.1 - - - +
93D VAL* 4.6 3.8 - - + -
123D TYR* 4.4 6.1 + - - -
141D LEU* 3.9 10.0 + - + +
144D ILE* 3.7 31.0 - - + -
145D GLY* 5.1 4.5 - - - +
150D VAL* 4.6 4.9 - - + -
152D GLY* 1.3 79.8 - - - +
154D HIS* 1.3 60.8 + - - +
172D LYS* 2.8 48.9 + - - +
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Residues in contact with HIS 154 (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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120C THR 5.8 0.4 - - - -
121C GLY* 4.9 14.4 - - - -
122C ASP* 5.9 2.0 + - - -
91D ILE* 3.7 0.2 - - - -
92D LEU* 2.8 50.3 + - + +
123D TYR* 3.5 41.5 - + + +
153D THR* 1.3 73.4 - - - +
155D THR* 1.3 73.7 + - - +
156D MET* 3.8 15.2 + - + +
172D LYS 3.7 3.7 + - - -
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Residues in contact with THR 155 (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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120C THR* 4.0 5.7 + - - -
89D ALA* 3.8 26.7 - - + -
90D PHE 3.6 4.5 - - - +
91D ILE* 3.8 10.1 - - + +
137D LEU* 4.2 12.8 - - + -
141D LEU* 3.2 23.0 - - + +
154D HIS* 1.3 80.4 + - - +
156D MET* 1.3 62.3 + - - +
157D ILE* 3.8 17.2 + - + +
172D LYS* 2.6 34.4 + - - +
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Residues in contact with MET 156 (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* 4.1 22.0 - - + -
119C THR* 3.6 28.0 - - + +
120C THR* 3.6 23.3 - - - +
121C GLY* 5.2 2.9 - - - -
123C TYR* 5.0 10.8 - - + +
126C VAL* 3.8 16.4 - - + -
89D ALA* 3.4 0.9 - - - -
90D PHE* 2.8 47.1 + - + +
92D LEU* 4.2 25.6 - - - -
154D HIS* 4.3 17.9 - - + +
155D THR* 1.3 74.3 - - - +
157D ILE* 1.3 65.4 + - - +
158D VAL* 3.6 0.5 + - - +
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Residues in contact with ILE 157 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119C THR* 3.4 3.2 - - - -
120C THR* 3.1 42.2 + - + +
87D MET* 4.0 27.4 - - + -
88D LEU 4.0 2.9 - - - -
89D ALA* 4.2 1.6 - - + -
134D SER* 5.0 5.6 - - - +
137D LEU* 4.0 22.2 - - + -
155D THR* 3.8 19.5 - - + +
156D MET* 1.3 71.7 - - - +
158D VAL* 1.3 74.0 + - - +
159D LEU* 3.4 10.1 + - + +
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Residues in contact with VAL 158 (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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117C TYR* 3.7 16.8 - - + -
118C GLU 3.4 5.4 - - - +
119C THR* 4.0 11.4 - - + -
87D MET* 5.8 0.2 - - - +
88D LEU* 3.0 47.0 + - + +
89D ALA* 4.6 0.2 - - - -
90D PHE* 3.9 28.9 - - + -
156D MET 3.6 0.2 + - - -
157D ILE* 1.3 79.5 - - - +
159D LEU* 1.3 61.9 + - - +
160D LYS* 3.5 23.6 - - - +
161D THR* 3.8 9.6 - - - +
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Residues in contact with LEU 159 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118C GLU* 2.6 21.0 + - + +
119C THR* 3.8 25.6 - - - +
120C THR* 3.9 26.0 - - + +
157D ILE* 4.1 8.5 - - + +
158D VAL* 1.3 75.2 - - - +
160D LYS* 1.3 59.2 + - - +
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Residues in contact with LYS 160 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101C SER* 5.5 6.3 + - - +
117C TYR* 3.4 3.6 - - - -
118C GLU* 2.8 52.8 + - + +
158D VAL* 3.5 7.2 - - - +
159D LEU* 1.3 80.4 - - + +
161D THR* 1.3 70.8 - - - +
162D HIS* 3.6 30.1 + - + +
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Residues in contact with THR 161 (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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116C VAL 4.0 2.5 - - - -
117C TYR* 3.5 30.4 - - + -
88D LEU* 4.2 5.5 - - - +
158D VAL* 3.8 7.1 - - - +
160D LYS* 1.3 80.2 - - - +
162D HIS* 1.3 64.4 + - - +
163D LYS 4.2 5.8 - - - +
164D GLU* 4.0 27.9 + - + +
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Residues in contact with HIS 162 (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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100C TYR 4.9 0.6 + - - -
101C SER* 5.1 7.0 + - - -
104C ALA* 3.4 35.3 - - + +
105C SER* 5.3 1.8 - - - -
108C ALA* 5.0 6.1 - - + +
116C VAL* 2.9 29.1 + - + +
118C GLU* 2.7 43.9 + - + +
125C MET* 5.1 0.2 - - - +
160D LYS* 3.6 27.8 + - + +
161D THR* 1.3 77.1 - - - +
163D LYS* 1.3 62.5 + - + +
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Residues in contact with LYS 163 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108C ALA* 2.9 37.3 + - + +
110C TYR 2.8 19.6 + - - -
111C PRO* 4.2 6.3 + - - +
113C ILE 2.7 29.5 + - - +
114C VAL 3.9 7.6 - - - +
115C GLU* 3.2 5.1 - - - +
116C VAL* 2.8 41.7 + - + +
117C TYR* 4.6 1.0 - - - -
161D THR* 4.2 4.1 - - - +
162D HIS* 1.3 80.1 - - - +
164D GLU* 1.3 66.9 + - - +
165D THR* 3.9 20.6 - - + -
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Residues in contact with GLU 164 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72C LYS* 4.6 16.0 + - - +
114C VAL 3.8 2.9 - - - -
115C GLU* 4.3 6.7 - - + +
117C TYR* 2.6 36.5 + - - +
80D PRO* 5.5 3.1 - - - +
88D LEU* 4.1 1.7 - - - +
128D LYS* 4.4 1.5 + - - +
130D ARG* 2.8 32.9 + - - -
161D THR* 4.0 14.8 + - + +
163D LYS* 1.3 76.3 - - - +
165D THR* 1.3 62.1 + - - +
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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