Contacts of the strand formed by residues 156 - 167 (chain B) in PDB entry 4ZIN
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 ALA 156 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B TYR* 4.2 2.0 - - - -
152B PRO* 3.4 4.0 - - - +
153B GLU 2.9 33.8 + - - +
154B ASP* 4.3 3.6 - - + +
155B GLY* 1.3 79.9 - - - +
157B LEU* 1.3 60.2 + - - +
158B LYS* 4.8 1.3 - - - -
180B THR* 3.9 22.0 - - + -
181B TYR 3.6 12.3 - - - +
182B LYS* 3.8 16.2 - - + +
189B LEU* 3.6 8.7 - - - +
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Residues in contact with LEU 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B TYR* 4.0 32.3 - - + -
83B LEU* 4.8 10.5 - - + -
150B MET* 3.9 28.3 - - + -
151B TYR* 3.6 30.7 - - - +
152B PRO* 4.1 1.8 - - + -
156B ALA* 1.3 71.5 - - - +
158B LYS* 1.3 60.2 + - - +
180B THR* 3.6 1.6 - - - -
181B TYR* 2.8 49.0 + - + +
189B LEU* 3.9 3.2 - - + +
190B PRO* 3.7 30.5 - - + -
193B TYR* 4.5 12.6 - - - +
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Residues in contact with LYS 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B ARG 4.4 0.2 - - - -
150B MET* 3.2 10.8 - - - +
151B TYR* 2.8 73.6 + - + +
153B GLU* 3.5 42.0 + - + +
154B ASP* 5.4 4.2 + - - -
156B ALA* 4.8 1.3 - - - -
157B LEU* 1.3 74.3 - - - +
159B GLY* 1.3 59.1 + - - +
178B LYS* 4.7 18.5 - - - +
179B THR 3.3 4.3 - - - +
180B THR* 3.5 37.6 + - + +
181B TYR* 4.6 0.2 - - - -
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Residues in contact with GLY 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148B GLU* 3.5 22.0 - - - +
149B ARG 3.3 8.1 - - - -
150B MET* 3.8 7.6 - - - -
151B TYR* 5.3 0.4 - - - -
158B LYS* 1.3 75.6 - - - +
160B GLU* 1.3 65.0 + - - +
161B ILE* 5.5 0.6 - - - +
177B VAL 4.0 0.3 - - - +
178B LYS* 3.3 4.9 - - - +
179B THR* 2.9 34.8 + - - -
181B TYR* 4.1 2.2 - - - -
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Residues in contact with GLU 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B GLU* 3.5 1.9 - - - +
149B ARG* 2.8 69.8 + - + +
151B TYR* 2.6 35.6 + - + +
159B GLY* 1.3 78.3 - - - +
161B ILE* 1.3 61.8 + - - +
177B VAL 3.4 6.7 - - - +
178B LYS* 3.7 27.3 + - + +
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Residues in contact with ILE 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B CH6 3.5 17.5 - - + -
95B ARG* 5.5 4.9 - - - +
146B SER* 3.8 17.7 - - - +
147B SER 3.4 24.7 - - - +
148B GLU* 3.9 23.8 - - + +
149B ARG* 3.3 7.6 - - - +
159B GLY 5.5 0.2 - - - -
160B GLU* 1.3 76.4 - - - +
162B LYS* 1.3 72.0 + - - +
163B GLN* 3.5 28.6 + - + +
176B GLU* 3.7 1.9 - - - -
177B VAL* 2.9 52.0 + - + +
179B THR* 5.9 0.7 - - - +
197B ILE* 5.7 0.2 - - + -
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Residues in contact with LYS 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B SER* 3.3 16.8 + - - -
147B SER 4.9 0.4 + - - -
149B ARG* 3.5 13.3 - - - +
161B ILE* 1.3 74.4 - - - +
163B GLN* 1.3 63.9 + - - +
164B ARG* 4.1 8.0 + - + +
174B ASP* 5.2 13.4 - - - +
175B ALA 3.5 6.1 - - - +
176B GLU* 3.3 45.5 + - + +
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Residues in contact with GLN 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B PRO* 4.5 3.6 - - - +
66B CH6 2.6 58.8 + - - -
97B MET* 5.0 2.0 - - - +
143B 4OO 3.2 42.5 + - + +
144B GLU 4.8 0.2 - - - +
146B SER* 3.4 10.6 + - - -
161B ILE* 3.5 13.6 - - + +
162B LYS* 1.3 76.0 - - - +
164B ARG* 1.3 62.3 + - - +
165B LEU 4.2 0.2 - - - -
173B TYR 4.8 0.2 - - - -
174B ASP* 3.4 6.3 - - - +
175B ALA* 2.8 35.2 + - + +
177B VAL* 3.8 16.4 - - + -
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Residues in contact with ARG 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B 4OO 3.5 8.0 - - - -
144B GLU* 2.9 42.4 + - + +
146B SER* 4.8 3.3 + - - +
162B LYS* 4.5 9.4 - - + +
163B GLN* 1.3 80.9 + - - +
165B LEU* 1.3 60.0 + - - +
172B HIS* 3.4 49.0 + - + +
173B TYR 3.7 0.4 - - - -
174B ASP* 2.9 38.2 + - - +
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Residues in contact with LEU 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B ALA* 6.2 0.2 - - + -
59B ASP* 3.6 22.2 - - + -
60B ILE* 4.8 7.2 - - + -
99B PHE* 4.6 11.7 - - + -
135B VAL* 5.6 0.4 - - + -
140B THR* 4.0 29.6 - - + -
142B GLY 3.4 10.8 - - - +
143B 4OO 3.2 57.2 - - + +
163B GLN 4.2 0.4 - - - -
164B ARG* 1.3 73.4 - - - +
166B LYS* 1.3 62.3 + - - +
172B HIS* 3.3 6.0 - - - -
173B TYR* 2.7 60.0 + - + +
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Residues in contact with LYS 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A LYS* 4.1 13.9 - - - +
32A GLU* 3.0 34.8 + - - +
117A GLU* 5.7 0.2 - - - +
140B THR* 3.2 7.1 - - - -
141B MET* 2.8 54.7 + - + -
142B GLY* 2.9 22.3 + - - +
143B 4OO 4.3 10.1 + - - -
144B GLU* 3.3 39.9 + - + +
165B LEU* 1.3 72.8 - - - +
167B LEU* 1.3 60.3 + - - +
171B GLY 3.9 0.9 - - - -
172B HIS* 3.8 10.1 - - - +
198B LYS* 5.6 5.3 - - - +
200B ASP* 5.8 2.0 + - - -
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Residues in contact with LEU 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A LYS* 3.1 20.2 - - - -
134B PRO* 3.6 32.8 - - + -
139B LYS* 3.6 14.4 - - + +
140B THR* 4.5 2.5 - - + -
141B MET* 4.1 0.4 - - - -
166B LYS* 1.3 78.3 - - - +
168B LYS* 1.3 66.4 + - - +
169B ASP* 3.1 3.4 - - + +
170B GLY* 3.1 27.1 + - - +
171B GLY* 3.1 6.4 + - - +
172B HIS 3.6 34.3 - - - +
173B TYR* 4.0 12.3 - - + +
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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