Contacts of the helix formed by residues 152 - 163 (chain B) in PDB entry 2Z1Z
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 TYR 152 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A TYR* 5.0 1.7 + - - -
309A ASN* 4.9 2.1 + - - -
37B TYR* 5.1 6.3 - - - -
39B PHE* 5.2 10.1 - + - -
129B LYS* 4.0 20.5 - - + +
132B ILE* 4.3 8.7 - - + -
151B SER* 1.3 75.0 + - - +
153B PRO* 1.3 79.9 - - + +
154B ALA* 3.3 30.9 + - + -
155B TYR* 3.4 39.7 + + + +
156B VAL* 4.3 3.8 + - - +
205B CYS* 5.6 0.7 - - - -
209B ASN* 3.5 29.9 + - - +
395B PHE* 4.3 5.4 - + - -
501B PLP 3.5 66.0 + + + +
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Residues in contact with PRO 153 (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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37B TYR* 3.6 24.0 - - + +
38B LEU* 4.6 15.0 - - + +
39B PHE* 4.9 8.3 - - + -
151B SER 3.3 6.7 - - - +
152B TYR* 1.3 92.1 - - + +
154B ALA* 1.3 60.8 + - - +
155B TYR 3.0 1.0 + - - -
156B VAL* 3.0 8.5 + - + +
157B ASP* 2.8 37.3 + - - +
394B GLY 3.9 20.6 - - - +
395B PHE* 4.0 13.0 - - + -
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Residues in contact with ALA 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A THR* 4.4 16.2 + - - +
37B TYR* 4.3 7.7 + - - +
129B LYS* 4.5 11.9 - - + -
132B ILE* 3.9 14.4 - - + +
152B TYR* 3.3 30.3 - - + -
153B PRO* 1.3 78.9 - - - +
155B TYR* 1.3 51.6 + - - +
157B ASP* 4.7 4.0 - - - +
158B SER* 2.4 40.7 + - - +
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Residues in contact with TYR 155 (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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132B ILE* 3.5 35.2 - - + -
136B GLN* 3.7 3.6 - - - +
145B ILE* 3.9 3.0 - - - +
147B VAL* 4.1 15.9 - - + -
148B GLN* 5.4 1.1 - - - -
151B SER* 3.3 29.6 - - - -
152B TYR* 3.4 28.6 - + + -
153B PRO 3.0 1.2 + - - -
154B ALA* 1.3 76.8 - - - +
156B VAL* 1.3 62.0 + - + +
158B SER* 3.1 14.9 + - - -
159B SER* 3.2 15.4 + - - -
203B PHE* 3.6 44.0 - + + -
204B PHE 5.6 0.7 - - - -
205B CYS* 3.7 15.9 - - + +
235B VAL* 5.8 1.8 - - + -
237B ASP* 2.6 36.9 + - + +
265B THR* 5.8 0.7 - - + -
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Residues in contact with VAL 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B ILE* 4.8 0.7 - - - -
147B VAL* 4.1 30.5 - - + -
151B SER* 5.9 2.7 - - - +
152B TYR 4.3 4.5 + - - +
153B PRO* 3.0 10.3 + - + +
155B TYR* 1.3 77.2 - - + +
157B ASP* 1.3 70.4 + - - +
159B SER* 3.0 17.7 + - - -
160B VAL* 3.0 15.9 + - - +
175B TYR* 3.6 35.9 - - + -
178B ILE* 4.2 13.5 - - + -
180B TYR* 4.1 14.6 - - + +
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Residues in contact with ASP 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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302A ARG* 3.5 17.9 + - - +
306A THR* 3.8 20.2 - - + +
33B LEU* 4.0 14.3 - - + +
37B TYR* 2.9 34.5 - - - -
153B PRO* 2.8 26.4 + - - +
154B ALA* 4.8 0.4 - - - +
156B VAL* 1.3 80.7 - - - +
158B SER* 1.3 56.3 + - - +
160B VAL* 3.4 3.5 + - - +
161B ILE* 3.0 34.4 + - - +
175B TYR* 4.5 7.1 + - - -
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Residues in contact with SER 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A THR* 4.2 9.8 + - - -
307A CYS* 4.8 9.9 - - - -
132B ILE* 3.4 17.2 - - - +
133B SER* 5.4 2.5 - - - -
136B GLN* 3.3 21.6 + - - +
154B ALA 2.4 28.4 + - - -
155B TYR 3.1 9.0 + - - -
157B ASP* 1.3 75.7 - - - +
159B SER* 1.3 56.6 + - - +
160B VAL 3.5 0.2 - - - -
161B ILE* 3.5 8.0 + - - +
162B MET* 3.2 33.3 + - - +
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Residues in contact with SER 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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136B GLN* 3.5 3.4 - - - -
145B ILE* 3.3 24.0 - - - +
155B TYR 3.2 14.8 + - - -
156B VAL* 3.0 14.3 + - - -
158B SER* 1.3 74.2 - - - +
160B VAL* 1.3 60.1 + - - +
162B MET* 3.1 6.6 + - - -
163B GLY 3.3 0.2 + - - -
164B GLN* 2.6 62.9 + - - +
165B THR* 3.6 11.0 - - - +
178B ILE* 4.7 0.6 - - - +
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Residues in contact with VAL 160 (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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29B ASN* 3.2 17.1 + - - +
32B LYS* 3.7 30.9 - - + +
33B LEU* 3.5 20.9 - - + +
156B VAL* 3.0 17.5 + - + +
157B ASP* 3.6 7.6 - - - +
159B SER* 1.3 70.7 - - - +
161B ILE* 1.3 66.8 + - - +
162B MET 3.0 1.2 + - - -
163B GLY* 3.1 10.7 + - - -
164B GLN 4.8 0.2 - - - +
165B THR* 3.7 24.4 + - + +
175B TYR* 3.8 39.3 - - + -
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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
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137A VAL* 3.5 31.9 - - + +
303A ILE* 3.6 22.4 - - + -
306A THR* 3.8 33.7 - - + +
307A CYS* 4.2 8.7 - - - -
27B ASN* 4.6 5.5 + - - -
29B ASN* 3.4 21.2 - - - +
30B MET* 4.3 11.9 - - + -
33B LEU* 3.9 25.4 - - + -
157B ASP 3.0 21.0 + - - +
158B SER* 3.7 7.0 - - - +
159B SER 3.2 0.4 - - - -
160B VAL* 1.3 76.7 - - - +
162B MET* 1.3 62.6 + - + +
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Residues in contact with MET 162 (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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137A VAL* 4.3 17.3 - - + -
162A MET* 4.2 21.8 - - + -
29B ASN* 4.0 3.0 - - - +
136B GLN* 3.9 30.3 - - + +
137B VAL* 3.7 30.7 - - + +
140B GLY* 4.2 14.1 - - - -
141B SER* 3.0 26.2 - - - +
158B SER* 3.2 18.6 + - - +
159B SER 3.1 5.7 + - - +
160B VAL 3.0 1.2 + - - -
161B ILE* 1.3 81.9 - - + +
163B GLY* 1.3 58.6 + - - +
164B GLN* 3.6 15.9 - - - +
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Residues in contact with GLY 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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29B ASN* 3.4 26.2 + - - -
32B LYS* 4.5 4.8 + - - -
141B SER* 3.2 19.3 - - - +
160B VAL 3.1 6.8 + - - -
161B ILE 3.3 1.4 + - - -
162B MET* 1.3 81.6 - - - +
164B GLN* 1.3 60.8 + - - +
165B THR 3.5 6.5 + - - +
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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