Contacts of the helix formed by residues 152 - 163 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A TYR* 3.9 8.2 + - - -
39A PHE* 4.4 4.7 - + - -
129A LYS* 4.2 12.2 - - + +
132A ILE* 4.5 5.8 - - + -
151A SER* 1.3 73.9 + - - +
153A PRO* 1.4 73.7 - - + +
154A ALA* 3.2 31.1 + - + -
155A TYR* 3.4 43.1 + + + +
156A VAL* 4.4 3.1 + - - +
205A CYS* 5.4 0.4 - - - -
209A ASN* 3.2 32.4 + - - +
395A PHE* 4.1 2.7 - + - -
433A MLT 2.9 54.5 + - - -
500A PLP 3.7 39.3 - + + -
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Residues in contact with PRO 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A TYR* 3.9 22.9 - - + +
38A LEU* 4.1 12.3 - - + +
39A PHE* 4.0 11.9 - - + -
151A SER 3.2 4.2 - - - +
152A TYR* 1.4 94.6 - - + +
154A ALA* 1.3 57.3 + - - +
155A TYR 3.3 0.7 - - - -
156A VAL* 3.8 8.6 + - + +
157A ASP* 3.0 35.9 + - - +
394A GLY 3.9 20.6 - - - +
395A PHE* 3.7 17.0 - - + -
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Residues in contact with ALA 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A TYR* 3.3 25.2 + - - +
129A LYS* 4.7 7.0 - - + +
132A ILE* 4.0 12.3 - - + +
152A TYR* 3.2 23.9 + - + +
153A PRO* 1.3 75.3 - - - +
155A TYR* 1.3 61.0 + - - +
157A ASP* 4.6 2.9 - - - +
158A SER* 3.0 31.6 + - - -
306B THR* 4.2 17.6 + - - +
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Residues in contact with TYR 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A ILE* 3.1 35.9 - - + -
136A GLN* 4.1 2.4 - - - +
145A ILE* 4.2 3.2 - - - +
147A VAL* 4.0 19.7 - - + -
148A GLN* 5.2 1.1 - - - -
151A SER* 3.7 23.6 - - - -
152A TYR* 3.4 25.5 + + + -
153A PRO 3.3 1.0 - - - -
154A ALA* 1.3 75.2 - - - +
156A VAL* 1.3 68.3 + - + +
158A SER* 3.1 18.1 + - - -
159A SER* 3.3 10.9 + - - -
203A PHE* 3.7 44.4 - + + -
204A PHE 5.5 0.4 - - - -
205A CYS* 3.4 20.0 - - + +
235A VAL* 6.4 0.4 - - + -
237A ASP* 2.8 35.1 + - + +
500A PLP 3.9 1.7 - - - +
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Residues in contact with VAL 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A ILE* 4.8 1.6 - - - -
147A VAL* 3.8 30.7 - - + -
151A SER* 5.9 3.6 - - - +
152A TYR 4.4 2.9 + - - +
153A PRO* 3.8 10.1 + - + +
155A TYR* 1.3 77.4 - - + +
157A ASP* 1.3 68.4 + - - +
159A SER* 2.9 18.5 + - - -
160A VAL* 3.1 15.1 + - - +
175A TYR* 3.5 36.1 - - + -
178A ILE* 4.5 10.3 - - + +
180A TYR* 4.1 19.3 - - + +
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Residues in contact with ASP 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A LEU* 4.0 3.7 - - + +
36A GLY 5.1 0.2 - - - +
37A TYR* 3.5 15.0 - - + -
38A LEU 5.0 0.5 + - - -
153A PRO* 3.0 24.1 + - - +
154A ALA* 4.6 2.0 - - - -
156A VAL* 1.3 87.7 - - - +
158A SER* 1.3 59.9 + - - +
160A VAL* 3.7 5.5 + - - +
161A ILE* 3.1 28.5 + - - +
175A TYR* 4.4 12.1 + - - -
302B ARG* 3.1 40.1 + - - +
306B THR* 4.0 10.8 - - - +
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Residues in contact with SER 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A ILE* 3.9 7.6 - - - +
133A SER* 3.8 22.2 - - - -
136A GLN* 3.3 26.7 + - - +
154A ALA 3.0 23.6 + - - -
155A TYR* 3.1 9.9 + - - -
156A VAL 3.3 0.2 - - - -
157A ASP* 1.3 75.5 - - - +
159A SER* 1.3 56.7 + - - +
161A ILE* 3.4 10.6 + - - +
162A MET* 2.9 33.7 + - - +
203A PHE* 5.2 0.2 - - - -
306B THR* 4.7 3.0 + - - -
307B CYS* 5.2 2.9 - - - -
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Residues in contact with SER 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A GLN* 3.7 3.6 - - - -
145A ILE* 3.5 23.2 - - - +
155A TYR 3.3 13.0 + - - -
156A VAL* 2.9 10.9 + - - -
158A SER* 1.3 76.3 + - - +
160A VAL* 1.3 66.2 + - - +
162A MET 3.2 1.6 + - - -
163A GLY 3.2 4.2 + - - -
164A GLN* 2.4 65.8 + - - +
165A THR* 3.7 10.6 - - - +
178A ILE* 4.6 0.4 - - - -
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Residues in contact with VAL 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A ASN* 3.2 28.0 + - - +
32A LYS* 3.6 20.5 + - + -
33A LEU* 3.1 29.8 - - + +
156A VAL* 3.4 13.7 - - + +
157A ASP* 3.8 2.2 - - - +
159A SER* 1.3 76.2 - - - +
161A ILE* 1.3 62.0 + - - +
163A GLY* 3.0 13.0 + - - -
165A THR* 3.6 19.6 + - + +
175A TYR* 3.6 41.7 - - + -
178A ILE* 5.0 0.2 - - + -
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Residues in contact with ILE 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A ASN* 4.3 7.1 + - - -
29A ASN* 3.5 20.1 - - - +
30A MET* 4.1 10.3 - - + -
33A LEU* 3.8 26.7 - - + -
157A ASP 3.1 20.9 + - - +
158A SER* 3.6 5.6 - - - +
159A SER 3.2 0.2 - - - -
160A VAL* 1.3 79.8 - - - +
162A MET* 1.3 63.0 + - + +
163A GLY 3.3 0.2 - - - -
137B VAL* 3.7 32.0 - - + +
302B ARG* 4.6 0.7 - - - +
303B ILE* 3.8 17.3 - - + -
306B THR* 3.7 26.5 - - + +
307B CYS* 3.8 17.0 - - - -
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Residues in contact with MET 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A ASN* 4.0 2.4 - - - +
133A SER 5.3 0.4 - - - +
136A GLN* 3.7 27.1 - - + +
137A VAL* 3.7 39.7 - - - +
140A GLY* 4.5 10.1 - - - +
141A SER* 2.7 34.4 - - - +
158A SER* 2.9 18.5 + - - +
159A SER 3.9 4.0 - - - +
160A VAL 3.2 0.6 - - - -
161A ILE* 1.3 76.7 - - + +
163A GLY* 1.3 51.6 + - - +
164A GLN* 3.3 15.7 - - - +
137B VAL* 4.5 18.6 - - - -
161B ILE 6.1 0.2 - - - +
162B MET* 4.2 25.1 - - + -
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Residues in contact with GLY 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A ASN* 3.4 29.1 + - - -
32A LYS* 4.4 0.9 + - - -
141A SER* 3.4 18.1 + - - +
160A VAL 3.0 10.2 + - - -
161A ILE 3.3 1.0 - - - -
162A MET* 1.3 78.6 - - - +
164A GLN* 1.4 57.4 - - - +
165A THR 3.2 11.2 + - - +
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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