Contacts of the helix formed by residues 160 - 172 (chain A) in PDB entry 2Z9O
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 PRO 160 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A GLU* 3.6 21.1 - - + +
158A THR 2.8 20.7 - - - +
159A ASN* 1.3 78.1 - - - +
161A TYR* 1.3 72.2 + - + +
163A MET* 3.6 18.3 - - + +
164A ARG* 2.6 49.5 + - - +
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Residues in contact with TYR 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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159A ASN* 2.5 28.3 + - - +
160A PRO* 1.3 91.4 - - + +
162A ALA* 1.3 66.7 + - - +
163A MET 3.2 0.9 - - - -
164A ARG* 3.7 10.1 - - - +
165A LEU* 2.9 23.2 + - - +
192A TYR* 3.4 26.2 - - - -
193A GLN 3.8 12.2 + - - -
194A LEU* 3.5 15.3 - - + -
195A PRO* 3.7 14.4 - - + +
198A TYR* 5.6 2.5 - + - -
208A PHE* 4.1 22.1 - + + -
212A CYS* 4.1 6.2 - - - -
23C T 5.3 1.1 - - - -
24C G 2.5 42.2 + - - -
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Residues in contact with ALA 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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157A ILE* 4.5 10.3 - - + -
159A ASN* 2.5 35.3 + - + +
161A TYR* 1.3 73.6 - - - +
163A MET* 1.3 53.2 - - - +
165A LEU* 3.0 3.2 + - - +
166A TYR* 2.8 37.0 + - - +
212A CYS* 3.6 23.7 - - + -
215A GLU* 4.4 19.5 - - + -
216A ILE* 3.9 8.3 - - + +
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Residues in contact with MET 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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26A GLU* 3.5 45.8 - - + +
29A TYR* 3.7 28.9 - - + -
30A SER* 5.1 0.2 - - - -
157A ILE* 2.8 48.4 - - + +
158A THR* 3.9 15.0 - - - +
159A ASN 3.5 6.1 - - - +
160A PRO* 3.6 20.6 - - + +
162A ALA* 1.3 76.4 - - - +
164A ARG* 1.3 64.8 + - + +
166A TYR* 3.3 9.5 + - - +
167A GLU* 3.0 29.5 + - - +
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Residues in contact with ARG 164 (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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21A SER* 3.9 26.4 - - - +
26A GLU* 2.6 37.8 + - - +
160A PRO* 2.6 35.2 + - - +
161A TYR* 3.3 11.7 + - - +
163A MET* 1.3 78.1 - - + +
165A LEU* 1.3 68.6 + - - +
167A GLU* 3.3 7.3 + - - +
168A SER* 3.1 21.8 + - - -
191A ARG 4.7 3.1 + - - +
192A TYR* 3.7 46.9 + - + +
193A GLN* 5.2 10.2 - - - +
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Residues in contact with LEU 165 (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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161A TYR 2.9 12.9 + - - +
162A ALA 3.3 6.3 - - - +
164A ARG* 1.3 74.3 - - - +
166A TYR* 1.3 52.7 + - - +
168A SER* 2.9 7.6 + - - -
169A LEU* 2.8 67.8 + - + -
183A LEU* 5.2 0.4 - - + -
192A TYR* 3.0 30.9 - - + +
208A PHE* 4.2 15.9 - - + -
212A CYS* 3.8 26.0 - - + -
213A VAL* 4.6 2.9 - - + +
216A ILE* 4.5 10.5 - - + -
224A LEU* 4.6 6.3 - - + -
240A PHE* 4.5 20.6 - - + -
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Residues in contact with TYR 166 (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 TYR* 3.9 32.8 - + - -
149A PHE* 3.1 29.6 + - + -
150A ARG* 5.1 1.2 - - - +
154A THR* 4.9 3.4 + - - -
157A ILE* 5.9 2.9 - - + -
162A ALA 2.8 15.8 + - - +
163A MET* 3.3 11.2 - - - +
165A LEU* 1.3 76.7 - - - +
167A GLU* 1.3 62.6 + - - +
169A LEU* 4.1 3.4 - - - +
170A CYS* 3.1 48.8 + - - +
173A ARG* 5.6 1.0 + - - -
216A ILE* 3.5 31.4 - - + +
220A THR* 3.1 32.3 - - + -
221A PRO* 3.7 20.8 - - - +
222A MET* 4.0 12.7 - - + +
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Residues in contact with GLU 167 (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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25A THR* 4.0 2.1 - - - +
29A TYR* 2.9 39.7 + - - +
145A ARG* 3.0 39.8 + - - -
149A PHE* 3.3 38.9 - - + -
163A MET* 3.0 18.5 + - - +
164A ARG* 3.3 6.0 + - - +
166A TYR* 1.3 74.4 - - + +
168A SER* 1.3 66.5 + - - +
171A GLN* 3.1 20.3 + - - +
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Residues in contact with SER 168 (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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164A ARG 3.1 4.5 + - - -
165A LEU 2.9 2.5 + - - -
167A GLU* 1.3 73.8 - - - +
169A LEU* 1.3 67.2 - - - +
171A GLN* 2.7 25.7 - - - +
172A TYR* 3.4 16.5 - - - -
183A LEU* 5.4 6.7 - - - -
192A TYR* 2.7 43.2 + - - -
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Residues in contact with LEU 169 (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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165A LEU* 2.8 43.6 + - + +
166A TYR* 4.1 3.1 - - - +
168A SER* 1.3 71.8 - - - +
170A CYS* 1.3 65.5 + - - +
172A TYR* 2.8 17.2 + - + +
181A VAL* 4.9 10.5 - - + -
183A LEU* 4.2 11.7 - - + -
216A ILE* 5.6 0.4 - - + -
222A MET* 3.8 9.0 - - + -
224A LEU* 3.2 43.5 - - + -
240A PHE* 3.7 32.8 - - + -
242A PHE* 3.0 32.1 - - + -
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Residues in contact with CYS 170 (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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148A GLN* 5.0 3.8 - - - +
149A PHE* 3.9 19.7 - - + -
166A TYR* 3.1 54.4 + - - +
167A GLU 3.7 4.9 - - - +
169A LEU* 1.3 76.1 - - - +
171A GLN* 1.3 53.8 + - - +
172A TYR 2.5 1.2 + - - -
173A ARG* 2.5 68.7 + - - +
222A MET* 3.7 13.6 - - - +
242A PHE* 4.6 1.1 - - - -
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Residues in contact with GLN 171 (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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148A GLN* 3.7 23.4 + - - +
167A GLU 3.1 10.9 + - - +
168A SER* 2.7 20.1 + - - +
170A CYS* 1.3 77.3 - - - +
172A TYR* 1.3 79.1 + - + +
173A ARG* 3.6 4.9 + - - +
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Residues in contact with TYR 172 (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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168A SER* 3.4 29.5 - - - -
169A LEU* 2.8 15.0 + - + +
170A CYS 2.5 6.5 + - - -
171A GLN* 1.3 94.2 - - + +
173A ARG* 1.3 64.1 + - - -
174A LYS* 5.1 3.6 - - - +
178A SER 4.3 3.1 - - - +
179A GLY* 4.6 4.2 - - - -
180A ILE 5.4 0.2 + - - -
181A VAL* 3.1 51.1 - - + +
183A LEU* 4.5 13.6 - - + +
187A TRP* 6.0 0.5 + - - -
242A PHE* 3.8 7.6 - - + -
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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