Contacts of the helix formed by residues 154 - 165 (chain C) in PDB entry 5Z7R
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 GLY 154 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151A ARG 5.6 4.9 - - - -
152A LEU* 5.6 5.6 - - - -
218A MET* 5.6 1.1 - - - -
150C SER* 2.8 18.7 + - - +
151C ARG 4.6 0.6 + - - -
152C LEU 3.7 0.8 - - - -
153C VAL* 1.3 80.5 - - - +
155C MET* 1.3 62.2 + - - -
156C GLY 3.5 2.5 - - - -
157C MET 4.5 0.2 - - - -
158C ALA* 3.1 28.8 + - - +
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Residues in contact with MET 155 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A GLU* 4.9 13.2 - - - +
120A ASP 4.6 0.2 - - - -
122A ARG* 5.6 0.4 - - - +
151A ARG* 5.6 7.2 + - + +
152A LEU* 4.1 23.9 - - + +
214A ILE* 3.9 29.4 - - - +
215A ASN* 4.2 9.6 - - - +
218A MET* 4.2 28.0 - - + +
219A GLN* 5.7 4.7 - - - +
150C SER* 4.2 8.5 - - - +
154C GLY* 1.3 71.8 - - - -
156C GLY* 1.3 59.6 + - - +
159C LYS* 2.9 60.6 + - + +
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Residues in contact with GLY 156 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A ASP 3.8 14.6 - - - -
121A ILE* 4.1 2.3 - - - +
122A ARG* 3.9 17.3 - - - +
152A LEU* 4.6 2.6 - - - +
180A ASN* 3.1 25.3 + - - -
154C GLY* 3.5 1.2 - - - -
155C MET* 1.3 77.4 - - - +
157C MET* 1.3 61.8 + - - +
159C LYS* 3.9 1.4 - - - +
160C GLN* 3.0 19.4 + - - +
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Residues in contact with MET 157 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A GLY* 6.5 0.7 - - - -
180A ASN* 3.5 39.2 + - - +
153C VAL* 3.9 24.4 + - + +
154C GLY 4.1 2.4 + - - -
155C MET 3.5 0.2 - - - -
156C GLY* 1.3 71.6 - - - +
158C ALA* 1.3 67.6 + - - +
159C LYS 3.2 0.2 + - - -
160C GLN* 3.2 15.3 + - - +
161C LEU* 2.9 55.2 + - + +
168C ILE* 4.9 1.3 - - + -
172C GLU* 3.6 20.9 - - - +
175C ARG* 4.2 11.7 - - - +
176C ILE* 3.8 28.3 - - + -
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Residues in contact with ALA 158 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A ILE* 5.3 0.2 - - + -
149C LEU* 3.7 20.4 - - + +
150C SER* 3.5 33.7 - - - +
153C VAL* 3.8 1.2 - - - +
154C GLY 3.1 22.5 + - - +
155C MET 3.9 1.8 - - - +
156C GLY 3.3 0.2 - - - -
157C MET* 1.3 78.4 - - - +
159C LYS* 1.3 59.0 + - + +
161C LEU* 3.4 1.2 + - - +
162C ILE* 2.9 41.8 + - + +
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Residues in contact with LYS 159 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A GLU* 4.7 6.5 + - - +
119A CYS 5.3 1.2 + - - -
120A ASP* 3.0 48.7 + - - +
121A ILE* 4.4 1.6 - - + -
211A LYS* 4.8 1.8 - - - -
214A ILE* 3.9 33.4 - - + -
215A ASN* 2.9 33.5 + - - +
155C MET* 2.9 40.1 + - + +
156C GLY 3.9 2.5 - - - +
158C ALA* 1.3 74.5 - - - +
160C GLN* 1.3 65.0 + - - +
163C PHE* 2.9 57.4 + - + -
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Residues in contact with GLN 160 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A ILE* 3.6 28.3 - - + +
123A ILE* 3.7 8.1 - - - +
180A ASN* 3.0 33.7 + - - +
181A LYS* 3.6 24.4 + - - +
195A ILE* 4.8 4.9 - - + -
156C GLY 3.0 13.8 + - - +
157C MET* 3.5 28.4 - - - +
159C LYS* 1.3 75.8 - - - +
161C LEU* 1.3 60.6 + - + +
164C THR* 2.8 46.9 + - + +
168C ILE* 6.2 0.6 - - - +
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Residues in contact with LEU 161 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130C PHE* 4.8 6.3 - - + +
131C GLY* 5.2 5.6 - - - -
132C GLN* 3.6 9.9 + - + +
149C LEU* 4.1 28.3 - - + -
157C MET* 2.9 49.8 + - + +
158C ALA 3.8 3.4 - - - +
160C GLN* 1.3 78.6 - - + +
162C ILE* 1.3 63.1 + - - +
164C THR* 3.6 4.4 + - - -
165C ALA* 2.9 28.4 + - - -
166C GLN* 3.7 17.7 + - + +
168C ILE* 4.2 34.5 - - + -
176C ILE* 5.2 3.4 - - + -
178C LEU* 5.8 1.6 - - + -
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Residues in contact with ILE 162 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A SER* 3.7 34.1 - - - +
214A ILE* 3.6 23.8 - - + -
132C GLN* 4.2 15.6 - - + +
135C VAL* 3.2 25.3 - - + +
141C PRO* 4.0 22.9 - - + -
145C GLY 3.8 23.1 - - - +
146C THR* 4.2 6.7 - - - -
149C LEU* 4.0 17.9 - - + -
150C SER* 5.8 0.4 - - - +
158C ALA* 2.9 25.3 + - + +
159C LYS 4.4 0.9 - - - +
161C LEU* 1.3 78.3 - - - +
163C PHE* 1.3 59.2 + - + +
165C ALA 3.8 1.0 + - - -
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Residues in contact with PHE 163 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A PRO* 4.0 18.2 - - + -
120A ASP* 3.9 19.5 - - + -
121A ILE* 4.1 9.0 - - + -
199A ILE* 3.8 28.4 - - + +
202A ASN* 3.0 18.9 + - - -
207A VAL* 3.8 25.9 - - + +
210A SER* 4.2 6.5 - - - -
211A LYS* 3.7 47.3 - - + -
214A ILE* 4.4 6.3 - - + -
135C VAL* 3.5 7.8 - - - +
159C LYS* 2.9 48.6 + - + +
160C GLN 4.1 0.9 - - - +
162C ILE* 1.3 81.0 - - + +
164C THR* 1.3 58.8 + - - +
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Residues in contact with THR 164 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A ILE* 4.1 30.7 - - + +
198A LYS* 4.3 16.6 - - + +
199A ILE* 4.2 11.2 - - + -
202A ASN* 3.2 11.1 + - - +
160C GLN* 2.8 31.8 + - + +
161C LEU* 3.6 2.8 + - - +
163C PHE* 1.3 75.1 - - - +
165C ALA* 1.3 70.9 + - - +
166C GLN* 3.0 33.7 + - - +
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Residues in contact with ALA 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A ASN* 4.1 8.3 - - - +
132C GLN 3.2 29.3 - - - +
133C PRO* 3.7 22.7 - - + +
135C VAL* 4.1 16.2 - - + -
136C GLY* 4.5 1.3 - - - +
161C LEU 2.9 7.8 + - - -
162C ILE 3.8 0.8 + - - -
163C PHE 3.4 2.2 - - - -
164C THR* 1.3 80.7 + - - +
166C GLN* 1.3 59.2 + - - +
167C ASN* 4.0 5.2 + - - -
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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