Contacts of the helix formed by residues 152 - 165 (chain C) in PDB entry 1ZSV
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 152 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149C ALA* 3.1 17.1 + - - -
151C ALA* 1.3 81.4 - - - +
153C ALA* 1.3 57.0 + - - -
154C VAL 3.3 3.1 - - - -
155C GLY 3.9 1.8 - - - -
156C SER* 2.7 36.1 + - - -
323C GLY 6.3 0.7 - - - -
419C CL 4.3 1.8 - - - +
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Residues in contact with ALA 153 (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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47C ASP* 5.8 0.4 - - - +
120C GLY* 5.6 0.8 - - - -
121C THR* 5.6 0.9 + - - -
125C PRO* 3.8 20.3 - - + +
152C GLY* 1.3 72.1 - - - +
154C VAL* 1.3 62.1 + - + +
156C SER* 3.7 3.8 + - - -
157C VAL* 3.4 23.2 - - - +
323C GLY 5.9 1.4 - - - -
324C LYS* 3.5 40.6 - - + +
405C CL 4.4 9.0 - - + -
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Residues in contact with VAL 154 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124C MET* 5.8 1.3 - - - -
125C PRO* 3.6 29.6 - - + +
128C THR* 3.9 17.3 - - + +
129C ALA* 3.5 18.8 - - - +
152C GLY 3.3 0.4 - - - -
153C ALA* 1.3 76.0 - - + +
155C GLY* 1.3 65.9 + - - +
157C VAL 3.1 4.7 + - - -
158C VAL* 3.0 21.5 + - - +
215C PHE* 3.7 34.8 - - + -
217C ASN* 4.3 8.1 - - - +
239C CYS* 4.2 4.9 - - - -
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Residues in contact with GLY 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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147C VAL* 3.8 22.4 - - - +
149C ALA 3.7 20.0 + - - -
150C ALA* 3.5 7.2 - - - +
152C GLY 3.4 2.6 + - - -
154C VAL* 1.3 78.3 - - - +
156C SER* 1.3 56.4 + - - +
158C VAL* 3.4 5.9 + - - +
159C GLY 3.1 23.9 + - - -
187C PHE* 3.9 5.0 - - - -
217C ASN* 4.2 5.1 - - - +
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Residues in contact with SER 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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150C ALA 3.2 15.1 + - - -
151C ALA* 4.3 7.3 + - - -
152C GLY 2.7 23.4 + - - -
153C ALA* 3.7 7.4 + - - -
155C GLY* 1.3 76.2 - - - +
157C VAL* 1.3 62.4 + - - +
159C GLY 3.9 0.6 + - - -
160C GLN* 2.9 35.4 + - - +
181C TYR* 4.2 19.6 + - - -
182C LEU* 4.5 6.7 - - - -
185C LEU* 4.6 3.6 - - - -
187C PHE* 4.1 7.2 - - - -
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Residues in contact with VAL 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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121C THR* 4.3 25.6 - - + +
126C GLY* 4.2 13.7 - - - -
129C ALA* 3.7 11.4 - - + -
153C ALA 3.4 18.6 - - - +
154C VAL 3.1 5.8 + - - +
156C SER* 1.3 78.9 + - - +
158C VAL* 1.3 64.6 + - - +
159C GLY 3.2 0.2 - - - -
160C GLN* 3.1 8.0 + - - +
161C ILE* 2.9 45.8 + - + +
287C LEU* 4.1 16.2 - - + -
296C ILE* 4.2 11.7 - - + -
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Residues in contact with VAL 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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129C ALA* 3.4 24.9 - - + +
133C LEU* 3.6 33.1 - - + +
145C VAL* 5.0 3.4 - - + -
147C VAL* 4.4 10.8 - - + -
154C VAL 3.0 12.4 + - - +
155C GLY* 3.4 8.3 + - - +
157C VAL* 1.3 75.0 - - - +
159C GLY* 1.3 57.6 - - - +
161C ILE* 3.4 1.1 + - - -
162C ALA* 3.0 28.7 + - + +
215C PHE* 3.6 47.6 - - + -
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Residues in contact with GLY 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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147C VAL* 4.6 0.8 - - - +
155C GLY 3.1 7.9 + - - -
156C SER 3.9 0.2 + - - -
158C VAL* 1.3 81.2 - - - +
160C GLN* 1.3 56.1 + - - +
162C ALA* 3.6 0.6 + - - -
163C LYS* 3.2 32.4 + - - +
169C VAL* 3.6 20.4 - - - +
187C PHE* 3.5 29.4 - - - -
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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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156C SER* 2.9 27.8 + - - +
157C VAL* 3.1 6.1 + - - +
159C GLY* 1.3 74.3 - - - +
161C ILE* 1.3 65.5 + - - +
163C LYS* 3.9 6.7 - - - +
164C LEU* 3.3 28.2 + - - +
185C LEU* 3.7 38.2 - - + +
187C PHE* 4.4 2.0 - - + -
295C LYS 4.0 15.3 - - - +
296C ILE* 3.6 17.9 - - + +
297C GLN* 2.9 52.3 + - - +
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Residues in contact with ILE 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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129C ALA 4.5 2.0 - - - -
130C TYR* 3.7 33.7 - - + +
133C LEU* 3.6 19.3 - - + -
134C LEU* 3.9 26.0 - - + -
157C VAL* 2.9 37.4 + - + +
158C VAL* 4.0 0.4 - - - +
160C GLN* 1.3 73.2 - - - +
162C ALA* 1.3 59.9 + - - +
164C LEU* 3.4 7.8 + - + +
165C LYS* 2.9 35.4 + - + +
287C LEU* 4.0 7.6 - - + -
290C TRP* 3.9 20.0 - - + -
296C ILE* 4.0 11.4 - - + -
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Residues in contact with ALA 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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133C LEU* 3.6 14.6 - - + +
145C VAL* 4.5 11.2 - - + -
158C VAL* 3.0 18.7 + - + +
159C GLY* 3.7 0.9 - - - +
160C GLN 3.4 0.2 - - - -
161C ILE* 1.3 75.0 - - - +
163C LYS* 1.3 60.5 + - - +
165C LYS* 3.4 2.7 + - - +
166C GLY 3.2 5.0 + - - -
167C CYS* 2.9 43.5 + - + -
169C VAL* 3.4 23.6 - - + -
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Residues in contact with LYS 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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159C GLY 3.2 21.8 + - - +
160C GLN* 3.9 7.0 - - - +
161C ILE 3.2 0.4 - - - -
162C ALA* 1.3 76.4 - - - +
164C LEU* 1.3 57.3 + - - +
166C GLY* 2.9 20.8 + - - -
167C CYS 2.7 28.2 + - - +
168C LYS* 4.3 0.2 - - - +
169C VAL* 3.6 12.3 - - + -
185C LEU 4.9 4.3 - - - +
186C GLY* 3.6 29.6 - - - +
187C PHE* 4.7 2.0 - - + +
188C ASP* 2.9 31.1 + - - +
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Residues in contact with LEU 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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160C GLN 3.3 18.2 + - - +
161C ILE* 3.5 14.4 - - - +
163C LYS* 1.3 78.8 - - - +
165C LYS* 1.3 74.9 + - - +
166C GLY 3.3 0.4 - - - -
290C TRP* 3.8 55.6 - - + +
295C LYS* 4.1 39.8 + - + +
296C ILE* 4.5 3.4 - - + -
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Residues in contact with LYS 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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134C LEU* 4.0 39.7 - - + +
139C VAL* 4.8 8.7 - - + +
140C LYS 4.2 6.8 - - - +
141C GLY* 3.2 24.0 - - - +
161C ILE* 2.9 20.3 + - + +
162C ALA* 3.4 5.6 + - - +
164C LEU* 1.3 95.2 - - - +
166C GLY* 1.3 57.3 + - - +
167C CYS* 4.5 7.9 - - - -
290C TRP* 3.8 21.9 - - - -
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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