Contacts of the helix formed by residues 154 - 165 (chain B) 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 VAL 154 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B MET* 6.0 1.8 - - - -
125B PRO* 3.8 26.0 - - + +
128B THR* 3.9 22.4 - - + -
129B ALA* 3.6 9.8 - - - +
153B ALA* 1.3 78.1 - - + +
155B GLY* 1.3 66.2 + - - +
157B VAL* 3.0 12.3 + - - +
158B VAL* 3.0 15.0 + - + +
215B PHE* 3.4 39.7 - - + -
217B ASN* 4.0 13.7 - - - +
239B CYS* 5.0 1.1 - - - -
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Residues in contact with GLY 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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147B VAL* 3.7 24.6 - - - +
149B ALA 3.7 20.4 + - - -
150B ALA 3.3 9.1 - - - +
152B GLY 3.6 2.2 + - - -
154B VAL* 1.3 79.7 - - - +
156B SER* 1.4 56.4 + - - +
158B VAL* 3.5 5.5 + - - +
159B GLY* 3.1 23.9 + - - -
187B PHE* 4.0 1.7 - - - -
217B ASN* 4.3 5.2 - - - +
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Residues in contact with SER 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B ALA 3.1 15.5 + - - -
151B ALA* 4.3 8.1 + - - -
152B GLY 2.5 24.8 + - - -
153B ALA* 3.6 6.4 + - - -
155B GLY* 1.4 71.9 - - - +
157B VAL* 1.3 68.0 + - - +
159B GLY* 3.7 0.7 + - - -
160B GLN* 2.8 41.2 + - - +
181B TYR* 5.3 3.8 - - - -
182B LEU* 4.5 9.2 - - - -
185B LEU* 4.6 4.7 - - - -
187B PHE* 4.3 5.1 - - - -
297B GLN 5.8 0.4 - - - -
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Residues in contact with VAL 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B THR* 4.2 28.9 - - + +
126B GLY* 4.2 11.0 - - - +
129B ALA* 3.7 12.1 - - + -
153B ALA 3.6 16.2 - - - +
154B VAL 3.0 8.0 + - - +
156B SER* 1.3 78.8 + - - +
158B VAL* 1.3 69.4 + - - +
160B GLN* 3.1 7.5 + - - +
161B ILE* 2.9 48.1 + - + +
287B LEU* 4.1 15.7 - - + -
296B ILE* 4.3 11.2 - - + -
297B GLN 5.7 0.2 - - - +
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Residues in contact with VAL 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B ALA* 3.3 32.3 - - + +
133B LEU* 3.4 25.2 - - + +
145B VAL* 4.8 4.9 - - + -
147B VAL* 4.3 12.6 - - + -
154B VAL* 3.0 14.5 + - + +
155B GLY* 3.6 9.2 - - - +
157B VAL* 1.3 76.9 - - - +
159B GLY* 1.3 56.8 - - - +
161B ILE* 4.8 1.1 - - - -
162B ALA* 2.9 31.8 + - + +
215B PHE* 3.6 48.0 - - + -
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Residues in contact with GLY 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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147B VAL* 4.6 1.1 - - - -
155B GLY 3.1 9.8 + - - -
157B VAL 3.1 1.0 - - - -
158B VAL* 1.3 80.2 - - - +
160B GLN* 1.3 56.4 + - - +
162B ALA* 3.5 1.7 + - - -
163B LYS* 3.0 32.1 + - - +
169B VAL* 3.6 17.7 - - - +
187B PHE* 3.5 29.4 - - - -
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Residues in contact with GLN 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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156B SER* 2.8 28.6 + - - +
157B VAL* 3.1 5.9 + - - +
159B GLY* 1.3 75.0 - - - +
161B ILE* 1.3 64.6 + - - +
162B ALA 3.2 0.7 - - - -
163B LYS* 3.6 7.6 + - - +
164B LEU* 3.1 26.9 + - - +
185B LEU* 3.7 35.0 - - + +
187B PHE* 4.4 5.4 - - + -
295B LYS 4.0 14.9 - - - +
296B ILE* 3.5 18.0 - - + +
297B GLN* 2.8 50.9 + - - +
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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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129B ALA 4.5 2.5 - - - +
130B TYR* 3.9 27.6 - - + +
133B LEU* 3.7 15.5 - - + -
134B LEU* 3.9 26.9 - - + -
157B VAL* 2.9 39.4 + - + +
158B VAL* 3.9 3.6 - - - +
160B GLN* 1.3 76.3 - - - +
162B ALA* 1.3 62.3 + - - +
164B LEU* 3.3 9.1 - - + +
165B LYS* 3.1 30.4 + - + +
287B LEU* 4.2 10.1 - - + -
290B TRP* 4.0 13.5 - - + -
296B ILE* 4.0 17.3 - - + -
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Residues in contact with ALA 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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133B LEU* 3.8 16.4 - - + -
139B VAL* 5.4 0.2 - - - -
145B VAL* 4.5 11.4 - - + -
158B VAL 2.9 20.4 + - - +
159B GLY* 3.6 0.7 - - - +
160B GLN 3.2 0.2 - - - -
161B ILE* 1.3 74.9 - - - +
163B LYS* 1.3 65.3 + - - +
165B LYS* 3.3 3.5 + - - -
166B GLY 3.2 5.4 + - - -
167B CYS* 2.9 38.5 + - + +
169B VAL* 3.5 21.5 - - + -
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Residues in contact with LYS 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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159B GLY 3.0 22.0 + - - +
160B GLN* 3.8 8.1 - - - +
161B ILE 3.3 0.2 - - - -
162B ALA* 1.3 76.9 - - - +
164B LEU* 1.3 56.7 + - - +
166B GLY* 3.0 22.0 + - - -
167B CYS 2.6 27.2 + - - +
168B LYS* 4.4 0.2 - - - +
169B VAL* 3.8 9.6 - - + -
185B LEU 5.1 4.3 - - - +
186B GLY* 3.7 27.6 - - - +
187B PHE* 4.6 2.5 - - + +
188B ASP* 3.1 33.6 + - - +
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Residues in contact with LEU 164 (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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160B GLN 3.1 15.1 + - - +
161B ILE* 3.3 18.6 - - - +
163B LYS* 1.3 79.6 - - - +
165B LYS* 1.3 83.5 + - + +
166B GLY 3.3 1.1 - - - -
290B TRP* 4.0 38.1 - - + +
295B LYS* 4.0 31.9 - - + +
296B ILE* 4.8 1.8 - - + -
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Residues in contact with LYS 165 (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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134B LEU* 4.1 31.9 - - + +
139B VAL* 4.9 7.9 - - + +
140B LYS 4.0 9.7 - - - +
141B GLY* 3.5 17.5 - - - -
161B ILE* 3.1 21.1 + - - +
162B ALA* 3.3 6.5 + - - +
163B LYS 3.2 0.2 - - - -
164B LEU* 1.3 92.0 - - + +
166B GLY* 1.3 59.7 + - - +
167B CYS* 3.7 6.7 - - - -
290B TRP* 4.1 25.5 - - - -
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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