Contacts of the helix formed by residues 157 - 167 (chain A) in PDB entry 6V3O
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 SER 157 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155A GLY 4.0 1.0 + - - -
156A LYS* 1.3 75.8 - - - +
158A PRO* 1.3 73.4 - - - +
159A GLU* 3.7 12.2 + - - +
160A GLU* 2.9 41.6 + - - +
161A VAL* 3.0 13.4 + - - +
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Residues in contact with PRO 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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151A VAL* 4.0 26.9 - - + -
156A LYS 3.9 0.2 - - - -
157A SER* 1.3 85.3 - - - +
159A GLU* 1.3 64.4 + - - +
161A VAL* 3.1 4.5 + - + +
162A PHE* 2.8 28.1 + - - +
270A ILE* 3.5 38.1 - - + +
271A GLY 5.5 0.7 - - - -
272A ILE* 4.0 20.1 - - + +
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Residues in contact with GLU 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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157A SER* 3.7 11.4 + - - +
158A PRO* 1.3 87.1 - - - +
160A GLU* 1.3 60.7 + - - +
162A PHE* 3.8 10.1 - - + +
163A GLU* 2.9 29.6 + - - +
272A ILE* 4.1 14.1 - - + -
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Residues in contact with GLU 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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156A LYS* 3.3 41.8 + - + +
157A SER* 2.9 32.7 + - - +
159A GLU* 1.3 77.0 - - - +
161A VAL* 1.3 57.0 + - - +
163A GLU* 3.5 6.2 + - + +
164A ALA* 3.0 27.2 + - - +
703A MET* 4.6 8.8 - - - +
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Residues in contact with VAL 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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147A LEU* 3.5 32.1 - - + -
150A LEU* 4.3 18.6 - - + -
151A VAL* 4.2 19.1 - - + -
156A LYS* 4.3 10.1 - - + -
157A SER 3.0 12.4 + - - +
158A PRO* 3.4 7.9 - - + +
160A GLU* 1.3 74.3 - - - +
162A PHE* 1.3 66.9 + - - +
164A ALA* 3.1 7.6 + - - +
165A LEU* 3.0 27.2 + - + +
267A LEU* 5.1 0.7 - - + -
270A ILE* 4.5 8.7 - - + -
699A LEU* 4.3 10.3 - - + -
703A MET* 4.4 7.4 - - + -
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Residues in contact with PHE 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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158A PRO 2.8 18.6 + - - +
159A GLU* 3.8 9.6 - - + +
160A GLU 3.4 0.2 - - - -
161A VAL* 1.3 72.3 - - - +
163A GLU* 1.3 62.4 + - - +
165A LEU* 3.4 2.9 + - + +
166A LYS* 3.1 56.3 + - + +
267A LEU* 3.7 39.7 - - + +
272A ILE* 4.1 24.0 - - + -
274A GLU* 3.3 28.9 - - + -
275A ARG 3.9 14.8 - - - -
276A LEU* 4.2 20.4 - - + -
277A PRO* 4.0 12.6 - - + -
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Residues in contact with GLU 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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159A GLU 2.9 18.8 + - - +
160A GLU* 3.7 6.7 - - + +
161A VAL 3.2 0.2 - - - -
162A PHE* 1.3 74.0 - - - +
164A ALA* 1.3 66.1 + - - +
166A LYS* 3.3 31.2 + - - +
167A ASN* 2.8 44.3 + - - +
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Residues in contact with ALA 164 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160A GLU 3.0 14.4 + - - +
161A VAL 3.1 8.3 + - - +
163A GLU* 1.3 75.5 - - - +
165A LEU* 1.3 63.0 + - - +
167A ASN* 3.0 16.9 + - - +
168A GLN* 3.2 13.9 + - - +
666A GLY* 5.8 0.5 - - - -
699A LEU* 3.6 20.6 - - + +
703A MET* 4.0 15.7 - - + -
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Residues in contact with LEU 165 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143A ILE* 5.2 4.3 - - + -
147A LEU* 4.5 7.4 - - + -
161A VAL* 3.0 17.2 + - + +
162A PHE* 3.7 7.2 - - - +
164A ALA* 1.3 75.3 - - - +
166A LYS* 1.3 62.0 + - - +
167A ASN 3.2 0.9 + - - -
168A GLN* 3.3 14.6 + - - +
263A VAL* 5.4 11.0 - - + -
267A LEU* 4.0 31.2 - - + -
276A LEU* 4.3 13.6 - - + +
280A VAL* 4.0 4.9 - - - +
282A LEU* 3.4 44.7 - - + +
695A THR* 4.3 12.1 - - + -
699A LEU* 3.9 32.5 - - + +
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Residues in contact with LYS 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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162A PHE* 3.1 55.2 + - + +
163A GLU* 3.6 25.2 + - - +
164A ALA 3.2 0.6 - - - -
165A LEU* 1.3 75.8 - - - +
167A ASN* 1.3 63.7 + - - +
168A GLN 3.5 0.6 - - - +
274A GLU* 5.0 1.4 + - - -
276A LEU* 4.1 15.9 - - + -
277A PRO* 4.2 19.2 - - + +
280A VAL* 3.9 26.8 - - + +
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Residues in contact with ASN 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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163A GLU* 2.8 47.0 + - - +
164A ALA* 3.0 11.2 + - - +
166A LYS* 1.3 81.8 - - - +
168A GLN* 1.3 59.7 + - - +
169A THR* 4.8 4.4 - - - +
634A LYS* 5.8 3.5 - - - -
665A ASN 5.3 0.2 - - - +
666A GLY* 3.7 12.5 - - - +
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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