Contacts of the helix formed by residues 162 - 172 (chain A) in PDB entry 6DWW
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 ILE 162 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158A LYS 3.2 13.2 - - - +
159A LYS* 4.5 4.7 - - - +
161A LEU* 1.3 80.4 - - + +
163A SER* 1.3 57.4 + - - +
164A ARG 2.9 6.5 + - - +
165A GLU* 3.7 27.6 - - + +
166A ILE* 2.9 51.3 + - + +
207A LEU* 5.0 4.0 - - + -
209A LEU* 6.4 0.7 - - + -
235A PHE* 4.8 3.8 - - + -
599A PHE* 4.0 18.6 - - + -
603A PHE* 3.7 39.9 - - + -
607A PHE* 4.0 22.0 - - + -
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Residues in contact with SER 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 LYS 3.2 18.5 + - - -
160A ALA* 3.1 12.5 + - - +
162A ILE* 1.3 77.4 - - - +
164A ARG* 1.3 55.1 + - - +
167A LYS* 3.5 20.4 + - - +
235A PHE* 3.3 33.0 - - - +
236A ASN* 5.3 1.1 - - - +
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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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160A ALA 4.3 3.4 + - - +
161A LEU 5.0 4.7 - - - +
162A ILE 2.9 1.4 - - - -
163A SER* 1.3 77.3 - - - +
165A GLU* 1.3 69.8 + - + +
166A ILE 3.1 1.3 - - - -
167A LYS* 3.3 4.9 + - - +
168A SER* 3.2 22.6 + - - -
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Residues in contact with GLU 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 LEU* 4.0 12.1 - - - +
162A ILE* 3.2 31.9 + - + +
164A ARG* 1.3 80.6 - - + +
166A ILE* 1.3 64.0 + - + +
168A SER* 3.7 10.8 + - - -
169A ALA* 3.8 11.8 + - - +
198A TYR* 4.7 12.0 + - - +
200A GLU* 4.7 7.4 - - - +
205A ARG* 5.4 0.3 + - - -
607A PHE* 3.9 20.1 - - + -
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Residues in contact with ILE 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 ILE* 2.9 37.0 + - + +
163A SER 4.7 2.9 - - - +
165A GLU* 1.3 74.1 - - - +
167A LYS* 1.3 68.5 + - - +
168A SER 3.0 3.0 + - - -
169A ALA* 3.1 14.4 + - - +
170A VAL* 3.3 14.6 + - + +
196A LEU* 3.7 33.3 - - + +
198A TYR* 3.7 20.9 - - + +
207A LEU* 3.7 18.2 - - + -
209A LEU* 4.9 7.2 - - + -
232A PHE* 6.2 2.2 - - + -
235A PHE* 4.5 21.3 - - + -
237A VAL* 4.4 16.2 - - + -
607A PHE* 5.5 0.2 - - + -
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Residues in contact with LYS 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 SER 3.5 19.3 + - - +
164A ARG* 3.3 6.5 + - - +
166A ILE* 1.3 81.0 - - - +
168A SER* 1.3 61.9 + - - +
170A VAL* 3.7 4.9 + - + +
171A GLU* 3.1 47.5 + - + +
235A PHE 4.7 0.7 - - - +
236A ASN* 3.2 35.8 + - + +
237A VAL* 4.5 14.8 - - + +
238A GLU 5.9 0.9 - - - +
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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* 3.2 14.4 + - - -
165A GLU* 3.9 9.0 - - - -
166A ILE 3.0 0.8 + - - -
167A LYS* 1.3 74.8 - - - +
169A ALA* 1.3 66.0 + - - +
171A GLU* 3.1 11.8 + - - +
172A LYS* 3.0 45.0 + - - +
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Residues in contact with ALA 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 GLU 3.8 7.0 + - - +
166A ILE 3.1 8.5 + - - +
168A SER* 1.3 78.1 - - - +
170A VAL* 1.3 61.5 + - + +
172A LYS* 3.5 7.9 + - - +
174A GLY* 3.2 27.9 + - - +
175A ALA* 3.6 7.9 + - + -
198A TYR* 3.9 41.7 - - + -
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Residues in contact with VAL 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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166A ILE* 3.3 18.5 + - + +
167A LYS* 3.9 8.5 - - + +
168A SER 3.2 0.4 - - - -
169A ALA* 1.3 74.8 - - - +
171A GLU* 1.3 66.7 + - + +
173A ASP* 3.3 9.5 + - - -
175A ALA* 3.9 19.3 - - + -
196A LEU* 5.1 5.8 - - + -
232A PHE* 5.6 1.6 - - + -
237A VAL* 4.2 26.7 - - + -
239A ASP* 5.4 6.3 - - + -
240A LEU 5.1 4.9 - - - +
242A SER* 3.3 21.0 - - - -
243A ILE* 3.8 33.4 - - + -
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Residues in contact with GLU 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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167A LYS* 3.1 44.0 + - + +
168A SER* 3.1 10.5 + - - +
170A VAL* 1.3 80.2 - - + +
172A LYS* 1.3 74.8 + - - +
173A ASP* 3.0 7.3 + - - +
242A SER* 4.6 5.5 + - - -
464A ILE* 3.9 29.9 - - + +
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Residues in contact with LYS 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* 3.0 32.1 + - - +
169A ALA* 3.5 4.9 + - - +
170A VAL 3.3 0.2 - - - -
171A GLU* 1.3 89.7 + - - +
173A ASP* 1.3 57.2 + - - +
174A GLY* 2.8 17.9 + - - +
461A LEU* 4.4 10.8 - - - +
464A ILE* 3.9 24.2 - - + -
465A ASN* 3.5 31.2 - - - +
468A SER* 4.1 14.2 + - - -
556A LYS* 5.8 2.2 - - - +
560A SER* 5.5 1.2 - - - -
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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