Contacts of the helix formed by residues 161 - 170 (chain A) in PDB entry 6OE7
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 PRO 161 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160A SER* 1.4 84.4 - - - +
162A GLU* 1.3 60.4 + - + +
163A ASN 3.5 0.2 - - - -
164A TRP* 4.2 5.5 - - + +
165A GLU* 3.4 26.0 + - - +
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Residues in contact with GLU 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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160A SER* 3.3 3.7 - - - -
161A PRO* 1.3 81.5 - - + +
163A ASN* 1.3 63.5 + - - +
165A GLU* 4.3 3.6 - - - +
166A LYS* 3.3 23.7 + - - +
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Residues in contact with ASN 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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160A SER* 3.5 25.7 + - - +
162A GLU* 1.3 75.0 - - - +
164A TRP* 1.3 64.3 + - - +
166A LYS* 3.4 5.9 + - - +
167A VAL* 3.1 31.0 + - + +
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Residues in contact with TRP 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 SER 3.2 15.4 + - - +
161A PRO* 4.4 5.4 - - + +
163A ASN* 1.3 76.9 - - - +
165A GLU* 1.3 63.4 + - - +
167A VAL* 3.0 19.6 + - - +
168A TRP* 3.1 38.1 + + - -
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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 PRO 3.4 18.7 + - - +
162A GLU* 4.5 3.8 - - - +
164A TRP* 1.3 78.1 - - - +
166A LYS* 1.3 60.4 + - - +
168A TRP* 3.6 4.6 + - - +
169A ASP* 3.2 35.0 + - - +
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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 GLU 3.3 19.2 + - - +
163A ASN* 3.4 6.4 + - - +
164A TRP 3.2 0.4 - - - -
165A GLU* 1.3 75.5 - - - +
167A VAL* 1.3 64.8 + - + +
169A ASP* 3.4 6.8 + - - +
170A ASN* 3.0 34.8 + - - +
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Residues in contact with VAL 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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146A GLN* 6.0 2.5 - - + -
163A ASN* 3.2 18.2 - - + +
164A TRP* 3.0 10.6 + - - +
166A LYS* 1.3 75.9 - - + +
168A TRP* 1.3 65.8 + - + +
170A ASN* 3.1 8.5 + - - +
171A TRP* 3.1 52.7 + - + -
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Residues in contact with TRP 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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8A HIS* 3.5 37.7 + + - +
9A LEU* 4.0 24.5 - - + +
13A VAL* 4.2 11.0 - - + +
42A TYR* 5.2 3.9 + + - -
123A ASP* 4.0 14.6 - - + -
141A PHE* 5.1 0.9 - + - -
164A TRP* 3.1 45.2 + + - +
165A GLU* 4.4 4.0 - - - +
167A VAL* 1.3 77.5 - - + +
169A ASP* 1.3 66.0 - - - +
170A ASN 3.5 0.3 + - - -
171A TRP* 3.1 76.2 + + + +
267A LEU* 4.4 27.3 - - + +
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Residues in contact with ASP 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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13A VAL* 4.5 21.0 - - - +
17A ALA* 5.7 4.2 - - - +
165A GLU* 3.2 28.3 + - - +
166A LYS* 3.6 8.0 - - - +
168A TRP* 1.3 79.5 - - - +
170A ASN* 1.3 66.2 + - - +
171A TRP 3.4 3.3 + - - +
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Residues in contact with ASN 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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146A GLN* 4.0 4.0 - - - +
147A ILE* 4.7 26.9 + - + +
166A LYS* 3.0 27.5 + - - +
167A VAL* 3.1 10.1 + - - +
169A ASP* 1.3 82.1 - - - +
171A TRP* 1.3 61.9 + - - +
172A ARG* 3.7 2.3 + - - +
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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