Contacts of the helix formed by residues 122 - 126 (chain B) in PDB entry 2QKW
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 LEU 122 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B ASN* 1.3 70.4 - - - +
123B LYS* 1.3 66.5 + - - +
125B HIS* 3.0 17.8 + - + +
126B LEU* 3.5 24.0 + - + +
136B MET* 3.8 25.8 - - + -
141B ARG 5.9 0.2 - - - +
144B ILE* 3.7 33.7 - - + -
145B CYS* 5.7 0.9 - - - -
167B SER* 3.4 13.0 + - - +
170B ILE* 2.9 28.3 + - + +
172B LEU* 4.4 6.7 - - + +
230B VAL* 4.0 18.4 - - + -
234B VAL* 3.7 27.4 - - + -
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Residues in contact with LYS 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B ASN* 3.2 11.1 + - - +
122B LEU* 1.3 77.8 - - - +
124B ARG* 1.3 58.3 + - - +
126B LEU* 2.9 28.7 + - - +
128B GLY* 3.8 11.6 + - - -
167B SER* 3.3 27.1 + - - +
168B ILE* 3.8 26.3 - - + +
207B TYR* 4.9 2.8 + - - -
233B GLU* 3.7 5.9 + - - -
239B SER* 2.5 47.7 + - - +
240B ALA* 4.7 2.3 - - - +
241B ILE* 5.1 2.8 - - - +
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Residues in contact with ARG 124 (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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118B GLU 4.8 3.8 + - - -
119B ASN* 3.6 28.8 + - - +
120B GLY* 4.2 5.9 - - - -
121B ASN* 2.9 32.2 + - - +
123B LYS* 1.3 76.7 - - - +
125B HIS* 1.3 66.9 + - - +
126B LEU 3.3 1.3 + - - -
127B TYR 5.0 0.3 + - - -
128B GLY* 4.3 15.0 + - - -
129B SER 4.5 19.5 + - - +
130B ASP 5.1 4.5 + - - +
131B LEU* 3.2 36.5 - - - +
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Residues in contact with HIS 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B ASN* 2.7 33.0 + - + +
121B ASN 3.1 24.9 - - - -
122B LEU* 3.0 10.2 + - - +
124B ARG* 1.3 87.3 - - + +
126B LEU* 1.3 66.0 + - - +
127B TYR 4.0 1.9 + - - -
135B SER* 5.4 2.9 - - - -
136B MET* 4.1 34.5 + - + +
141B ARG* 5.0 2.1 + - - -
172B LEU* 3.5 20.4 - - + +
176B PHE* 3.6 24.0 - + - -
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Residues in contact with LEU 126 (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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122B LEU* 3.5 33.2 - - + +
123B LYS* 2.9 9.9 + - - +
124B ARG 3.3 0.8 - - - -
125B HIS* 1.3 85.2 - - - +
127B TYR* 1.3 64.5 + - - +
128B GLY 3.2 1.4 + - - -
136B MET* 4.0 12.6 - - + -
141B ARG* 3.6 33.9 - - + +
167B SER* 5.4 2.0 - - - -
233B GLU* 3.9 8.7 - - + +
234B VAL* 3.7 36.1 - - + +
237B ALA* 4.1 10.1 - - + -
239B SER* 2.7 41.4 + - - +
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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