Contacts of the helix formed by residues 117 - 123 (chain A) in PDB entry 2KK0
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 TYR 117 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79A LEU* 3.4 35.2 - - + -
80A VAL* 4.7 1.1 - - + -
113A MET* 3.5 21.8 - - + +
115A TYR 3.6 0.4 + - - -
116A LEU* 1.3 73.5 - - - +
118A PRO* 1.4 82.2 - - + +
119A TYR* 2.8 9.8 + - - +
120A GLU* 3.0 34.7 + - - +
121A CYS* 3.2 9.8 + - + -
127A SER* 3.1 33.7 + - - -
128A ASN 3.0 33.3 + - - -
129A PRO* 3.1 17.2 - - + +
132A LEU* 4.3 13.0 - - + +
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Residues in contact with PRO 118 (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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42A LEU* 6.2 1.1 - - + -
45A PHE* 3.7 9.7 - - + -
46A MET* 5.1 5.2 - - + -
49A ARG* 3.6 44.0 + - - +
51A THR* 5.1 8.7 - - + -
113A MET 4.8 4.3 - - - +
114A LYS 5.0 2.9 - - - +
115A TYR 4.2 10.8 - - - +
117A TYR* 1.4 103.4 - - + +
119A TYR* 1.3 55.8 + - + +
121A CYS* 4.0 4.3 - - + +
122A GLU* 3.0 33.4 + - - +
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Residues in contact with TYR 119 (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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38A PHE* 3.5 32.8 - + - -
41A ASP* 2.9 31.9 + - + +
42A LEU* 4.0 32.8 - - + -
45A PHE* 3.9 24.8 - + + -
70A TYR* 3.2 30.5 - + + +
117A TYR 2.8 5.1 + - - +
118A PRO* 1.3 79.4 - - - +
120A GLU* 1.3 59.7 + - - +
122A GLU* 4.6 0.9 - - - -
123A LYS* 2.9 68.8 + - + +
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Residues in contact with GLU 120 (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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70A TYR* 3.3 24.6 + - + +
74A THR* 4.4 0.9 - - + -
78A GLY* 3.8 4.3 - - - -
79A LEU* 3.1 19.0 + - - +
112A TYR* 2.9 29.8 + - - -
117A TYR* 3.0 34.1 + - + +
119A TYR* 1.3 78.9 - - - +
121A CYS* 1.3 52.9 + - + +
124A ARG* 3.1 15.3 + - - +
125A GLY 2.7 28.2 + - - -
126A LEU* 3.4 27.3 + - + +
127A SER* 2.9 30.2 + - - -
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Residues in contact with CYS 121 (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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117A TYR* 3.2 18.9 + - + +
118A PRO* 4.2 5.2 - - + +
120A GLU* 1.3 83.0 - - + +
122A GLU* 1.3 60.1 + - - +
125A GLY* 3.1 28.0 + - - +
126A LEU 4.2 0.7 - - - +
127A SER 3.1 26.9 - - - +
128A ASN* 4.6 12.6 - - - -
129A PRO* 4.8 8.3 - - - -
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Residues in contact with GLU 122 (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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45A PHE* 3.7 24.0 - - + -
49A ARG* 3.5 21.7 + - - +
118A PRO 3.0 20.3 + - - +
119A TYR* 4.0 1.6 - - - +
121A CYS* 1.3 80.7 - - - +
123A LYS* 1.3 72.0 + - + +
124A ARG 4.9 0.3 - - - -
125A GLY 4.7 0.5 + - - -
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Residues in contact with LYS 123 (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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41A ASP* 4.7 4.8 + - - -
45A PHE* 5.0 16.1 - - - -
70A TYR* 5.1 1.3 - - - +
119A TYR* 2.9 71.2 + - + +
122A GLU* 1.3 81.1 - - + +
124A ARG* 1.3 77.1 + - + +
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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