Contacts of the helix formed by residues 140 - 149 (chain B) in PDB entry 1KK8
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 ASP 140 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102B LYS 3.9 2.3 - - - +
103B LYS* 4.3 25.5 - - + +
133B PRO* 3.3 24.0 + - + +
138B LYS 3.8 2.4 + - - +
139B PHE* 1.3 70.7 - - - +
141B TYR* 1.3 54.8 + - - +
142B VAL* 2.7 34.1 - - - +
143B LYS* 3.0 29.4 + - + +
144B PHE* 2.9 26.9 + - - +
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Residues in contact with TYR 141 (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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90B ARG* 3.9 21.3 - - + -
93B PHE* 3.4 40.7 - + + -
94B ALA* 3.9 14.4 - - + +
97B ASP* 2.6 32.3 + - + +
102B LYS* 3.4 26.9 + - + +
103B LYS* 3.4 26.7 - - - -
104B LEU* 3.7 19.1 - - + -
139B PHE* 3.1 22.0 + - + -
140B ASP* 1.3 69.2 + - - +
142B VAL* 1.3 75.6 + - + +
144B PHE* 3.7 2.1 - - - +
145B THR* 2.4 38.8 + - - -
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Residues in contact with VAL 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B GLU* 5.0 0.9 - - - +
90B ARG* 4.2 24.8 + - - +
102B LYS* 4.1 28.0 - - + +
140B ASP* 2.7 28.9 - - - +
141B TYR* 1.3 100.4 - - + +
143B LYS* 1.3 63.8 + - + +
145B THR* 3.4 6.4 + - - -
146B ALA* 3.1 21.8 + - - +
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Residues in contact with LYS 143 (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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133B PRO* 4.2 19.0 - - + +
140B ASP* 3.0 30.8 + - + +
142B VAL* 1.3 82.4 - - + +
144B PHE* 1.3 59.0 + - - +
146B ALA* 3.1 9.4 + - + +
147B MET* 2.9 34.3 + - + +
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Residues in contact with PHE 144 (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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815A ILE* 3.7 39.5 - - + -
818A TRP* 4.3 24.5 - + - -
89B ILE* 6.3 0.2 - - + -
93B PHE* 4.1 19.7 - + - -
128B THR* 4.1 26.2 - - + -
132B ALA* 4.4 3.4 - - + -
133B PRO* 3.9 21.0 - - + +
139B PHE* 3.6 30.5 - + + -
140B ASP 2.9 17.0 + - - +
141B TYR* 3.8 3.4 - - - +
143B LYS* 1.3 76.8 - - - +
145B THR* 1.3 59.3 + - - +
147B MET* 3.6 12.8 - - - +
148B ILE* 3.0 33.1 + - + +
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Residues in contact with THR 145 (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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86B GLU* 3.3 39.9 - - + +
89B ILE* 3.9 11.9 - - + -
90B ARG* 3.9 17.8 - - + +
93B PHE* 3.8 19.4 - - - -
141B TYR 2.4 25.8 + - - -
142B VAL* 3.6 7.6 - - - -
143B LYS 3.1 0.2 - - - -
144B PHE* 1.3 76.7 - - - +
146B ALA* 1.3 64.1 + - - +
147B MET 3.1 1.3 - - - -
148B ILE* 2.7 26.0 - - + +
149B LYS* 3.1 9.5 + - - +
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Residues in contact with ALA 146 (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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86B GLU* 3.6 21.5 + - - +
142B VAL 3.1 13.2 + - - +
143B LYS* 3.5 11.2 - - + +
145B THR* 1.3 77.4 - - - +
147B MET* 1.3 54.7 + - - +
149B LYS* 3.6 4.0 + - - +
151B SER* 2.7 52.4 + - - +
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Residues in contact with MET 147 (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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818A TRP* 4.0 26.3 + - + -
131B GLU* 4.0 23.1 - - - +
133B PRO* 4.0 30.5 - - + -
143B LYS* 2.9 20.8 + - + +
144B PHE* 3.6 13.7 - - - +
146B ALA* 1.3 77.6 - - - +
148B ILE* 1.3 65.7 + - - +
150B GLY* 3.5 10.6 + - - -
151B SER 4.1 10.1 - - - +
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Residues in contact with ILE 148 (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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814A ASN* 3.1 41.1 - - + +
815A ILE* 4.4 10.5 - - + -
818A TRP* 3.4 45.4 - - + +
89B ILE* 4.4 14.8 - - + -
144B PHE* 3.0 25.0 + - + +
145B THR* 2.7 34.8 - - + +
147B MET* 1.3 72.7 - - - +
149B LYS* 1.3 70.0 + - + +
150B GLY 3.0 10.3 + - - -
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Residues in contact with LYS 149 (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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83B THR* 2.9 28.5 + - - -
84B ASP 2.3 32.2 + - - -
85B SER* 3.7 11.3 - - - +
86B GLU* 3.3 42.7 - - + +
89B ILE* 3.8 11.9 - - + -
145B THR* 3.1 9.5 + - + +
147B MET 3.3 0.2 - - - -
148B ILE* 1.3 86.7 - - + +
150B GLY* 1.3 54.6 + - - +
151B SER* 3.3 8.9 + - - -
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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