Contacts of the helix formed by residues 85 - 95 (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 SER 85 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84B ASP* 1.3 79.9 - - - +
86B GLU* 1.3 65.6 + - - +
87B GLU* 3.4 7.3 - - - +
88B THR* 2.8 24.6 + - - -
89B ILE* 3.3 21.0 + - - +
149B LYS* 3.7 4.9 - - - +
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Residues in contact with GLU 86 (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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85B SER* 1.3 73.1 - - - +
87B GLU* 1.3 62.0 + - - +
89B ILE 3.4 0.5 + - - -
90B ARG* 2.8 54.5 + - - +
142B VAL 5.0 0.3 - - - +
145B THR* 3.3 22.4 - - + +
146B ALA* 3.6 30.9 + - - +
149B LYS* 3.3 35.9 - - + +
151B SER* 4.6 6.6 + - - -
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Residues in contact with GLU 87 (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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85B SER* 3.4 6.3 - - - +
86B GLU* 1.3 79.2 - - - +
88B THR* 1.3 53.6 + - - +
90B ARG* 3.2 21.4 + - - +
91B ASN* 2.7 58.5 + - - +
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Residues in contact with THR 88 (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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810A VAL* 4.5 13.7 - - + -
84B ASP* 4.0 26.1 - - + +
85B SER* 2.8 27.1 + - - -
86B GLU 3.3 0.4 - - - -
87B GLU* 1.3 79.3 - - - +
89B ILE* 1.3 58.6 + - - +
91B ASN* 3.1 8.5 + - - +
92B ALA* 2.9 26.5 + - - +
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Residues in contact with ILE 89 (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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810A VAL* 3.8 25.1 - - + -
811A ILE* 5.0 4.3 - - + -
814A ASN* 3.4 38.1 - - + +
84B ASP* 3.6 10.8 - - + +
85B SER 3.3 18.4 + - - +
86B GLU 3.9 2.7 - - - +
88B THR* 1.3 72.8 - - - +
90B ARG* 1.3 67.0 + - - +
92B ALA* 3.1 10.7 + - - +
93B PHE* 3.3 32.1 + - + -
145B THR* 3.9 15.5 - - + +
148B ILE* 4.4 16.6 - - + -
149B LYS* 3.8 12.8 - - + -
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Residues in contact with ARG 90 (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* 2.8 56.6 + - - +
87B GLU* 3.4 33.8 - - - +
89B ILE* 1.3 77.3 - - - +
91B ASN* 1.3 64.7 - - - +
93B PHE* 3.4 7.0 + - - +
94B ALA* 3.2 23.3 + - + +
102B LYS* 5.7 6.3 - - - +
141B TYR* 3.9 6.4 - - + -
142B VAL* 4.2 34.8 + - + +
145B THR* 3.9 16.1 - - + +
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Residues in contact with ASN 91 (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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87B GLU* 2.7 40.4 + - - +
88B THR* 3.5 7.1 - - - +
90B ARG* 1.3 87.6 + - - +
92B ALA* 1.3 61.3 + - - +
93B PHE 3.3 0.2 - - - -
94B ALA* 3.5 16.5 + - - +
95B MET* 3.3 26.1 + - + +
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Residues in contact with ALA 92 (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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807A GLY* 3.6 32.9 - - - +
810A VAL* 3.9 13.7 - - + -
811A ILE* 3.5 13.0 - - + -
88B THR* 2.9 11.9 + - + +
89B ILE 3.1 10.0 + - - +
91B ASN* 1.3 76.3 - - - +
93B PHE* 1.3 62.7 + - - +
95B MET* 3.4 16.4 + - + +
96B PHE* 3.5 19.2 - - - -
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Residues in contact with PHE 93 (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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811A ILE* 3.6 42.6 - - + -
815A ILE* 4.7 2.5 - - + -
89B ILE* 3.3 33.6 + - + -
90B ARG 3.7 2.0 - - - +
92B ALA* 1.3 75.9 - - - +
94B ALA* 1.3 55.9 + - - +
95B MET 3.0 5.4 - - - -
96B PHE* 2.9 28.0 + + - +
97B ASP* 3.7 5.0 + - - +
104B LEU* 3.8 20.6 - - + +
109B ILE* 4.1 13.9 - - + -
139B PHE* 3.9 17.5 - + - -
141B TYR* 3.4 35.9 - + + -
144B PHE* 4.1 28.3 - + - -
145B THR* 3.8 16.4 - - - -
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Residues in contact with ALA 94 (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* 3.2 13.0 + - + +
91B ASN* 3.7 20.2 - - - +
92B ALA 3.3 0.4 - - - -
93B PHE* 1.3 78.1 - - - +
95B MET* 1.3 60.3 + - + +
96B PHE 3.1 1.7 + - - -
97B ASP* 3.2 22.2 + - - +
98B GLU* 5.1 0.5 - - - -
100B GLU* 6.5 0.9 - - + -
102B LYS* 5.0 8.7 - - - +
141B TYR* 3.9 20.1 - - + +
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Residues in contact with MET 95 (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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800A LYS* 5.3 1.7 - - - +
803A ASP* 3.5 43.1 - - + +
804A GLN* 2.7 39.8 + - + +
806A ILE* 5.1 7.0 - - + -
807A GLY* 4.3 14.6 - - - +
91B ASN* 3.3 21.8 - - + +
92B ALA* 3.5 12.8 - - - +
93B PHE 3.0 1.2 - - - -
94B ALA* 1.3 77.2 - - - +
96B PHE* 1.3 56.9 + - + +
97B ASP 3.5 0.9 - - - -
98B GLU* 4.5 3.3 - - - +
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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