Contacts of the helix formed by residues 89 - 104 (chain B) in PDB entry 1K86
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 GLY 89 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B LYS* 5.2 3.0 - - - +
87B ARG 3.3 0.4 + - - -
88B ASN* 1.3 74.4 - - - +
90B THR* 1.3 63.6 + - - +
91B ASP* 3.4 3.5 - - - +
92B LYS* 3.3 20.2 + - - +
93B ASP* 3.3 18.2 + - - +
233B ARG* 5.9 3.1 - - - -
234B SER 3.9 16.2 - - - -
235B PRO* 4.0 8.1 + - - +
236B GLY* 5.6 0.7 - - - -
238B GLY* 3.7 5.3 - - - -
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Residues in contact with THR 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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74B ASN* 2.8 27.5 + - - +
76B LYS* 3.5 31.4 - - + -
87B ARG* 2.8 47.1 + - - +
88B ASN 3.9 0.2 + - - -
89B GLY* 1.3 75.9 - - - +
91B ASP* 1.3 71.8 + - - +
93B ASP* 3.1 11.4 + - - +
94B ALA* 2.9 23.7 + - - +
142B LEU* 3.8 9.2 - - - +
233B ARG* 5.8 1.4 - - - +
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Residues in contact with ASP 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B ASN* 3.1 21.7 - - - +
76B LYS* 3.3 41.3 + - - +
89B GLY* 3.4 1.4 - - - +
90B THR* 1.3 82.8 - - - +
92B LYS* 1.3 57.7 + - - +
94B ALA* 3.4 1.7 + - - +
95B GLU* 2.9 31.2 + - - +
112B ASN* 5.0 2.1 + - - -
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Residues in contact with LYS 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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89B GLY* 3.3 16.1 + - - +
90B THR 3.1 0.6 - - - -
91B ASP* 1.3 80.5 - - - +
93B ASP* 1.3 62.1 + - - +
95B GLU* 3.4 6.0 + - - +
96B ALA* 3.1 24.1 + - + +
236B GLY 2.5 24.3 + - - +
237B ARG* 3.3 35.9 - - - +
238B GLY* 3.7 1.6 - - - +
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Residues in contact with ASP 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B ARG* 5.2 3.8 + - - -
89B GLY 3.3 11.2 + - - +
90B THR* 3.1 12.5 + - - +
92B LYS* 1.3 75.4 - - - +
94B ALA* 1.3 58.6 + - - +
96B ALA* 3.2 3.5 + - - +
97B LEU* 2.8 36.7 + - - +
142B LEU* 4.3 10.8 - - + +
184B GLN* 5.0 4.0 - - - +
233B ARG* 5.3 2.1 - - - +
237B ARG 4.6 0.7 - - - +
238B GLY* 3.1 8.5 - - - -
239B SER* 2.9 42.3 + - - +
242B VAL* 3.5 32.0 - - + +
243B GLN* 4.9 0.7 + - - -
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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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72B ILE* 4.1 10.2 - - + +
74B ASN* 3.4 35.4 - - + +
90B THR 2.9 11.7 + - - +
91B ASP* 3.7 3.6 - - - +
93B ASP* 1.3 77.8 - - - +
95B GLU* 1.3 55.9 + - - +
97B LEU* 4.0 3.6 - - - +
98B PHE* 3.0 31.0 + - - +
110B VAL* 4.8 8.2 - - + +
112B ASN* 5.5 0.2 - - - +
142B LEU* 3.9 12.7 - - + +
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Residues in contact with GLU 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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91B ASP 2.9 17.5 + - - +
92B LYS* 3.8 6.5 - - - +
94B ALA* 1.3 74.2 - - - +
96B ALA* 1.3 63.4 + - - +
98B PHE* 3.5 21.5 - - - -
99B LYS* 3.1 57.1 + - - +
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Residues in contact with ALA 96 (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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92B LYS* 3.1 18.6 + - + +
93B ASP* 3.6 5.8 - - - +
95B GLU* 1.3 75.7 - - - +
97B LEU* 1.3 60.1 + - - +
99B LYS* 3.3 7.2 + - - +
100B CYS* 2.9 30.5 + - - +
242B VAL* 4.8 2.7 - - + -
243B GLN* 6.3 1.1 - - - -
246B CYS* 3.8 19.8 - - + +
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Residues in contact with LEU 97 (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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72B ILE* 4.0 12.3 - - + -
93B ASP 2.8 22.5 + - - +
94B ALA 4.0 3.4 - - - +
96B ALA* 1.3 77.5 - - - +
98B PHE* 1.3 52.3 + - - +
100B CYS* 4.2 0.2 - - - -
101B PHE* 2.8 51.2 + - + +
140B ILE* 3.9 29.8 - - + -
142B LEU* 3.9 19.1 - - + -
242B VAL* 3.4 24.2 - - + +
245B LEU* 4.0 24.9 - - + -
246B CYS* 3.5 20.0 - - - -
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Residues in contact with PHE 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B ILE* 3.7 15.9 - - + +
94B ALA 3.0 17.5 + - - +
95B GLU* 3.5 30.1 - - - -
96B ALA 3.3 0.2 - - - -
97B LEU* 1.3 75.1 - - - +
99B LYS* 1.3 78.0 + - + +
102B ARG* 2.9 70.2 + - - +
108B VAL* 3.8 24.5 - - + +
110B VAL* 4.3 13.7 - - + -
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Residues in contact with LYS 99 (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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95B GLU* 3.1 46.6 + - - +
96B ALA* 3.7 5.4 - - - +
98B PHE* 1.3 94.2 - - + +
100B CYS* 1.3 62.8 + - - +
102B ARG* 3.2 22.6 + - - +
103B SER* 3.0 25.8 + - - -
250B GLU* 4.5 5.3 - - - +
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Residues in contact with CYS 100 (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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96B ALA 2.9 18.7 + - - +
97B LEU 3.6 3.4 - - - +
99B LYS* 1.3 76.8 - - - +
101B PHE* 1.3 64.0 + - - +
103B SER* 3.1 18.2 + - - -
104B LEU* 3.2 9.6 + - - +
246B CYS* 3.9 24.2 - - + -
249B LEU* 3.5 45.5 - - - -
250B GLU* 3.7 26.6 + - - +
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Residues in contact with PHE 101 (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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70B CYS* 3.5 31.0 - - + -
97B LEU* 2.8 37.8 + - + +
98B PHE* 4.9 0.2 - - - -
100B CYS* 1.3 77.3 - - + +
102B ARG* 1.3 60.8 + - - +
104B LEU* 3.5 12.9 + - + -
106B PHE* 3.1 48.4 + + + +
108B VAL* 3.9 7.9 - - + -
138B ALA* 4.1 11.0 - - + -
140B ILE* 4.0 17.3 - - + -
182B PHE* 3.7 39.0 - + - -
245B LEU* 4.6 2.2 - - + -
249B LEU* 3.5 30.1 - - + -
301B PHE* 5.8 2.2 - + - -
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Residues in contact with ARG 102 (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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98B PHE* 2.9 54.6 + - + +
99B LYS* 3.6 24.7 + - - +
100B CYS 3.1 0.2 - - - -
101B PHE* 1.3 74.7 - - - +
103B SER* 1.3 59.1 - - - +
104B LEU 3.0 1.6 - - - -
105B GLY* 2.8 22.0 + - - -
106B PHE 4.0 9.8 + - - +
108B VAL* 3.7 12.3 - - + +
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Residues in contact with SER 103 (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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99B LYS 3.0 12.7 + - - -
100B CYS 3.1 6.9 + - - -
102B ARG* 1.3 78.1 - - - +
104B LEU* 1.3 59.8 + - - +
105B GLY* 3.5 0.7 + - - -
250B GLU* 3.0 29.3 + - - -
254B LYS* 3.5 21.9 + - - -
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Residues in contact with LEU 104 (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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67B LEU* 3.0 16.6 - - + +
100B CYS* 3.2 14.3 + - - +
101B PHE* 3.6 16.8 - - + +
102B ARG 3.0 0.8 - - - -
103B SER* 1.3 78.4 + - - +
105B GLY* 1.3 58.2 + - - +
106B PHE* 4.0 20.2 - - + -
249B LEU* 4.0 24.9 - - + +
250B GLU* 5.7 0.4 - - - +
253B GLY* 4.0 27.4 - - - +
254B LYS* 3.9 26.6 - - + +
301B PHE* 3.9 38.6 - - + +
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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