Contacts of the helix formed by residues 97 - 112 (chain B) in PDB entry 1KYO
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 97 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74B LEU* 3.6 41.2 - - + +
93B PHE* 4.4 3.1 - - + -
94B LEU* 3.5 17.3 + - - +
95B LYS 3.1 2.0 - - - -
96B ASP* 1.3 82.2 - - - +
98B LEU* 1.3 63.5 + - - +
99B PRO* 3.3 7.6 - - - -
100B TYR* 3.3 10.4 + - + +
101B TYR* 3.1 34.1 + - + -
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Residues in contact with LEU 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B LEU* 4.4 7.6 - - + -
93B PHE* 3.9 21.7 - - + -
95B LYS* 3.3 14.1 + - + +
96B ASP 3.2 1.5 - - - -
97B ASP* 1.3 75.1 - - - +
99B PRO* 1.3 70.1 - - + +
101B TYR* 3.3 7.2 + - - +
102B VAL* 3.3 33.9 + - + +
192B VAL* 3.3 32.1 - - + -
193B VAL* 4.0 20.4 - - + +
196B ASP* 4.8 9.2 - - + -
197B LEU* 4.1 16.2 - - + +
200B PHE* 4.7 9.9 - - + -
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Residues in contact with PRO 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B ASP 4.3 6.7 - - - +
97B ASP* 3.4 4.5 - - - +
98B LEU* 1.3 94.8 - - + +
100B TYR* 1.3 64.9 + - + +
102B VAL* 3.0 7.7 + - + +
103B ASN* 3.0 35.7 + - - +
200B PHE* 4.0 40.1 - - + -
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Residues in contact with TYR 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B ARG* 3.8 16.4 + - - -
67B LEU* 3.6 17.8 + - - +
70B GLU* 3.0 49.1 + - + +
71B SER* 4.2 15.9 - - - -
74B LEU* 3.4 29.4 - - + -
78B PHE* 4.4 12.1 - + - -
97B ASP* 3.3 12.0 + - + +
99B PRO* 1.3 80.9 - - + +
101B TYR* 1.3 67.3 + + + +
103B ASN* 3.4 5.2 + - - +
104B ALA* 2.7 37.4 + - + +
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Residues in contact with TYR 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B LEU* 4.0 6.3 - - + -
71B SER* 4.0 2.3 + - - -
74B LEU* 3.5 22.1 - - + +
75B GLY 3.8 1.7 + - - -
76B GLY* 3.5 28.8 + - - -
77B THR 4.7 0.7 - - - -
78B PHE* 4.0 27.4 - + - -
91B ALA* 4.3 10.3 - - + -
92B THR 4.6 1.3 - - - -
93B PHE* 3.3 54.0 - + + +
97B ASP* 3.1 34.7 + - + +
98B LEU 3.3 4.9 + - - +
99B PRO 3.3 0.4 - - - -
100B TYR* 1.3 90.3 - + - +
102B VAL* 1.3 61.1 + - - +
104B ALA* 3.7 6.1 - - - -
105B LEU* 2.9 34.1 + - - +
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Residues in contact with VAL 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B LEU* 3.5 20.4 - - + -
98B LEU* 3.3 31.0 + - + +
99B PRO* 3.0 9.0 + - + +
101B TYR* 1.3 75.7 - - - +
103B ASN* 1.3 63.4 + - - +
104B ALA 3.2 0.2 + - - -
105B LEU* 3.8 2.1 - - - +
106B ALA* 2.9 30.1 + - - +
197B LEU* 4.1 9.9 - - + -
200B PHE* 3.4 39.0 - - + +
201B VAL* 4.1 11.4 - - + -
204B SER* 4.3 7.2 - - - +
206B LEU* 4.4 7.1 - - + +
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Residues in contact with ASN 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B ARG* 5.2 1.3 - - - +
99B PRO* 3.0 29.5 + - - +
100B TYR* 3.9 3.7 - - - +
102B VAL* 1.3 76.9 - - - +
104B ALA* 1.3 54.1 + - - +
106B ALA* 3.5 5.5 - - - +
107B ASP* 2.8 37.1 + - - +
200B PHE* 4.8 3.8 + - - +
203B GLU* 5.0 2.0 + - - +
204B SER* 3.5 29.5 - - - +
205B LEU* 4.5 12.2 - - + +
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Residues in contact with ALA 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B ARG* 3.6 28.1 + - - +
67B LEU* 4.5 2.8 - - + +
78B PHE* 4.1 22.4 - - + -
100B TYR* 2.7 21.9 + - + +
101B TYR* 3.6 10.1 - - - +
103B ASN* 1.3 73.8 - - - +
105B LEU* 1.3 66.6 + - - +
107B ASP* 3.2 5.9 - - - +
108B VAL* 3.2 26.2 + - - +
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Residues in contact with LEU 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B LEU* 3.7 34.1 - - + +
33B VAL* 3.8 23.1 - - + -
56B PHE* 3.6 29.2 - - + -
78B PHE* 4.4 2.2 - - + -
89B LEU* 3.5 32.8 - - + +
91B ALA* 4.0 14.4 - - + -
101B TYR 2.9 22.1 + - - +
102B VAL* 3.8 2.7 - - - +
104B ALA* 1.3 74.2 - - - +
106B ALA* 1.3 63.9 + - - +
108B VAL* 3.1 16.4 + - - +
109B LEU* 2.9 21.2 - - + +
206B LEU* 5.6 1.6 - - + -
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Residues in contact with ALA 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B VAL 2.9 18.6 + - - +
103B ASN* 3.5 8.5 - - - +
105B LEU* 1.3 75.7 - - - +
107B ASP* 1.3 65.7 + - - +
109B LEU* 2.8 20.6 + - - +
110B TYR* 3.0 15.9 + - - +
204B SER* 4.3 1.6 - - - +
205B LEU* 4.2 12.1 - - + +
206B LEU* 3.5 42.6 - - + +
209B LEU* 6.0 0.2 - - - +
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Residues in contact with ASP 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B THR* 3.0 34.3 + - + +
61B THR* 3.4 16.8 + - - -
62B ARG* 3.8 15.0 + - - +
103B ASN 2.8 22.8 + - - +
104B ALA* 3.2 9.4 - - - +
106B ALA* 1.3 72.1 - - - +
108B VAL* 1.3 56.9 + - - +
110B TYR* 4.8 2.2 - - - -
111B LYS* 3.0 51.9 + - - +
205B LEU* 4.3 14.1 - - - +
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Residues in contact with VAL 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B ASN* 4.0 18.3 + - + +
56B PHE* 3.9 45.1 - - + +
59B THR* 4.2 11.7 - - + -
62B ARG* 6.3 0.4 - - - +
67B LEU* 4.8 7.0 - - + -
89B LEU* 4.3 10.8 - - + -
104B ALA 3.2 15.7 - - - +
105B LEU* 3.2 9.2 - - - +
106B ALA 2.9 1.4 + - - -
107B ASP* 1.3 76.9 - - - +
109B LEU* 1.3 64.1 + - + +
112B THR* 3.1 48.7 + - + -
180B TYR* 6.0 0.2 - - - -
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Residues in contact with LEU 109 (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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33B VAL* 4.3 14.6 - - + -
35B VAL* 4.1 8.1 - - + -
89B LEU* 3.9 18.4 - - + -
105B LEU* 2.9 33.6 + - + +
106B ALA* 2.8 11.7 + - - +
108B VAL* 1.3 77.5 - - - +
110B TYR* 1.3 63.4 + - - +
112B THR* 4.8 2.3 + - - -
180B TYR* 3.3 60.7 - - + +
185B LEU* 3.7 28.3 - - + -
206B LEU* 4.7 4.7 - - + -
209B LEU* 4.4 16.5 - - + +
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Residues in contact with TYR 110 (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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106B ALA 3.0 14.1 + - - +
107B ASP 4.3 2.2 - - - +
109B LEU* 1.3 81.8 - - - +
111B LYS* 1.3 68.8 + - + +
112B THR 3.9 1.1 + - - -
205B LEU* 3.5 45.1 - - + +
208B THR* 4.3 32.8 + - + +
209B LEU* 3.9 23.3 - - + -
210B PRO* 5.1 5.4 - - + -
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Residues in contact with LYS 111 (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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59B THR* 3.2 1.9 - - - +
60B ASN* 2.9 50.7 + - - +
61B THR* 4.1 24.8 - - - +
107B ASP* 3.0 45.5 + - - +
110B TYR* 1.3 88.1 - - + +
112B THR* 1.3 65.6 + - - +
205B LEU* 3.7 26.6 - - + +
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Residues in contact with THR 112 (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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54B PHE* 4.6 8.5 - - - +
55B ASN* 5.0 4.0 + - - +
56B PHE 4.5 9.6 - - - +
57B GLN* 4.6 5.8 - - + +
58B ASN 3.3 13.2 - - - +
59B THR* 3.9 7.6 - - + +
60B ASN* 4.6 0.9 + - - +
107B ASP 4.1 0.2 + - - -
108B VAL* 3.1 44.0 + - + +
109B LEU 4.8 2.4 + - - -
110B TYR 3.9 1.4 + - - -
111B LYS* 1.3 75.0 - - - +
113B ALA* 1.3 56.8 + - - +
114B PHE* 2.8 54.3 - - + -
180B TYR* 5.8 2.6 - - - -
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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