Contacts of the helix formed by residues 99 - 116 (chain B) in PDB entry 1OLY
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 THR 99 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217A THR* 4.3 11.9 - - - +
218A SER* 5.4 5.2 - - - +
97B ASP 5.9 0.2 - - - +
98B HIS* 1.4 71.0 - - - +
100B ASP* 1.4 61.7 + - - +
101B PHE* 3.6 7.5 + - - +
102B THR* 3.1 26.6 + - - -
103B LYS* 2.8 31.0 + - - -
134B GLN* 5.0 8.5 - - - +
137B ALA* 4.1 24.5 - - + +
141B THR* 3.9 7.3 + - - -
488B VIB 6.0 2.2 - - - -
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Residues in contact with ASP 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B ALA* 4.0 1.9 - - - +
46B ASP* 2.7 48.2 - - + +
69B ASN* 3.5 2.6 - - - +
70B GLY* 3.5 13.7 - - - -
71B ASP 3.2 17.9 + - - -
93B THR* 3.7 2.9 + - - +
99B THR* 1.4 72.0 - - - +
101B PHE* 1.3 59.9 + - - +
103B LYS* 2.7 21.8 + - - +
104B CYS* 2.8 32.1 + - - +
488B VIB 3.4 27.8 - - + +
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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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22B VAL* 4.4 7.4 - - + -
24B LEU* 3.0 36.3 - - + -
45B ALA* 4.3 2.8 - - - +
46B ASP* 4.9 0.4 + - - -
99B THR* 3.1 8.6 + - - +
100B ASP* 1.3 77.6 - - - +
102B THR* 1.3 60.3 + - - +
104B CYS* 3.2 11.6 + - - +
105B LEU* 3.2 35.9 + - + +
124B THR* 3.3 40.6 - - + -
138B SER* 4.4 8.3 - - - +
141B THR* 3.0 47.6 - - + +
142B LEU* 5.0 2.2 - - + -
153B ILE* 4.7 4.5 - - + -
155B ILE* 4.4 19.3 - - + -
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Residues in contact with THR 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 HIS* 4.6 12.5 - - + +
99B THR* 3.1 20.2 + - - -
101B PHE* 1.3 77.2 - - - +
103B LYS* 1.3 65.5 + - + +
105B LEU* 3.1 14.1 + - - +
106B LYS* 3.3 8.9 + - + +
141B THR* 3.2 25.5 + - + +
144B GLN* 2.9 31.4 + - + +
148B ILE* 3.7 23.4 - - + +
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Residues in contact with LYS 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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69B ASN* 3.5 2.8 - - - +
93B THR* 3.2 46.0 + - + +
95B ASP* 3.1 28.9 - - + -
98B HIS* 2.9 36.0 + - + -
99B THR 2.8 29.6 + - - +
100B ASP* 2.7 34.4 + - - +
102B THR* 1.3 78.4 - - + +
104B CYS* 1.3 63.4 + - - +
106B LYS* 3.1 11.0 + - + +
107B MET* 3.1 19.6 + - - +
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Residues in contact with CYS 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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22B VAL* 4.0 29.6 - - + -
43B ALA* 4.3 4.9 - - - -
44B CYS 4.2 4.7 - - - -
45B ALA* 4.0 7.6 - - + -
67B PHE* 3.9 15.9 - - - -
69B ASN* 2.7 37.4 + - - +
100B ASP 2.8 15.2 + - - +
101B PHE* 3.4 6.1 - - - +
102B THR 3.2 0.4 - - - -
103B LYS* 1.3 77.1 - - - +
105B LEU* 1.3 57.3 + - + +
107B MET* 3.1 3.7 + - - +
108B LEU* 2.8 25.7 + - - +
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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
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22B VAL* 4.5 18.6 - - + -
101B PHE* 3.2 30.7 + - + +
102B THR 3.1 7.0 + - - +
104B CYS* 1.3 76.6 - - + +
106B LYS* 1.3 59.0 + - - +
108B LEU* 3.2 9.4 + - + +
109B GLN* 2.9 28.9 + - - +
122B ILE* 4.5 11.9 - - + -
124B THR* 5.0 0.2 - - - +
141B THR* 3.4 31.2 - - + -
142B LEU* 6.1 0.2 - - + -
145B ALA* 4.1 8.1 - - + -
148B ILE* 3.8 17.2 - - + +
149B THR* 5.7 2.9 - - + +
153B ILE* 3.7 31.4 - - + -
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Residues in contact with LYS 106 (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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102B THR 3.3 7.7 + - - +
103B LYS* 3.1 14.1 + - + +
105B LEU* 1.3 79.2 - - - +
107B MET* 1.4 62.5 + - - +
109B GLN* 3.2 5.2 + - + +
110B LYS* 3.1 19.8 + - + +
148B ILE* 3.9 21.4 - - + +
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Residues in contact with MET 107 (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 PHE* 3.5 35.7 - - + -
69B ASN* 4.9 4.9 - - + -
89B GLU* 5.1 0.2 - - + -
91B ILE* 2.9 42.6 - - + -
103B LYS 3.1 7.7 + - - +
104B CYS* 3.1 10.3 + - - +
106B LYS* 1.4 77.2 - - - +
108B LEU* 1.3 63.6 + - - +
110B LYS* 3.0 28.8 + - - +
111B LYS* 2.9 55.1 + - + +
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Residues in contact with LEU 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B CYS* 4.1 20.0 - - + -
21B LEU 6.2 0.4 - - - +
22B VAL* 4.3 10.3 - - + -
41B LEU* 4.1 29.8 - - + -
43B ALA* 5.3 2.7 - - + -
67B PHE* 4.0 18.1 - - + -
104B CYS* 2.8 15.7 + - - +
105B LEU* 3.5 13.2 - - + +
107B MET* 1.3 77.4 - - - +
109B GLN* 1.3 61.3 + - - +
111B LYS* 3.1 3.0 + - - +
112B ILE* 2.9 36.1 + - + +
122B ILE* 3.5 48.2 - - + -
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Residues in contact with GLN 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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105B LEU 2.9 14.8 + - - +
106B LYS* 3.2 8.5 + - + +
108B LEU* 1.3 75.6 - - - +
110B LYS* 1.3 63.6 + - - +
112B ILE* 3.2 10.6 + - - +
113B GLU* 2.9 59.1 + - - +
148B ILE* 3.6 24.9 - - + +
149B THR* 2.6 31.3 + - - -
150B PRO* 4.4 7.7 - - - +
151B PHE* 4.0 16.7 - - - -
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Residues in contact with LYS 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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91B ILE* 5.4 4.6 - - - +
106B LYS 3.1 12.1 + - - +
107B MET* 3.0 36.5 + - - +
109B GLN* 1.3 76.9 - - - +
111B LYS* 1.3 52.8 + - - +
113B GLU* 3.1 13.9 + - - +
114B GLU* 2.8 64.6 + - + +
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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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41B LEU* 3.8 14.6 - - + -
66B GLU* 5.6 2.2 - - - -
67B PHE* 4.1 13.5 - - + -
89B GLU* 4.4 19.4 + - - +
107B MET* 2.9 51.2 + - + +
108B LEU* 3.5 9.4 - - - +
110B LYS* 1.3 78.0 - - - +
112B ILE* 1.3 58.0 + - - +
114B GLU* 3.2 19.4 + - - +
115B LYS* 2.9 76.3 + - + +
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Residues in contact with ILE 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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20B CYS* 4.4 5.8 - - - -
41B LEU* 5.4 0.2 - - + -
108B LEU* 2.9 47.2 + - + +
109B GLN* 3.6 21.8 - - - +
111B LYS* 1.3 76.8 - - - +
113B GLU* 1.3 52.0 + - - +
116B ASP* 2.6 30.1 + - - -
117B LEU* 2.9 47.3 + - + +
119B VAL* 4.2 23.1 - - + -
122B ILE* 4.8 6.1 - - + -
151B PHE* 4.4 23.3 - - + -
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Residues in contact with GLU 113 (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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109B GLN* 2.9 53.1 + - - +
110B LYS* 3.5 11.5 - - - +
112B ILE* 1.3 74.6 - - + +
114B GLU* 1.4 63.6 + - + +
116B ASP* 2.8 28.2 + - - +
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Residues in contact with GLU 114 (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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110B LYS* 2.8 58.6 + - + +
111B LYS* 3.7 21.6 + - - +
113B GLU* 1.4 74.9 - - + +
115B LYS* 1.3 62.8 + - + +
116B ASP* 3.8 8.0 - - - +
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Residues in contact with LYS 115 (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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41B LEU* 3.6 14.1 - - - +
66B GLU* 4.0 17.8 - - - +
111B LYS* 2.9 54.5 + - + +
114B GLU* 1.3 76.7 - - + +
116B ASP* 1.4 70.5 + - - +
117B LEU* 3.2 38.8 + - + +
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Residues in contact with ASP 116 (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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112B ILE 2.6 14.9 + - - -
113B GLU* 2.8 22.1 + - - +
114B GLU 3.8 7.0 - - - +
115B LYS* 1.4 77.1 - - - +
117B LEU* 1.4 62.7 + - - +
118B LYS* 3.8 1.6 + - - +
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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