Contacts of the helix formed by residues 88 - 102 (chain B) in PDB entry 2IK8
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 88 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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182A THR* 3.6 39.3 + - - +
83B LEU* 3.0 34.4 + - - +
86B GLU* 4.1 10.5 + - - +
87B PHE* 1.3 77.8 - - - +
89B GLU* 1.3 63.9 + - - +
90B GLU* 3.2 13.3 + - - -
91B ASN* 3.5 22.0 + - - +
167B SER* 4.6 0.5 + - - -
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Residues in contact with GLU 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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80B HIS* 3.8 19.0 + - + +
83B LEU* 3.6 15.4 + - + +
84B LYS* 4.1 33.3 - - + +
87B PHE* 3.3 15.7 - - - -
88B SER* 1.3 81.0 + - - +
90B GLU* 1.3 70.0 + - + +
91B ASN 3.1 4.4 + - - -
92B LEU* 3.2 14.1 + - - +
93B GLU* 3.2 29.4 + - - +
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Residues in contact with GLU 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A THR* 4.0 1.6 + - - -
207A GLU* 4.8 0.7 - - - +
210A LYS* 2.9 40.9 + - - -
87B PHE 3.8 4.2 - - - +
88B SER* 3.2 4.8 - - - -
89B GLU* 1.3 85.6 + - + +
91B ASN* 1.3 88.1 + - - +
93B GLU* 3.7 10.5 - - - +
94B PHE* 3.1 25.5 + - - +
121B PHE* 3.9 3.0 - - - -
128B LYS* 3.5 40.6 - - + +
129B GLU 3.8 13.5 - - - +
130B VAL* 3.9 9.3 - - + +
131B ASN 5.3 0.5 + - - -
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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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182A THR* 3.1 39.3 + - - +
83B LEU* 5.6 0.4 - - - +
88B SER* 3.5 15.2 + - - +
90B GLU* 1.3 90.5 + - - +
92B LEU* 1.3 63.2 + - - +
94B PHE* 3.4 1.0 + - - +
95B TRP* 3.1 18.2 + - - +
130B VAL* 4.0 17.2 - - - +
131B ASN 4.5 1.4 + - - -
159B THR* 3.4 22.0 - - + +
162B LEU* 3.8 20.3 - - - +
163B MET* 3.8 21.9 - - + +
167B SER* 5.5 0.4 + - - -
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Residues in contact with LEU 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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70B LEU* 4.0 25.8 - - + -
76B VAL* 3.7 32.8 - - + +
79B PHE* 3.8 15.3 - - + -
80B HIS* 3.9 26.9 - - + -
83B LEU* 3.6 17.2 - - + +
88B SER 4.4 0.4 + - - -
89B GLU 3.2 6.4 + - - +
91B ASN* 1.3 79.2 - - - +
93B GLU* 1.3 64.1 + - - +
95B TRP* 3.3 8.2 + - + +
96B LEU* 3.0 39.8 + - + +
163B MET* 3.6 12.7 - - - -
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Residues in contact with GLU 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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80B HIS* 3.3 29.9 + - + +
89B GLU* 3.2 27.8 + - - +
90B GLU* 3.7 8.8 - - - +
91B ASN 3.2 0.2 - - - -
92B LEU* 1.3 73.6 - - - +
94B PHE* 1.3 55.7 + - - +
96B LEU* 2.9 13.5 + - + +
97B ALA* 2.7 33.4 + - - +
121B PHE* 4.0 11.2 - - + -
128B LYS* 3.2 40.3 + - - +
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Residues in contact with PHE 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 GLU 3.1 14.7 + - - +
91B ASN 3.7 2.5 - - - +
93B GLU* 1.3 77.6 - - - +
95B TRP* 1.3 55.7 + - - +
97B ALA* 2.8 5.9 + - - +
98B CYS* 2.7 53.7 + - - -
117B ILE* 3.4 24.7 - - + -
121B PHE* 3.5 39.3 - + + -
122B ILE* 3.4 27.1 - - + -
130B VAL* 4.1 9.2 - - + -
152B PHE* 3.7 10.3 - + + -
155B ALA* 3.7 31.4 - - + -
156B GLN* 4.1 2.2 - - - -
159B THR* 3.7 21.3 - - + -
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Residues in contact with TRP 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B LEU* 3.7 51.6 - - + -
76B VAL* 5.8 0.2 - - + -
91B ASN 3.1 11.6 + - - +
92B LEU* 3.5 18.2 - - + +
93B GLU 3.2 0.2 - - - -
94B PHE* 1.3 80.8 - - - +
96B LEU* 1.3 89.2 + - + +
98B CYS* 3.5 7.3 + - - +
99B GLU* 3.3 45.3 + - + +
156B GLN* 3.0 46.1 - - + +
159B THR* 4.7 4.3 - - + -
160B ARG* 4.3 25.9 - - + +
163B MET* 4.3 11.2 - - + -
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Residues in contact with LEU 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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70B LEU 5.4 0.7 - - - +
76B VAL* 3.9 27.1 - - + -
80B HIS* 5.6 4.0 - - + -
92B LEU* 3.0 34.4 + - + +
93B GLU* 2.9 12.1 + - + +
95B TRP* 1.3 99.6 - - + +
97B ALA* 1.3 62.7 + - - +
98B CYS 3.2 0.4 - - - -
99B GLU* 3.4 6.1 + - + +
100B GLU* 3.3 26.7 + - - +
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Residues in contact with ALA 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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93B GLU 2.7 15.8 + - - +
94B PHE 3.2 12.1 - - - +
96B LEU* 1.3 72.2 - - - +
98B CYS* 1.3 56.0 + - - +
100B GLU* 3.6 5.1 + - - +
101B PHE* 3.1 28.2 + - - +
113B ARG* 5.8 0.2 - - - +
117B ILE* 3.4 21.3 - - + +
121B PHE* 3.9 22.2 - - + -
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Residues in contact with CYS 98 (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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94B PHE* 2.7 58.1 + - - +
95B TRP 3.7 6.3 - - - +
96B LEU 3.2 0.2 - - - -
97B ALA* 1.3 73.1 - - - +
99B GLU* 1.3 62.2 + - - +
101B PHE* 3.7 8.8 - - + +
102B LYS* 3.3 28.9 + - - +
117B ILE* 4.7 1.1 - - - -
152B PHE* 3.5 24.7 - - + -
156B GLN* 3.6 27.3 - - + +
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Residues in contact with GLU 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 TRP* 3.3 47.1 + - + +
96B LEU* 3.4 8.7 + - + +
98B CYS* 1.3 74.5 - - - +
100B GLU* 1.3 63.6 + - - +
102B LYS* 3.1 37.2 + - - +
103B LYS* 3.2 30.7 - - - +
156B GLN* 3.2 12.7 + - - +
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Residues in contact with GLU 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 LEU 3.3 12.8 + - - +
97B ALA* 3.8 9.4 - - - +
99B GLU* 1.3 76.8 - - - +
101B PHE* 1.3 65.5 + - - +
103B LYS* 3.0 30.1 + - + +
104B ILE* 3.9 6.5 + - - +
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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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97B ALA 3.1 17.4 + - - +
98B CYS* 3.7 8.3 - - + +
100B GLU* 1.3 79.2 - - - +
102B LYS* 1.3 61.6 + - - +
104B ILE* 3.2 30.3 + - + +
110B LEU* 3.4 30.9 - - + +
113B ARG* 3.6 24.0 - - + -
114B ALA* 3.5 39.0 - - + -
117B ILE* 3.6 15.3 - - + -
147B ALA* 4.5 0.9 - - + -
148B THR 3.3 27.4 - - - -
149B ALA 3.7 13.7 - - - -
151B CYS* 4.1 11.2 - - + -
152B PHE* 4.2 13.0 - + + -
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Residues in contact with LYS 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 CYS 3.3 17.2 + - - +
99B GLU* 3.1 42.6 + - - +
100B GLU 3.1 0.2 + - - -
101B PHE* 1.3 77.1 - - + +
103B LYS* 1.3 66.2 + - + +
104B ILE 3.2 4.7 + - - +
149B ALA* 3.7 40.1 - - + +
153B ASP* 3.9 13.9 + - - -
156B GLN* 3.3 20.0 + - - +
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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