Contacts of the helix formed by residues 111 - 126 (chain B) in PDB entry 1IC8
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 111 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110B GLU* 1.3 77.4 + - - +
112B PRO* 1.3 73.5 - - - +
113B TRP* 2.6 36.2 + - - +
114B ARG* 2.7 39.8 + - + +
115B VAL* 3.1 12.7 + - - +
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Residues in contact with PRO 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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110B GLU 3.1 6.4 - - - +
111B ASP* 1.3 88.8 - - - +
113B TRP* 1.3 57.3 + - - +
115B VAL* 3.5 4.9 - - + +
116B ALA* 3.1 23.6 + - - +
147B HIS* 3.7 12.8 + - - +
154B MET 6.3 0.7 - - - +
159B ARG* 3.4 48.2 - - - +
163B TYR* 3.9 7.2 + - - +
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Residues in contact with TRP 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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111B ASP* 2.6 17.9 + - - +
112B PRO* 1.3 72.6 - - - +
114B ARG* 1.3 101.2 + - - +
115B VAL 3.0 1.3 - - - -
116B ALA* 2.9 15.2 + - + +
117B LYS* 2.9 56.7 + - + +
147B HIS* 4.3 6.0 + + + -
148B LEU 4.7 6.5 + - - -
149B ASN 5.4 2.7 - - - -
150B LYS* 4.2 23.9 + - - +
151B GLY* 4.7 9.4 - - - -
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Residues in contact with ARG 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 GLU* 5.0 6.7 - - - +
111B ASP* 2.7 35.6 + - + +
113B TRP* 1.3 102.5 - - - +
115B VAL* 1.3 63.4 + - + +
117B LYS* 3.1 39.3 + - - +
118B MET* 3.1 37.2 + - + +
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Residues in contact with VAL 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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107B LEU* 3.5 51.4 - - + +
110B GLU* 4.0 9.0 - - + -
111B ASP 3.1 16.4 + - - +
112B PRO 3.5 6.7 - - - +
113B TRP 3.0 0.4 - - - -
114B ARG* 1.3 74.9 - - + +
116B ALA* 1.3 54.5 + - - +
118B MET* 2.8 16.5 + - + +
119B VAL* 2.7 38.0 + - + +
163B TYR* 3.3 36.6 - - + +
166B TYR* 5.5 0.7 - - + -
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Residues in contact with ALA 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 PRO 3.1 11.3 + - - +
113B TRP* 2.9 24.1 + - + +
115B VAL* 1.3 77.8 - - - +
117B LYS* 1.3 65.4 + - - +
119B VAL* 2.6 7.7 + - - +
120B LYS* 2.6 25.5 + - - +
147B HIS* 4.1 17.3 - - + +
148B LEU* 3.6 28.6 - - + +
162B LEU* 5.8 1.1 - - - -
163B TYR* 5.4 0.6 - - - -
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Residues in contact with LYS 117 (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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113B TRP* 2.9 62.5 + - + +
114B ARG* 3.1 41.2 + - - +
116B ALA* 1.3 71.2 - - - +
118B MET* 1.3 63.4 + - - +
120B LYS* 3.5 13.4 - - + +
121B SER* 2.9 31.5 + - - +
148B LEU 5.4 0.4 - - - +
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Residues in contact with MET 118 (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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107B LEU* 4.5 19.5 - - + -
110B GLU* 5.2 9.6 - - - +
114B ARG* 3.1 31.3 + - + +
115B VAL* 2.8 19.3 + - + +
117B LYS* 1.3 81.9 - - + +
119B VAL* 1.3 61.0 + - - +
121B SER* 3.2 5.4 + - - -
122B TYR* 3.0 22.3 + - - +
166B TYR* 3.8 20.9 + - + +
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Residues in contact with VAL 119 (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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115B VAL* 2.7 24.5 + - + +
116B ALA* 2.6 12.6 + - - +
118B MET* 1.3 73.0 - - - +
120B LYS* 1.3 55.6 + - - +
122B TYR* 3.4 2.8 + - - +
123B LEU* 3.0 44.3 + - + +
148B LEU* 4.3 16.2 - - + -
162B LEU* 4.5 20.2 - - + -
163B TYR* 4.6 8.5 - - + -
165B TRP* 4.8 6.1 - - + -
166B TYR* 3.8 43.7 - - + -
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Residues in contact with LYS 120 (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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116B ALA 2.6 19.7 + - - +
117B LYS* 3.5 13.7 - - + +
119B VAL* 1.3 70.5 - - - +
121B SER* 1.3 59.1 + - - +
123B LEU* 3.1 11.1 + - - +
124B GLN* 2.6 79.0 + - + +
148B LEU* 3.4 32.5 - - + +
149B ASN* 4.0 20.0 - - - +
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Residues in contact with SER 121 (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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117B LYS* 2.9 20.5 + - - +
118B MET* 3.7 5.1 - - - -
120B LYS* 1.3 77.3 + - - +
122B TYR* 1.3 64.8 + - - +
124B GLN* 4.2 3.9 + - - -
125B GLN* 2.7 47.6 + - - +
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Residues in contact with TYR 122 (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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118B MET 3.0 9.0 + - - +
119B VAL 3.6 3.1 - - - +
121B SER* 1.3 78.4 - - - +
123B LEU* 1.3 68.1 + - + +
125B GLN* 4.7 0.9 - - - -
126B HIS* 2.9 53.8 + + - +
128B ILE* 3.9 25.4 - - + -
165B TRP* 5.5 0.7 - + - -
166B TYR* 3.6 33.7 - + + +
169B LYS* 4.1 13.7 - - + -
170B GLN* 4.2 32.4 - - + -
172B GLU* 2.5 37.8 + - - -
173B VAL* 4.8 4.8 - - + +
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Residues in contact with LEU 123 (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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119B VAL* 3.0 27.5 + - + +
120B LYS* 3.5 5.8 - - - +
122B TYR* 1.3 79.4 - - + +
124B GLN* 1.3 62.6 + - + +
127B ASN* 2.9 17.3 + - - -
128B ILE* 3.0 42.5 + - + +
129B PRO 5.5 0.2 - - - +
130B GLN* 5.2 11.4 - - + -
133B VAL* 4.1 13.2 - - + -
144B LEU* 6.0 0.2 - - + -
148B LEU* 3.8 28.5 - - + -
162B LEU* 6.5 0.4 - - + -
165B TRP* 3.4 34.3 - - + -
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Residues in contact with GLN 124 (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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120B LYS* 2.6 67.1 + - + +
121B SER* 4.7 2.8 + - - -
123B LEU* 1.3 73.4 - - + +
125B GLN* 1.3 74.9 + - - +
127B ASN* 2.7 28.1 + - - +
208B PRO* 5.6 5.4 - - - +
243B GLN* 4.5 1.4 + - - -
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Residues in contact with GLN 125 (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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121B SER* 2.7 35.8 + - - +
122B TYR* 3.8 3.4 - - - +
124B GLN* 1.3 91.4 + - - +
126B HIS* 1.3 69.9 + - + +
127B ASN 3.3 2.1 + - - -
208B PRO* 5.5 2.9 - - - +
243B GLN* 2.9 51.0 + - - +
244B ARG* 3.4 19.6 + - + +
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Residues in contact with HIS 126 (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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122B TYR* 2.9 54.2 + + - +
125B GLN* 1.3 82.1 - - + +
127B ASN* 1.3 72.5 + - - +
128B ILE* 3.2 22.5 + - + +
172B GLU* 3.8 18.4 + - - +
176B GLN* 4.5 10.0 + - + -
244B ARG* 3.6 53.0 + - + +
246B VAL* 5.4 1.1 - - + -
257B ASN* 3.7 4.0 - - - +
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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