Contacts of the helix formed by residues 107 - 119 (chain B) in PDB entry 1CI1
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 ASN 107 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100B ARG* 2.7 33.5 + - - +
106B THR* 1.3 76.7 - - - +
108B GLU* 1.3 64.0 + - - +
110B VAL* 3.4 2.8 + - - +
111B ALA* 2.9 30.9 + - - +
146B THR* 3.8 26.5 + - - +
147B GLN* 3.4 26.9 - - - +
150B ALA* 4.0 16.7 - - + +
151B VAL* 5.4 0.9 - - - +
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Residues in contact with GLU 108 (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 THR* 2.8 33.1 + - - +
107B ASN* 1.3 82.8 + - - +
109B ILE* 1.3 67.2 + - + +
111B ALA* 3.5 6.0 + - - +
112B GLU* 3.2 23.7 + - - +
150B ALA* 5.6 0.9 - - - -
154B LYS* 4.3 6.4 - - - +
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Residues in contact with ILE 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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104B GLY 4.0 10.3 - - - +
105B GLU* 4.4 17.9 - - + +
106B THR* 3.3 30.0 + - + +
107B ASN 3.3 0.2 - - - -
108B GLU* 1.3 83.1 - - + +
110B VAL* 1.3 61.7 + - - +
112B GLU* 3.4 5.9 + - - +
113B LYS* 3.1 43.6 + - - +
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Residues in contact with VAL 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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94B LEU* 4.4 1.1 - - + -
95B GLY* 3.7 32.3 - - - +
100B ARG* 3.9 24.0 - - - +
105B GLU* 3.7 28.9 - - + +
106B THR 3.0 18.6 + - - +
107B ASN* 3.9 3.8 - - - +
109B ILE* 1.3 77.6 - - - +
111B ALA* 1.3 62.4 + - - +
113B LYS* 3.4 8.5 + - - +
114B VAL* 3.0 23.9 + - + +
126B VAL* 4.1 17.3 - - + -
151B VAL* 5.1 3.4 - - + -
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Residues in contact with ALA 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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107B ASN 2.9 18.5 + - - +
108B GLU* 3.9 3.1 - - - +
109B ILE 3.3 0.2 - - - -
110B VAL* 1.3 73.8 - - - +
112B GLU* 1.3 61.2 + - - +
114B VAL* 3.2 2.2 + - - +
115B ALA* 2.8 31.2 + - - +
150B ALA* 3.6 21.5 - - + +
151B VAL* 3.8 20.9 - - + +
154B LYS* 3.4 25.1 - - + +
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Residues in contact with GLU 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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70B THR* 4.0 9.9 - - + +
108B GLU 3.2 17.2 + - - +
109B ILE* 3.8 5.8 - - - +
111B ALA* 1.3 76.0 - - - +
113B LYS* 1.3 57.7 + - - +
115B ALA* 3.4 3.9 + - - +
116B GLN* 2.8 73.0 + - + +
154B LYS* 2.5 33.6 + - - +
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Residues in contact with LYS 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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67B ASN* 2.9 27.9 + - - +
68B ALA 3.1 23.4 + - - +
69B ILE* 4.4 14.2 - - - +
70B THR* 3.7 18.8 - - + +
78B GLU* 5.4 0.2 + - - -
81B LEU* 4.3 3.9 - - - +
94B LEU* 3.6 24.2 - - + +
99B ARG* 5.5 0.2 - - - +
105B GLU* 3.0 30.6 + - - +
109B ILE* 3.1 29.6 + - + +
110B VAL* 3.5 11.9 - - - +
112B GLU* 1.3 76.9 - - - +
114B VAL* 1.3 55.8 + - - +
116B GLN* 4.0 1.6 - - - +
117B ALA* 3.0 28.2 + - - +
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Residues in contact with VAL 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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94B LEU* 3.9 22.9 - - + -
110B VAL* 3.0 18.6 + - + +
111B ALA* 3.7 6.3 - - - +
113B LYS* 1.3 73.8 - - - +
115B ALA* 1.3 67.5 + - - +
117B ALA* 3.2 2.6 + - - +
118B CYS* 2.9 38.0 + - - -
124B VAL* 4.2 6.7 - - + -
126B VAL* 3.7 43.1 - - + -
151B VAL* 4.7 8.5 - - + -
155B LEU* 4.4 16.6 - - + -
163B VAL* 5.0 0.9 - - + -
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Residues in contact with ALA 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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111B ALA 2.8 21.2 + - - +
112B GLU* 3.7 12.1 - - - +
114B VAL* 1.3 73.4 - - - +
116B GLN* 1.3 62.5 + - - +
118B CYS* 3.4 2.9 + - - +
119B ALA* 3.0 27.9 + - - +
154B LYS* 3.9 33.2 - - + +
155B LEU* 3.8 13.8 - - - +
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Residues in contact with GLN 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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70B THR* 3.5 31.4 + - + +
81B LEU* 3.7 11.1 - - + +
112B GLU* 2.8 42.6 + - + +
113B LYS 4.0 0.2 - - - +
115B ALA* 1.3 79.2 - - - +
117B ALA* 1.3 65.0 + - - +
119B ALA* 3.3 12.8 + - - +
120B ALA* 3.0 23.7 + - - +
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Residues in contact with ALA 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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81B LEU* 3.5 27.5 - - + +
92B VAL* 4.2 2.0 - - + -
94B LEU* 4.1 8.3 - - + -
113B LYS 3.0 19.2 + - - +
114B VAL 3.2 4.7 + - - +
116B GLN* 1.3 75.8 - - - +
118B CYS* 1.3 61.2 - - - +
120B ALA 3.2 5.9 + - - -
121B GLY 3.4 0.5 + - - -
122B PHE* 3.0 37.1 + - + +
124B VAL* 3.8 17.9 - - + -
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Residues in contact with CYS 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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114B VAL* 2.9 20.3 + - - +
115B ALA 3.6 5.2 - - - +
117B ALA* 1.3 71.7 - - - +
119B ALA* 1.3 65.7 + - - +
120B ALA 3.0 1.6 - - - -
121B GLY 3.0 0.7 + - - -
122B PHE 4.3 5.2 - - - -
124B VAL* 3.9 13.5 - - - -
155B LEU* 4.0 18.6 - - + -
159B ALA* 4.3 17.3 - - + -
162B ARG* 2.5 41.9 + - - +
163B VAL* 3.9 28.0 - - - -
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Residues in contact with ALA 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 ALA 3.0 16.4 + - - +
116B GLN* 3.3 18.4 + - - +
118B CYS* 1.3 76.9 - - - +
120B ALA* 1.3 59.4 + - - +
121B GLY 3.6 0.3 + - - -
162B ARG* 5.2 0.4 - - - +
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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