Contacts of the helix formed by residues 111 - 120 (chain I) in PDB entry 7C97
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 TYR 111 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20I ILE* 4.1 8.9 - - + +
21I TYR* 3.3 47.8 - + - -
24I GLN* 2.4 27.2 + - - -
72I SER* 5.2 0.2 + - - -
106I ILE 3.0 5.6 + - - -
107I GLU* 3.4 49.8 - - + +
109I ASP 3.6 0.6 - - - +
110I TRP* 1.3 75.4 - - - +
112I THR* 1.3 59.8 + - + +
113I LEU 3.1 2.0 - - - -
114I MET* 2.6 29.7 + - + +
115I ASN* 3.1 21.2 + - - +
160I TYR* 4.2 2.6 - + - -
164I LEU* 3.3 45.5 - - + -
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Residues in contact with THR 112 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107I GLU 5.0 5.2 - - - +
108I LYS* 4.3 19.2 + - + +
109I ASP 4.0 11.3 + - - +
111I TYR* 1.3 78.2 - - + +
113I LEU* 1.3 62.0 + - - +
114I MET 3.2 0.2 - - - -
115I ASN* 3.7 13.5 - - + +
116I THR* 2.3 42.8 + - - -
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Residues in contact with LEU 113 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109I ASP* 3.8 18.6 - - - +
110I TRP* 4.2 7.3 - - + +
111I TYR 3.0 1.0 + - - -
112I THR* 1.3 85.2 - - - +
114I MET* 1.3 62.2 + - - +
116I THR* 4.4 4.5 - - - +
117I ILE* 3.0 32.9 + - - +
128I ALA* 3.7 18.6 - - + +
131I GLN* 4.2 17.0 - - + +
132I LEU* 3.3 60.3 - - + +
135I GLU* 4.6 5.8 - - - +
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Residues in contact with MET 114 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110I TRP 3.4 19.5 - - - +
111I TYR* 2.6 18.9 + - + +
113I LEU* 1.3 75.1 - - - +
115I ASN* 1.3 59.1 + - - +
117I ILE* 3.4 5.4 + - - +
118I ILE* 3.0 28.2 + - - +
132I LEU* 4.2 20.6 - - - -
164I LEU* 4.0 28.3 - - + +
167I ARG* 4.0 38.4 - - + +
171I LEU* 4.5 25.3 - - + +
173I ILE* 5.3 3.1 - - + -
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Residues in contact with ASN 115 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111I TYR* 3.1 36.2 + - - +
112I THR* 3.6 11.3 + - - +
114I MET* 1.3 74.1 - - - +
116I THR* 1.3 61.0 + - - +
118I ILE* 2.9 32.9 + - + +
119I ASN* 3.0 15.5 + - - +
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Residues in contact with THR 116 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112I THR* 2.3 30.5 + - - -
113I LEU* 4.4 6.3 - - - +
115I ASN* 1.3 76.5 - - - +
117I ILE* 1.3 55.7 + - - +
119I ASN 4.5 1.3 - - - +
120I GLY* 2.5 40.4 + - - +
124I GLU* 3.2 33.3 - - + +
128I ALA* 5.0 8.7 - - + -
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Residues in contact with ILE 117 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113I LEU 3.0 20.9 + - - +
114I MET* 3.7 5.2 - - - +
115I ASN 3.2 0.4 - - - -
116I THR* 1.3 77.4 - - - +
118I ILE* 1.3 59.3 + - - +
119I ASN 3.4 0.2 - - - -
120I GLY 4.5 2.5 + - - +
125I ALA* 3.8 35.8 - - + +
128I ALA* 3.3 28.9 - - + -
129I ARG* 3.9 11.7 - - + +
132I LEU* 4.9 3.1 - - + -
171I LEU* 3.3 48.0 - - + +
172I GLY 5.7 0.2 - - - +
173I ILE* 4.7 12.6 - - + -
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Residues in contact with ILE 118 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114I MET 3.0 13.1 + - - +
115I ASN* 2.9 27.4 + - + +
117I ILE* 1.3 80.2 - - - +
119I ASN* 1.3 85.7 + - - +
120I GLY 3.8 0.2 - - - -
171I LEU* 4.3 15.5 - - + -
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Residues in contact with ASN 119 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115I ASN* 3.0 8.9 + - - +
116I THR* 3.4 2.9 - - - -
118I ILE* 1.3 112.0 - - + +
120I GLY* 1.3 59.2 + - - +
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Residues in contact with GLY 120 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116I THR* 2.5 25.0 + - - -
117I ILE* 4.3 3.5 + - - +
118I ILE 3.8 1.0 - - - -
119I ASN* 1.3 75.7 - - - +
121I SER* 1.3 67.9 + - - +
124I GLU* 4.3 15.5 - - - -
125I ALA* 5.1 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