Contacts of the helix formed by residues 110 - 121 (chain A) in PDB entry 3IIV
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 PRO 110 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106A ALA 2.9 16.8 - - - +
107A VAL 3.8 4.7 - - - +
108A GLU 3.7 1.6 - - - -
109A ASN* 1.3 86.7 - - - +
111A SER* 1.3 62.0 + - - +
112A LEU 3.0 0.2 - - - -
113A ILE* 3.0 27.4 + - + +
114A THR 3.8 0.2 + - - -
156A TRP* 4.0 22.7 - - + -
159A GLU* 4.8 2.7 - - + -
163A ARG* 3.6 32.9 - - + +
250B LEU 4.3 1.6 - - - +
251B GLU* 3.6 36.6 - - + +
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Residues in contact with SER 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A ASN* 3.0 12.9 + - - -
110A PRO* 1.3 77.9 - - - +
112A LEU* 1.3 58.4 + - - +
114A THR* 3.1 9.6 + - - -
115A GLN* 2.9 44.2 + - - +
163A ARG* 3.4 10.9 + - - +
235B ARG* 4.2 10.0 + - - -
250B LEU 5.0 0.2 + - - -
253B LEU* 3.1 34.1 + - - +
254B GLY* 3.8 4.2 - - - -
257B GLU* 5.8 0.2 - - - -
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Residues in contact with LEU 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A TYR 3.7 24.9 - - - +
85A ASP* 3.6 5.2 - - - +
86A PHE* 3.4 32.1 - - - +
102A ILE* 4.0 24.9 - - + -
105A ALA* 3.8 20.9 - - + +
106A ALA* 4.9 0.9 - - - -
109A ASN* 2.9 25.2 + - - +
111A SER* 1.3 78.7 - - - +
113A ILE* 1.3 64.4 + - - +
115A GLN* 3.3 15.9 + - - +
116A ILE* 3.1 41.5 + - + +
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Residues in contact with ILE 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A ILE* 3.7 24.0 - - + -
106A ALA* 4.0 8.3 - - + -
110A PRO* 3.0 15.6 + - + +
112A LEU* 1.3 78.0 - - - +
114A THR* 1.3 58.2 + - - +
116A ILE* 3.4 2.3 + - - +
117A ALA* 3.0 27.5 + - - +
125A VAL* 4.1 7.0 - - + +
127A VAL* 4.1 17.0 - - + -
156A TRP* 3.9 27.1 - - + -
160A VAL* 4.2 9.4 - - + -
163A ARG* 3.6 20.4 - - + +
164A GLY 3.6 3.6 - - - -
165A ALA* 3.2 36.6 - - + +
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Residues in contact with THR 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A SER* 3.1 11.6 + - - -
113A ILE* 1.3 73.7 - - - +
115A GLN* 1.3 58.1 + - - +
117A ALA* 3.9 0.2 - - - +
118A GLN* 2.7 46.9 + - + +
163A ARG* 2.7 42.5 + - - +
254B GLY 5.9 0.2 - - - -
257B GLU* 3.8 17.9 + - + +
258B HIS 3.5 35.9 - - - +
259B HIS* 3.7 5.8 - - - +
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Residues in contact with GLN 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A PHE* 3.3 44.0 + - + +
109A ASN* 4.5 8.5 - - - +
111A SER* 2.9 36.8 + - - +
112A LEU* 3.6 16.4 - - - +
114A THR* 1.3 76.8 - - - +
116A ILE* 1.3 65.0 + - - +
118A GLN* 3.5 24.8 + - - +
119A THR* 3.6 3.1 + - - -
235B ARG* 6.0 1.0 - - - +
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Residues in contact with ILE 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A PHE* 3.8 13.2 - - + -
89A ALA* 3.7 25.6 - - + -
93A ILE* 4.1 6.1 - - + -
100A VAL* 4.0 22.2 - - + -
102A ILE* 4.1 18.8 - - + -
112A LEU* 3.1 39.5 + - + +
113A ILE 3.9 0.2 - - - +
115A GLN* 1.3 75.9 - - - +
117A ALA* 1.3 57.5 + - - +
119A THR 3.2 2.6 + - - -
120A PHE* 2.9 46.2 + - + +
124A ALA 5.0 0.4 - - - +
125A VAL* 3.6 21.3 - - + -
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Residues in contact with ALA 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A ILE 3.0 16.6 + - - +
116A ILE* 1.3 73.7 - - - +
118A GLN* 1.3 63.3 + - - +
121A GLY* 2.8 36.5 + - - -
122A SER* 3.9 10.5 - - - +
125A VAL* 3.8 3.3 - - + +
164A GLY* 3.4 27.1 - - - +
259B HIS* 3.7 24.7 - - + +
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Residues in contact with GLN 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A THR* 2.7 30.8 + - + +
115A GLN* 3.6 20.5 + - - +
116A ILE 3.3 0.4 - - - -
117A ALA* 1.3 75.1 - - - +
119A THR* 1.3 60.8 + - - +
121A GLY 5.0 0.2 + - - -
258B HIS 4.0 8.8 - - - +
259B HIS* 3.8 26.5 - - - +
260B HIS 5.0 0.6 - - - +
261B HIS* 3.1 45.3 + - - +
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Residues in contact with THR 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A PHE* 3.7 22.3 - - + -
115A GLN 3.6 2.0 + - - -
116A ILE 3.2 3.1 + - - -
118A GLN* 1.3 79.5 - - - +
120A PHE* 1.3 98.3 + - + +
121A GLY 3.6 0.8 + - - -
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Residues in contact with PHE 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A PHE* 3.9 9.9 - + - -
90A SER* 3.4 46.4 - - - -
93A ILE* 3.5 37.2 - - + -
94A LEU* 4.1 17.9 - - + -
116A ILE* 2.9 23.5 + - + +
119A THR* 1.3 99.5 - - + +
121A GLY* 1.3 61.4 + - - +
123A GLN* 4.2 12.8 - - - +
124A ALA* 3.7 27.0 - - + +
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Residues in contact with GLY 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A ALA* 2.8 27.0 + - - -
118A GLN 4.7 0.2 - - - -
119A THR 3.6 1.2 - - - -
120A PHE* 1.3 81.9 - - - +
122A SER* 1.3 65.5 + - - -
123A GLN* 3.1 9.4 - - - -
124A ALA* 3.2 11.6 + - - +
125A VAL* 4.0 1.9 - - - +
259B HIS* 5.4 1.1 - - - -
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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