Contacts of the helix formed by residues 108 - 121 (chain A) in PDB entry 1IV4
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 HIS 108 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A ILE* 3.8 36.7 - - + +
26A PRO* 3.8 25.6 - - + +
103A PRO* 5.8 1.1 - - + -
104A LYS 3.7 20.7 + - - -
105A LEU* 2.7 13.9 + - - +
107A PRO* 1.3 85.8 - - + +
109A ARG* 1.3 65.5 + - - +
110A LYS 3.3 2.5 - - - -
111A ALA* 3.1 13.3 + - + +
112A LEU* 2.9 38.1 + - + +
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Residues in contact with ARG 109 (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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105A LEU 3.2 3.6 + - - -
106A GLY* 3.0 23.6 + - - +
107A PRO 3.4 0.8 - - - -
108A HIS* 1.3 77.1 - - - +
110A LYS* 1.3 63.9 + - - +
112A LEU* 3.3 1.1 + - - +
113A VAL* 3.0 35.0 + - + +
129A LEU* 3.9 16.1 + - + +
131A PHE* 3.5 38.2 - - + -
1602A C5P 3.5 8.1 + - - -
255B GLY* 4.0 5.4 - - - -
256B ASP* 3.0 48.1 + - - +
259B LEU* 3.8 28.3 - - - +
1064D THR* 3.8 26.4 - - - +
1066D PRO* 5.6 1.8 - - - -
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Residues in contact with LYS 110 (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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107A PRO 5.2 1.7 + - - +
108A HIS 3.3 0.6 - - - -
109A ARG* 1.3 78.3 - - - +
111A ALA* 1.3 60.4 + - - +
113A VAL* 3.8 2.8 - - - +
114A ASP* 2.8 55.8 + - - +
1063D ASP* 5.6 1.6 - - - +
1064D THR* 5.7 6.2 + - - +
1069D ARG* 3.0 60.3 - - - +
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Residues in contact with ALA 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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23A LEU* 3.6 20.4 - - + +
108A HIS* 3.1 15.4 + - + +
110A LYS* 1.3 80.8 - - + +
112A LEU* 1.3 59.3 + - - +
114A ASP* 3.3 8.3 + - - +
115A SER* 2.8 30.3 + - - -
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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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20A LEU* 3.3 31.9 - - + +
21A CYS* 3.6 13.7 - - + +
23A LEU* 4.2 7.6 - - + -
25A ILE* 4.0 15.5 - - + -
98A LEU* 5.3 0.7 - - + -
105A LEU* 4.3 17.0 - - + -
108A HIS* 2.9 36.2 + - + +
109A ARG 3.8 1.6 - - - +
111A ALA* 1.3 78.1 - - - +
113A VAL* 1.3 62.5 + - - +
115A SER* 3.2 4.9 + - - -
116A LEU* 3.0 27.2 + - - +
129A LEU* 3.7 16.6 - - + -
131A PHE* 3.8 29.2 - - + -
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Residues in contact with VAL 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A ARG* 3.0 27.2 + - + +
110A LYS* 3.9 3.6 - - - +
112A LEU* 1.3 74.3 - - - +
114A ASP* 1.3 67.9 + - - +
116A LEU* 3.3 1.6 + - - +
117A SER* 2.9 22.7 + - - -
124A GLN* 3.6 31.9 - - + +
127A ILE* 4.2 26.9 - - + +
129A LEU* 3.8 31.4 - - + +
253B GLY 6.2 0.2 - - - +
1069D ARG* 6.1 0.4 - - - +
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Residues in contact with ASP 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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110A LYS* 2.8 54.5 + - - +
111A ALA* 3.5 8.7 - - - +
113A VAL* 1.3 78.6 - - - +
115A SER* 1.3 56.0 + - - +
117A SER* 3.4 1.7 + - - -
118A ARG* 3.0 30.5 + - - +
124A GLN* 2.5 37.2 + - - +
1069D ARG* 3.8 6.9 + - - -
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Residues in contact with SER 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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21A CYS 2.8 26.4 + - - -
22A GLY* 4.4 1.6 - - - -
23A LEU* 3.9 20.6 - - - +
111A ALA 2.8 17.7 + - - -
112A LEU 3.5 3.8 - - - -
113A VAL 3.1 0.2 - - - -
114A ASP* 1.3 78.9 - - - +
116A LEU* 1.3 58.2 + - - +
118A ARG* 3.2 12.2 + - - +
119A LEU* 2.8 47.2 + - - +
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Residues in contact with LEU 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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21A CYS* 3.7 29.6 - - + +
41A MET* 3.4 32.3 - - + -
44A LEU* 3.8 15.5 - - + -
96A LEU* 4.0 22.4 - - + -
112A LEU 3.0 18.4 + - - +
113A VAL 3.9 2.9 - - - +
115A SER* 1.3 75.9 - - - +
117A SER* 1.3 58.2 + - - +
119A LEU* 3.9 2.9 - - + +
120A MET* 2.9 48.5 + - + +
127A ILE* 3.9 24.7 - - + -
129A LEU* 4.6 6.7 - - + -
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Residues in contact with SER 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 VAL 2.9 18.7 + - - -
114A ASP 3.6 4.5 - - - -
116A LEU* 1.3 76.3 - - - +
118A ARG* 1.3 57.1 + - - +
121A ARG* 2.9 26.0 + - - -
122A LEU 2.6 32.0 + - - +
123A PRO* 4.5 0.5 - - - +
124A GLN* 4.0 26.0 + - - +
127A ILE* 3.9 14.4 - - - +
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Residues in contact with ARG 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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23A LEU* 6.2 1.4 - - - +
74A GLU* 4.6 7.1 + - - -
78A ARG* 4.2 18.0 + - - +
114A ASP 3.0 17.9 + - - +
115A SER* 3.7 10.7 + - - +
117A SER* 1.3 78.1 + - - +
119A LEU* 1.3 82.4 + - - +
120A MET 3.6 0.2 + - - -
121A ARG* 3.6 13.4 + - - +
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Residues in contact with LEU 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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21A CYS 4.3 2.2 - - - +
22A GLY* 4.8 3.8 - - - -
41A MET* 3.5 31.4 - - + -
74A GLU* 3.5 39.9 - - + +
77A LEU* 4.1 10.7 - - + +
78A ARG* 3.8 18.0 + - - +
81A MET* 3.7 17.7 - - - +
115A SER* 2.8 36.2 + - - +
116A LEU* 3.9 4.0 - - - +
118A ARG* 1.3 108.4 - - - +
120A MET* 1.3 62.6 + - + +
121A ARG* 3.6 2.6 + - - +
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Residues in contact with MET 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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44A LEU* 3.8 24.7 - - + -
48A LEU* 5.7 3.1 - - + -
77A LEU* 4.6 14.6 - - + -
81A MET* 3.9 22.3 - - - +
91A LEU* 3.8 29.5 - - + +
94A ALA* 3.7 28.0 - - + -
116A LEU* 2.9 33.4 + - + +
119A LEU* 1.3 79.8 - - + +
121A ARG* 1.3 73.5 + - - +
122A LEU* 3.4 15.6 + - + +
127A ILE* 3.6 25.4 - - + -
148A VAL* 5.6 1.6 - - - -
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Residues in contact with ARG 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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78A ARG* 6.0 2.2 - - - +
81A MET* 4.7 8.3 - - + +
85A GLU* 2.9 32.9 + - - -
117A SER 2.9 10.8 + - - -
118A ARG* 3.6 11.6 + - - +
119A LEU 3.3 4.6 - - - +
120A MET* 1.3 82.7 + - - +
122A LEU* 1.3 62.7 + - - +
123A PRO* 4.5 1.9 - - - +
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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