Contacts of the helix formed by residues 114 - 126 (chain A) in PDB entry 1IVH
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 GLU 114 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68A GLN* 4.0 11.1 + - - +
69A TYR* 2.7 22.7 + - - -
113A ASN* 1.3 73.8 - - - +
115A ALA* 1.3 56.5 + - - +
117A LYS* 3.0 29.3 + - - +
118A GLU* 2.9 40.3 + - + +
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Residues in contact with ALA 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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113A ASN* 3.2 13.5 - - - +
114A GLU* 1.3 78.3 - - - +
116A GLN* 1.3 58.1 + - + +
118A GLU* 3.2 6.2 + - - +
119A LYS* 2.8 33.8 + - - +
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Residues in contact with GLN 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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108A LEU* 5.0 3.9 - - + +
111A ASN 4.2 1.0 - - - +
112A GLY* 2.9 28.3 - - - -
113A ASN* 2.8 34.6 + - - +
115A ALA* 1.3 72.7 - - + +
117A LYS* 1.3 57.8 + - - +
119A LYS* 4.5 0.7 - - - -
120A TYR* 2.8 52.6 + - + +
197A ILE* 3.8 22.2 - - + +
234A ALA 3.4 21.8 + - - +
235A ASN* 4.1 0.4 - - - -
236A ILE 2.9 31.0 + - - +
237A LEU* 3.6 6.4 - - - +
238A GLY 4.8 0.7 + - - -
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Residues in contact with LYS 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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69A TYR* 3.4 35.7 - - + +
108A LEU* 3.9 13.0 - - - +
109A VAL* 3.5 24.7 + - - +
110A ARG 5.8 0.4 + - - -
112A GLY* 2.9 26.8 + - - +
113A ASN* 3.0 19.0 + - - +
114A GLU* 3.0 20.3 + - - +
116A GLN* 1.3 75.1 - - - +
118A GLU* 1.3 59.5 + - - +
121A LEU* 2.7 54.9 + - + +
122A PRO* 3.2 0.7 - - - +
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Residues in contact with GLU 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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68A GLN* 4.1 11.2 - - - +
69A TYR* 2.8 36.9 - - + +
114A GLU* 2.9 32.0 + - + +
115A ALA* 3.6 4.9 - - - +
117A LYS* 1.3 75.0 - - - +
119A LYS* 1.3 63.0 + - - +
122A PRO* 3.1 23.0 - - - +
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Residues in contact with LYS 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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115A ALA 2.8 18.4 + - - +
116A GLN* 3.8 3.4 - - - +
118A GLU* 1.3 79.3 - - - +
120A TYR* 1.3 100.5 + - + +
122A PRO* 4.7 1.6 - - - +
123A LYS* 5.4 3.6 + - - +
129A TYR* 4.9 7.6 - - - -
199A GLU* 3.9 14.2 + - - -
235A ASN* 4.9 4.9 + - - -
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Residues in contact with TYR 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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108A LEU* 3.9 11.4 - - + -
116A GLN* 2.8 41.6 + - + +
119A LYS* 1.3 109.4 + - + +
121A LEU* 1.3 65.4 - - - +
122A PRO* 3.5 1.3 - - - -
123A LYS* 3.3 8.0 + - - +
124A LEU* 3.1 34.6 + - + +
129A TYR* 4.4 10.9 - + - -
175A VAL* 3.4 28.0 - - + -
197A ILE* 3.7 29.2 - - + -
199A GLU* 3.0 32.3 + - + -
235A ASN* 3.3 21.0 + - - -
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Residues in contact with LEU 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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65A ALA* 5.2 0.2 - - + -
69A TYR* 3.5 37.0 - - + -
105A ILE* 3.8 35.9 - - + +
108A LEU* 4.2 15.5 - - + -
109A VAL* 3.9 24.0 - - + -
117A LYS* 2.7 45.3 + - + +
120A TYR* 1.3 72.4 - - - +
122A PRO* 1.3 52.4 - - + -
124A LEU* 2.8 9.6 + - - +
125A ILE* 2.7 44.7 + - + +
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Residues in contact with PRO 122 (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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69A TYR* 3.9 27.8 - - + +
117A LYS 3.2 5.6 - - - +
118A GLU* 3.1 29.2 - - - +
119A LYS 4.5 1.3 - - - +
120A TYR 3.5 2.2 - - - -
121A LEU* 1.3 91.5 - - + +
123A LYS* 1.3 61.4 + - + +
125A ILE* 3.5 2.1 + - + +
126A SER* 2.8 29.0 + - - -
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Residues in contact with LYS 123 (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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119A LYS 5.4 3.3 + - - +
120A TYR 3.3 3.9 + - - +
121A LEU 3.3 0.6 - - - -
122A PRO* 1.3 78.9 - - + +
124A LEU* 1.3 64.6 + - - +
126A SER* 3.2 5.8 + - - +
128A GLU* 3.1 41.3 + - + +
129A TYR* 3.0 78.6 + - + +
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Residues in contact with LEU 124 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61A LEU* 4.2 1.4 - - - +
100A HIS* 2.8 28.2 + - - +
104A CYS* 4.4 4.0 - - - -
105A ILE* 3.6 25.4 - - + -
108A LEU* 4.2 6.5 - - + -
120A TYR* 3.1 38.1 + - + +
121A LEU* 2.8 9.5 + - + +
123A LYS* 1.3 76.2 - - - +
125A ILE* 1.3 62.0 - - - +
127A GLY 3.3 9.0 + - - -
129A TYR* 3.6 31.6 - - + +
130A ILE 3.8 18.4 - - - +
131A GLY* 3.8 6.3 - - - +
175A VAL* 3.5 28.0 - - + -
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Residues in contact with ILE 125 (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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56A GLY* 3.5 19.4 - - - +
59A GLY* 5.8 3.2 - - - +
61A LEU* 3.6 7.4 - - - +
62A GLY* 3.9 25.7 + - - +
65A ALA* 3.7 24.7 - - + -
69A TYR* 3.3 35.2 - - + +
70A GLY* 3.2 25.6 - - - +
71A GLY* 3.9 3.8 - - - +
105A ILE* 4.2 10.8 - - + -
121A LEU* 2.7 27.7 + - + +
122A PRO 3.8 4.0 - - - +
124A LEU* 1.3 74.7 - - - +
126A SER* 1.3 59.1 + - - +
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Residues in contact with SER 126 (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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52A TRP 3.7 1.0 - - - +
53A LYS* 3.7 19.8 - - - +
56A GLY* 3.7 13.7 - - - -
122A PRO 2.8 21.7 + - - -
123A LYS* 3.2 14.6 + - - +
125A ILE* 1.3 77.4 - - - +
127A GLY* 1.3 57.9 + - - +
128A GLU* 3.3 19.9 + - - +
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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