Contacts of the helix formed by residues 110 - 124 (chain A) in PDB entry 4D10
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 LEU 110 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78A GLU* 6.5 0.2 - - + -
79A ASN 3.3 26.7 - - - +
80A PRO* 4.7 11.4 - - + +
82A LEU* 4.3 27.8 - - + +
84A LEU* 3.8 28.4 - - + +
103A ILE* 5.0 5.3 - - + +
107A CYS* 3.9 21.5 - - - +
108A PRO 2.8 9.4 + - - +
109A THR* 1.3 80.1 + - - +
111A ARG* 1.3 62.5 + - - +
112A VAL 3.3 1.8 - - - -
113A GLU* 3.6 9.3 + - + +
114A ALA* 3.3 23.0 + - - +
390A LEU* 5.0 0.7 - - + -
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Residues in contact with ARG 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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104A ALA* 2.8 29.0 + - + +
105A ASP* 3.8 19.0 + - - -
107A CYS 3.6 11.9 + - - +
108A PRO* 3.8 35.3 - - + +
109A THR 3.2 3.3 - - - +
110A LEU* 1.3 75.4 - - - +
112A VAL* 1.3 58.1 + - + +
114A ALA* 3.5 6.1 + - - +
115A LEU* 2.8 57.3 + - + +
137A LYS* 5.8 1.6 - - - -
141A ALA* 5.1 9.4 - - + -
144A GLU* 4.5 15.2 + - - -
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Residues in contact with VAL 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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109A THR* 4.1 16.4 - - - +
110A LEU 3.3 0.6 - - - -
111A ARG* 1.3 78.3 - - + +
113A GLU* 1.3 59.0 + - + +
115A LEU* 3.3 9.9 + - - +
116A LYS* 2.9 49.9 + - + +
138A LEU* 5.0 8.7 - - + -
141A ALA* 5.4 6.1 - - + -
145A LEU* 3.9 39.3 - - + -
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Residues in contact with GLU 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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84A LEU* 3.8 24.7 - - + -
85A GLU* 3.8 9.2 - - - +
109A THR 5.3 0.2 + - - -
110A LEU* 3.6 7.1 + - + +
112A VAL* 1.3 80.0 - - + +
114A ALA* 1.3 59.2 + - - +
116A LYS* 2.9 36.3 + - + +
117A MET* 3.0 57.5 + - + +
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Residues in contact with ALA 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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84A LEU* 4.4 11.3 - - + +
100A LEU* 3.7 38.9 - - + +
103A ILE* 4.4 3.1 - - + -
104A ALA* 4.0 15.0 - - + +
110A LEU 3.3 16.5 + - - +
111A ARG 3.6 4.9 - - - +
113A GLU* 1.3 79.7 - - - +
115A LEU* 1.3 56.2 + - - +
118A ALA* 2.9 31.4 + - - +
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Residues in contact with LEU 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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104A ALA* 4.6 8.5 - - + -
111A ARG* 2.8 45.3 + - + +
112A VAL* 3.3 5.4 + - - +
114A ALA* 1.3 71.3 - - - +
116A LYS* 1.3 60.3 + - - +
118A ALA* 4.2 2.2 - - - -
119A LEU* 2.9 30.8 + - - +
134A ILE* 3.5 46.0 - - + +
137A LYS* 3.7 36.3 - - + +
138A LEU* 4.0 18.7 - - + +
141A ALA* 4.0 13.7 - - + -
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Residues in contact with LYS 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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112A VAL* 2.9 40.6 + - + +
113A GLU* 2.9 29.3 + - - +
115A LEU* 1.3 74.2 - - - +
117A MET* 1.3 61.0 + - + +
119A LEU* 3.4 8.3 + - - +
120A SER* 3.0 29.0 + - - -
138A LEU* 4.8 14.6 - - + -
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Residues in contact with MET 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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84A LEU* 3.9 26.5 - - + +
85A GLU* 3.4 43.1 - - + +
88A ALA* 4.2 12.3 - - + -
100A LEU* 3.9 20.3 - - + +
113A GLU* 3.0 34.9 + - - +
116A LYS* 1.3 74.0 - - + +
118A ALA* 1.3 66.5 + - - +
120A SER* 2.7 22.4 + - - +
121A PHE* 3.0 14.6 + - - +
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Residues in contact with ALA 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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97A ILE* 5.4 7.6 - - + +
100A LEU* 3.9 25.0 - - + +
101A GLN 5.4 0.2 - - - +
114A ALA 2.9 21.9 + - - +
115A LEU 3.7 4.7 - - - +
117A MET* 1.3 76.6 - - - +
119A LEU* 1.3 52.0 + - - +
121A PHE* 3.4 2.3 + - - +
122A VAL* 2.8 44.0 + - + +
134A ILE* 3.8 24.9 - - + -
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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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115A LEU 2.9 19.2 + - - +
116A LYS* 3.6 7.0 - - - +
118A ALA* 1.3 76.5 - - - +
120A SER* 1.3 62.7 + - - +
122A VAL* 3.2 5.8 + - - +
123A GLN* 3.0 33.7 + - + +
131A TYR* 3.7 37.2 - - + +
134A ILE* 3.8 23.5 - - + +
135A HIS* 4.4 15.3 - - + +
138A LEU* 4.4 19.1 - - + -
160A PRO* 4.7 12.3 - - + -
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Residues in contact with SER 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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116A LYS 3.0 12.2 + - - -
117A MET* 2.7 27.0 + - - +
119A LEU* 1.3 77.8 - - - +
121A PHE* 1.3 59.5 + - - +
123A GLN* 3.7 19.3 + - - +
124A ARG* 2.9 30.2 + - - +
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Residues in contact with PHE 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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92A SER* 5.3 0.7 - - - -
93A GLY* 3.2 48.7 - - - -
96A ARG* 3.2 44.9 - - + +
97A ILE* 3.6 25.7 - - + +
100A LEU* 5.4 2.0 - - + -
117A MET 3.0 15.4 + - - +
118A ALA* 4.1 3.4 - - - +
120A SER* 1.3 74.5 + - - +
122A VAL* 1.3 59.5 + - - +
123A GLN 3.2 2.0 - - - -
124A ARG* 3.1 49.4 + - + +
125A THR* 4.5 18.1 + - + -
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Residues in contact with VAL 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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97A ILE* 4.3 25.8 - - + -
118A ALA* 2.8 30.9 + - + +
119A LEU* 3.2 6.5 + - - +
121A PHE* 1.3 70.4 - - - +
123A GLN* 1.3 61.6 + - - +
124A ARG 3.0 12.9 - - - +
127A ASN* 3.7 23.8 + - + +
130A MET* 3.7 25.1 - - + -
131A TYR* 3.4 43.7 - - + +
134A ILE* 4.6 7.6 - - + -
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Residues in contact with GLN 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 LEU* 3.0 24.9 + - + +
120A SER* 3.8 11.4 - - - +
121A PHE 3.2 0.2 - - - -
122A VAL* 1.3 76.0 - - - +
124A ARG* 1.3 60.0 + - + +
126A PHE* 3.9 9.9 + - - -
131A TYR* 4.1 26.9 + - + -
163A ASP* 5.1 6.1 + - - -
166A TRP* 3.4 48.9 + - + +
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Residues in contact with ARG 124 (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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96A ARG* 5.5 1.3 - - - +
120A SER* 2.9 45.6 + - - +
121A PHE* 3.1 39.3 + - + +
122A VAL* 3.0 11.8 - - - +
123A GLN* 1.3 73.1 - - + +
125A THR* 1.3 71.1 + - + +
126A PHE* 2.9 11.9 + - - -
127A ASN* 5.3 0.2 - - - +
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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