Contacts of the helix formed by residues 108 - 125 (chain A) in PDB entry 4G98
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 THR 108 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49A LEU* 4.4 12.6 - - + -
53A SER* 4.5 4.4 + - - +
106A PRO* 4.5 10.5 - - + -
107A TYR* 1.3 76.5 - - - +
109A PRO* 1.3 70.9 - - + +
111A THR* 2.7 31.7 + - - +
112A GLN* 2.9 26.2 + - - +
213A LEU* 3.9 0.5 - - - +
216A GLU* 2.5 28.9 + - - +
217A LEU* 4.3 9.6 - - + -
220A LEU* 4.0 20.9 - - + -
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Residues in contact with PRO 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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107A TYR 4.4 1.8 - - - +
108A THR* 1.3 86.7 - - - +
110A ALA* 1.3 55.8 + - - +
112A GLN* 3.1 18.5 + - + +
113A HIS* 2.8 28.4 + - - +
216A GLU* 3.3 12.1 - - - +
220A LEU* 6.0 1.6 - - + -
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Residues in contact with ALA 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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109A PRO* 1.3 72.3 - - - +
111A THR* 1.3 60.8 + - - +
113A HIS* 3.5 9.5 + - - +
114A TYR* 3.2 22.0 + - - +
209A LEU* 5.1 5.0 - - - +
212A GLU* 4.0 8.5 - - + +
213A LEU* 3.9 25.1 - - - +
216A GLU* 2.7 41.1 + - + +
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Residues in contact with THR 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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53A SER* 3.1 44.6 + - - +
56A HIS* 3.7 21.5 - - + -
57A ILE* 4.0 11.0 - - + -
107A TYR* 4.0 6.5 - - + -
108A THR* 2.7 34.3 + - - -
110A ALA* 1.3 75.7 - - - +
112A GLN* 1.3 63.3 + - - +
114A TYR* 3.3 5.1 + - - +
115A VAL* 3.0 28.6 + - - +
213A LEU* 3.3 9.0 - - - +
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Residues in contact with GLN 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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107A TYR* 3.1 55.0 + - + +
108A THR 2.9 16.8 + - - +
109A PRO* 3.4 17.7 - - + +
111A THR* 1.3 75.2 - - - +
113A HIS* 1.3 58.8 + - - +
115A VAL* 3.4 1.7 + - - +
116A LYS* 2.9 30.1 + - - +
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Residues in contact with HIS 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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109A PRO 2.8 15.9 + - - +
110A ALA* 3.7 9.6 - - - +
111A THR 3.2 0.2 - - - -
112A GLN* 1.3 76.3 - - - +
114A TYR* 1.3 61.5 + - - +
116A LYS* 3.3 22.2 + - + +
117A ARG* 3.1 25.0 + - + +
209A LEU* 3.6 25.0 - - + +
212A GLU* 3.8 16.2 + - + -
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Residues in contact with TYR 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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57A ILE* 3.4 36.8 - - + -
110A ALA 3.2 16.8 + - - +
111A THR 3.7 4.5 - - - +
113A HIS* 1.3 75.0 - - - +
115A VAL* 1.3 57.9 + - - +
117A ARG* 3.2 3.5 + - - +
118A LEU* 2.9 47.0 + - + +
132A HIS* 4.0 20.7 + - - -
135A THR* 4.7 3.1 - - - +
136A ARG* 3.3 23.1 - - + +
206A ALA* 4.3 3.3 + - - +
209A LEU* 3.9 41.0 - - + +
210A ASN* 3.0 44.1 + - - -
213A LEU* 5.2 2.5 - - + -
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Residues in contact with VAL 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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56A HIS* 3.8 33.7 - - + +
57A ILE* 4.3 5.2 - - - +
60A ALA* 3.8 8.7 - - + -
107A TYR* 3.6 23.8 - - - +
111A THR* 3.0 21.7 + - + +
112A GLN 3.7 4.5 - - - +
114A TYR* 1.3 72.9 - - - +
116A LYS* 1.3 65.8 + - - +
118A LEU* 3.1 10.2 + - - +
119A HIS* 3.0 47.5 + - + +
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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 GLN 2.9 18.3 + - - +
113A HIS* 3.3 22.8 + - + +
115A VAL* 1.3 77.6 - - - +
117A ARG* 1.3 64.1 + - - +
119A HIS* 3.2 8.2 + - - +
120A GLU* 2.9 49.7 + - + +
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Residues in contact with ARG 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 HIS* 3.1 15.1 + - + +
114A TYR 3.2 7.6 + - - +
116A LYS* 1.3 80.3 - - + +
118A LEU* 1.3 62.9 + - - +
120A GLU* 3.0 34.1 + - - +
121A VAL* 2.9 34.0 + - - +
125A HIS* 4.2 15.5 + - - -
128A LEU* 4.2 11.5 - - - +
132A HIS* 4.3 2.7 - - + +
202A GLU* 2.7 43.9 + - - +
205A THR* 5.0 7.2 - - + +
209A LEU* 4.1 24.2 - - + -
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Residues in contact with LEU 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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57A ILE* 3.6 30.7 - - + +
60A ALA* 4.0 18.6 - - + +
61A LEU* 4.0 21.5 - - + +
64A GLU* 3.6 9.2 - - - +
114A TYR* 2.9 43.5 + - + +
115A VAL* 3.1 7.8 + - - +
117A ARG* 1.3 76.8 - - - +
119A HIS* 1.3 57.5 + - - +
121A VAL* 3.4 5.1 + - - +
122A GLY* 2.9 22.9 + - - -
129A LEU* 4.6 5.4 - - + +
132A HIS* 3.6 38.8 - - + +
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Residues in contact with HIS 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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60A ALA* 3.8 18.5 - - + +
63A GLU* 3.1 28.9 + - + -
64A GLU* 2.7 29.1 + - + +
67A ARG* 4.7 3.0 + - - -
115A VAL* 3.0 43.8 + - + +
116A LYS* 3.8 7.6 - - - +
118A LEU* 1.3 72.2 - - - +
120A GLU* 1.3 61.6 + - - +
123A GLY* 2.8 27.5 + - - -
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Residues in contact with GLU 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* 2.9 51.6 + - + +
117A ARG* 3.0 43.0 + - - +
119A HIS* 1.3 71.7 - - - +
121A VAL* 1.3 62.5 + - - +
124A THR* 2.7 35.7 + - - +
125A HIS* 3.3 10.5 + - + +
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Residues in contact with VAL 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 ARG* 2.9 36.5 + - - +
118A LEU* 3.7 3.8 - - - +
120A GLU* 1.3 77.0 - - - +
122A GLY* 1.3 58.1 + - - +
125A HIS* 2.8 47.1 + - + +
126A PRO* 2.9 2.9 - - - +
128A LEU* 3.7 9.0 - - + +
129A LEU* 3.5 41.5 - - + +
132A HIS* 3.9 10.5 - - + +
202A GLU* 3.4 28.3 - - - +
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Residues in contact with GLY 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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64A GLU* 3.1 35.2 - - - +
67A ARG* 3.9 3.3 - - - -
68A ASN* 3.1 27.0 + - - +
118A LEU 2.9 11.8 + - - -
121A VAL* 1.3 77.2 - - - +
123A GLY* 1.3 59.7 + - - +
126A PRO* 4.0 6.1 - - - +
129A LEU* 4.5 6.3 - - - -
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Residues in contact with GLY 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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64A GLU* 3.6 3.3 + - - -
67A ARG* 4.5 11.2 - - - -
119A HIS 2.8 17.3 + - - -
122A GLY* 1.3 79.0 - - - +
124A THR* 1.3 62.9 + - - +
126A PRO* 4.6 3.5 - - - +
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Residues in contact with THR 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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120A GLU* 2.7 21.9 + - - -
123A GLY* 1.3 76.0 - - - +
125A HIS* 1.3 81.8 + - + +
126A PRO* 3.4 9.3 - - - +
127A GLU* 4.7 0.5 - - - +
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Residues in contact with HIS 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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117A ARG* 4.2 23.3 + - - -
120A GLU* 3.3 21.6 + - + +
121A VAL* 2.8 20.7 + - - +
124A THR* 1.3 94.3 + - + +
126A PRO* 1.3 57.1 - - - +
127A GLU* 3.0 20.4 + - - +
128A LEU* 2.8 45.5 + - + +
198A ARG* 5.0 4.6 + - - -
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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