Contacts of the helix formed by residues 108 - 121 (chain A) in PDB entry 3GHZ
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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23A VAL* 3.9 19.0 - - + +
24A ARG 4.9 1.3 - - - -
25A ILE* 3.5 39.7 - - + +
26A PRO* 4.5 13.0 - - + +
104A LYS 3.4 25.1 + - - -
105A MET 2.9 6.4 + - - +
107A PRO* 1.3 92.6 + - + +
109A ILE* 1.3 64.2 + - - +
110A PRO 3.3 2.9 - - - -
111A GLN* 3.2 10.5 + - - +
112A MET* 3.1 38.5 + - + +
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Residues in contact with ILE 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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98A ILE* 4.7 0.7 - - + -
105A MET* 3.2 14.8 + - + +
106A LEU* 3.4 26.2 + - + +
108A HIS* 1.3 77.3 - - - +
110A PRO* 1.3 72.5 - - + +
112A MET* 3.2 14.2 + - + +
113A ARG* 3.0 34.9 + - - +
129A VAL* 3.6 48.9 - - + +
130A LYS* 3.9 21.1 - - - -
131A ALA* 4.0 9.0 - - + +
55B GLY* 6.4 0.4 - - - -
59B LYS* 6.2 2.2 - - - +
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Residues in contact with PRO 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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106A LEU 3.6 11.7 - - - +
107A PRO 3.9 7.9 - - - +
108A HIS 3.6 2.5 - - - -
109A ILE* 1.3 96.7 - - + +
111A GLN* 1.3 61.4 + - - +
113A ARG* 3.2 13.7 + - - +
114A VAL* 3.1 25.3 + - - +
124A MET* 4.6 2.9 - - + +
59B LYS* 6.4 1.8 - - - -
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Residues in contact with GLN 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 VAL* 3.8 22.7 - - + -
107A PRO 5.4 0.2 + - - -
108A HIS* 3.2 10.9 + - - +
110A PRO* 1.3 75.8 - - - +
112A MET* 1.3 66.0 + - - +
114A VAL* 3.2 23.0 + - - +
115A PHE* 3.0 57.8 + - + -
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Residues in contact with MET 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 ILE* 3.5 44.0 - - + +
21A GLY* 3.4 22.4 - - - +
23A VAL* 3.6 5.1 - - + +
25A ILE* 4.0 8.5 - - + -
40A ALA* 5.3 0.9 - - - -
98A ILE* 3.8 25.1 - - + -
105A MET* 4.2 8.7 - - - +
108A HIS* 3.1 35.5 + - + +
109A ILE* 3.2 11.0 + - + +
111A GLN* 1.3 74.5 - - - +
113A ARG* 1.3 58.4 + - - +
115A PHE* 3.2 2.6 + - - +
116A ILE* 2.9 35.7 + - + +
129A VAL* 4.0 20.2 - - + -
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Residues in contact with ARG 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 ILE* 3.0 33.1 + - + +
110A PRO* 3.5 11.7 - - - +
111A GLN 3.2 0.2 - - - -
112A MET* 1.3 75.6 - - - +
114A VAL* 1.3 58.0 + - - +
116A ILE* 4.1 0.9 - - - +
117A ALA* 2.9 33.8 + - - +
124A MET* 2.9 61.5 + - + +
125A ASP* 4.3 2.2 - - - +
127A VAL* 2.9 33.7 + - + +
128A ASN* 4.4 4.8 - - - +
129A VAL* 4.3 20.6 - - + +
53B ALA* 4.2 21.1 + - - +
59B LYS* 5.2 9.9 - - - +
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Residues in contact with VAL 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 PRO 3.1 17.1 + - - +
111A GLN* 3.2 28.2 + - - +
113A ARG* 1.3 77.9 - - - +
115A PHE* 1.3 60.2 + - + +
117A ALA* 3.5 2.0 + - - +
118A GLU* 3.0 35.8 + - + +
124A MET* 3.8 21.8 - - - -
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Residues in contact with PHE 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 GLY 3.6 22.2 - - - +
22A GLY* 3.3 28.3 - - - -
23A VAL* 3.8 13.5 - - + -
41A LEU* 6.3 0.4 - - + -
74A ARG* 3.3 40.6 - - - +
111A GLN* 3.0 40.0 + - + -
112A MET 3.6 4.9 - - - +
114A VAL* 1.3 77.5 - - + +
116A ILE* 1.3 64.5 + - + +
118A GLU* 3.3 7.9 + - - +
119A ASP* 3.0 30.2 + - - +
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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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21A GLY* 4.9 4.7 - - - +
40A ALA* 6.2 1.6 - - + -
41A LEU* 3.8 28.0 - - + -
44A LEU* 3.5 30.7 - - + -
77A LEU* 4.9 1.8 - - + -
94A VAL* 4.5 0.9 - - + -
96A VAL* 4.8 4.7 - - + -
112A MET* 2.9 25.4 + - + +
113A ARG 4.1 0.2 - - - +
115A PHE* 1.3 75.2 - - + +
117A ALA* 1.4 57.5 + - - +
119A ASP* 3.1 7.8 + - - +
120A LEU* 2.9 44.3 + - + +
127A VAL* 3.6 25.8 - - + -
129A VAL* 3.9 27.1 - - + -
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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 ARG 2.9 19.2 + - - +
114A VAL 3.9 2.9 - - - +
116A ILE* 1.4 73.2 - - - +
118A GLU* 1.3 65.5 + - - +
121A GLY* 2.9 18.9 + - - -
122A CYS* 3.0 39.3 + - - +
123A HIS 4.1 1.8 - - - -
124A MET* 4.0 26.9 - - + +
127A VAL* 4.2 2.9 - - + +
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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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74A ARG* 3.1 22.5 + - - +
78A ARG* 5.6 0.3 + - - -
114A VAL* 3.0 26.1 + - + +
115A PHE* 3.5 9.6 - - - +
117A ALA* 1.3 77.0 - - - +
119A ASP* 1.3 65.2 + - - +
121A GLY* 3.1 13.1 + - - -
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Residues in contact with ASP 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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41A LEU* 5.0 0.5 - - - +
74A ARG* 2.9 42.0 + - - +
77A LEU* 3.9 23.0 - - + +
78A ARG* 2.8 55.6 + - + +
81A TRP* 3.8 13.2 - - - +
115A PHE 3.0 19.7 + - - +
116A ILE* 3.1 4.0 + - - +
118A GLU* 1.3 79.7 - - - +
120A LEU* 1.3 62.3 + - - +
121A GLY 3.7 0.2 + - - -
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Residues in contact with LEU 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* 4.6 4.3 - - + -
48A LEU* 3.8 26.2 - - + -
77A LEU* 4.1 14.1 - - + -
81A TRP* 3.1 57.3 + - + +
85A GLN* 5.1 2.3 + - - -
91A LEU* 4.3 22.6 - - + +
94A VAL* 4.6 7.0 - - + -
116A ILE* 2.9 39.5 + - + +
119A ASP* 1.3 79.7 - - - +
121A GLY* 1.3 65.5 + - - +
122A CYS* 3.2 16.7 + - + +
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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 2.9 7.4 + - - -
118A GLU* 3.1 11.2 + - - -
119A ASP 3.3 0.8 - - - -
120A LEU* 1.3 79.2 - - - +
122A CYS* 1.3 58.3 + - - +
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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