Contacts of the helix formed by residues 108 - 126 (chain A) in PDB entry 3G2V
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 SER 108 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A GLU* 2.7 32.4 + - - +
106A ARG 4.1 1.0 + - - -
107A THR* 1.3 80.7 - - - +
109A GLU* 1.3 64.0 + - - +
110A LYS* 3.7 2.6 + - - -
111A VAL* 3.3 23.1 + - - +
112A LYS* 3.1 18.4 + - - +
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Residues in contact with GLU 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 THR 4.0 1.6 - - - +
108A SER* 1.3 69.2 - - - +
110A LYS* 1.3 55.5 + - - +
112A LYS* 3.1 32.4 + - - +
113A ASN* 2.8 55.0 + - - +
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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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60A GLU* 3.8 20.0 + - - +
61A TRP* 4.9 9.3 - - - -
64A ILE* 3.7 40.8 - - + +
108A SER* 3.7 8.2 + - - +
109A GLU* 1.3 79.0 - - - +
111A VAL* 1.3 57.4 + - - +
113A ASN* 3.9 5.4 - - - +
114A LYS* 3.0 28.7 + - + +
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Residues in contact with VAL 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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55A ILE 4.5 10.8 - - - +
60A GLU* 3.8 14.1 - - + -
63A ALA* 4.2 14.1 - - + -
64A ILE* 3.7 24.7 - - + -
67A LEU* 3.8 13.6 - - + +
97A VAL* 3.7 15.0 - - + -
107A THR* 3.5 27.6 - - + -
108A SER* 3.3 15.7 + - - +
110A LYS* 1.3 75.1 - - - +
112A LYS* 1.3 65.5 + - - +
114A LYS* 3.3 3.3 + - - +
115A ILE* 3.1 23.2 + - + +
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Residues in contact with LYS 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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97A VAL 3.6 20.0 - - - +
98A VAL* 3.8 25.2 - - + +
104A GLY* 2.9 30.0 + - - +
105A SER* 5.2 0.4 - - - +
107A THR* 3.2 28.7 + - + +
108A SER 3.1 5.4 + - - +
109A GLU* 3.1 41.1 + - - +
111A VAL* 1.3 75.1 - - - +
113A ASN* 1.3 67.4 + - - +
115A ILE* 3.2 4.4 + - - +
116A LEU* 3.0 31.2 + - + +
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Residues in contact with ASN 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 GLU* 2.8 42.6 + - - +
110A LYS* 3.9 5.2 - - - +
112A LYS* 1.3 75.5 - - - +
114A LYS* 1.3 57.4 + - - +
116A LEU* 3.3 15.9 + - - +
117A GLU* 2.9 29.8 + - - +
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Residues in contact with LYS 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ILE* 4.8 8.7 - - + +
67A LEU* 3.9 33.9 - - + -
68A THR* 5.1 6.0 + - - -
71A GLU* 2.8 30.5 + - - -
110A LYS* 3.0 19.3 + - + +
111A VAL* 3.6 4.7 - - - +
112A LYS 3.2 0.2 - - - -
113A ASN* 1.3 75.2 - - - +
115A ILE* 1.3 63.7 + - - +
117A GLU* 3.0 32.7 + - - +
118A LEU* 2.9 39.0 + - + +
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Residues in contact with ILE 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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55A ILE* 4.2 11.9 - - + -
67A LEU* 3.6 21.1 - - + -
94A LEU* 4.0 26.2 - - + +
97A VAL* 3.3 39.7 - - + -
98A VAL* 3.6 18.8 - - + -
111A VAL* 3.1 18.8 + - + +
112A LYS 3.2 6.3 + - - +
114A LYS* 1.3 74.7 - - - +
116A LEU* 1.3 57.7 + - - +
118A LEU* 3.3 9.2 + - - +
119A LEU* 2.9 45.4 + - + +
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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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98A VAL* 4.1 18.4 - - + -
112A LYS* 3.0 23.7 + - + +
113A ASN* 3.8 18.6 - - - +
115A ILE* 1.3 73.0 - - - +
117A GLU* 1.3 67.0 + - - +
119A LEU* 3.4 6.9 + - + +
120A TYR* 3.0 23.0 + - - +
136A TYR* 3.8 7.0 + - + -
139A LEU* 4.1 20.2 - - + -
144A ILE* 4.1 25.4 - - + +
145A VAL* 3.9 27.1 - - + -
146A LYS 5.9 2.0 - - - +
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Residues in contact with GLU 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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71A GLU* 4.5 8.0 - - - +
113A ASN 2.9 14.0 + - - +
114A LYS* 3.0 43.6 + - - +
116A LEU* 1.3 76.6 - - - +
118A LEU* 1.3 61.3 + - - +
120A TYR* 3.4 8.7 + - + +
121A SER* 2.9 32.2 + - - -
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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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67A LEU* 3.8 44.6 - - + +
70A LEU* 4.3 3.6 - - + -
71A GLU* 3.6 41.3 - - + +
94A LEU* 6.4 0.2 - - + -
114A LYS* 2.9 26.1 + - + +
115A ILE* 3.6 7.2 - - - +
117A GLU* 1.3 79.9 - - - +
119A LEU* 1.3 62.7 + - - +
121A SER* 2.9 23.0 + - - +
122A TRP* 3.0 48.7 + - + +
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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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91A LEU* 4.0 27.4 - - + -
94A LEU* 4.1 12.6 - - + -
95A ILE* 6.0 1.8 - - + -
115A ILE* 2.9 37.2 + - + +
116A LEU* 3.7 6.5 - - + +
118A LEU* 1.3 74.4 - - - +
120A TYR* 1.3 65.2 + - - +
122A TRP* 3.3 20.3 + - + +
123A THR* 3.1 26.7 + - - +
132A ILE* 4.1 12.4 - - + +
135A ALA* 5.3 4.7 - - + -
136A TYR* 3.7 20.0 - - + +
139A LEU* 3.7 29.8 - - + -
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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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116A LEU 3.0 14.0 + - - +
117A GLU* 3.6 11.4 - - + +
119A LEU* 1.3 74.5 - - - +
121A SER* 1.3 68.0 + - - +
123A THR* 2.6 27.5 + - - -
124A VAL* 3.2 30.4 + - + +
136A TYR* 3.6 36.8 - + - +
140A LYS* 6.3 0.4 - - - -
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Residues in contact with SER 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 GLU* 2.9 20.0 + - - -
118A LEU* 2.9 26.4 + - - +
120A TYR* 1.3 83.3 - - - +
122A TRP* 1.3 66.1 + - - +
124A VAL* 3.4 6.4 + - - +
125A GLY* 2.8 26.5 + - - -
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Residues in contact with TRP 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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70A LEU* 3.6 36.3 - - + -
71A GLU* 4.9 2.4 + - - +
74A MET* 3.6 43.2 - - + +
85A VAL* 4.0 12.8 - - + -
91A LEU* 5.0 0.7 - - + -
94A LEU* 4.1 9.2 - - + -
118A LEU* 3.0 46.6 + - + +
119A LEU* 4.0 25.8 - - + +
120A TYR 3.2 0.2 - - - -
121A SER* 1.3 78.1 + - - +
123A THR* 1.3 62.6 + - - +
124A VAL 3.2 0.4 - - - -
125A GLY* 4.2 0.9 - - - +
126A LEU* 2.8 40.5 + - + +
132A ILE* 3.9 33.4 - - + -
150A IOD 3.6 24.2 - - + +
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Residues in contact with THR 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 3.1 15.3 + - - +
120A TYR* 2.6 27.2 + - - -
122A TRP* 1.3 76.2 - - - +
124A VAL* 1.3 64.5 + - - +
126A LEU 4.9 1.6 - - - -
127A PRO* 3.9 18.3 - - - +
129A GLU 6.1 0.2 - - - -
132A ILE* 4.2 4.7 - - + +
133A ALA* 3.8 30.0 - - - +
136A TYR* 3.8 32.5 - - + -
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Residues in contact with VAL 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 TYR* 3.2 46.8 + - + +
121A SER* 3.8 6.7 - - - +
123A THR* 1.3 83.6 + - - +
125A GLY* 1.3 62.5 + - - +
126A LEU 3.8 0.2 + - - -
127A PRO* 3.8 9.2 - - - +
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Residues in contact with GLY 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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121A SER 2.8 20.8 + - - -
124A VAL* 1.3 75.3 - - - +
126A LEU* 1.3 70.1 - - - +
127A PRO* 3.4 6.7 - - - +
128A GLU* 4.3 1.0 - - - +
150A IOD 4.6 9.2 - - - -
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Residues in contact with LEU 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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74A MET* 3.5 32.8 - - + +
82A HIS* 3.6 37.9 - - + +
122A TRP* 2.8 28.9 + - + +
123A THR* 4.5 1.0 - - - +
125A GLY* 1.3 82.3 - - - +
127A PRO* 1.3 62.2 - - - +
128A GLU* 3.0 27.5 + - - +
129A GLU* 3.2 26.2 + - + +
132A ILE* 5.0 0.6 - - + +
150A IOD 4.1 18.2 - - + -
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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