Contacts of the helix formed by residues 104 - 123 (chain A) in PDB entry 2G8I
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 104 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77A ASN* 3.3 7.6 - - - -
78A PRO* 4.3 2.0 - - + -
81A VAL* 3.7 10.7 - - - +
103A GLY* 1.3 78.1 - - - +
105A ASN* 1.3 65.2 + - - +
106A ASN 3.6 0.3 + - - -
107A MET* 3.0 23.1 + - - +
108A GLY* 3.1 17.8 + - - -
149A LEU* 3.8 33.7 - - + -
158A ILE* 5.5 0.2 - - - +
3C G 3.3 34.7 + - - +
4C T 2.7 20.3 + - - +
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Residues in contact with ASN 105 (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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72A VAL* 3.8 17.6 - - + +
74A SER* 5.5 7.8 - - - +
77A ASN* 3.0 21.6 + - + +
81A VAL* 4.8 1.3 - - - +
104A THR* 1.3 71.4 - - - +
106A ASN* 1.3 73.7 + - - -
108A GLY* 3.2 2.9 + - - -
109A GLU* 2.9 32.8 + - - +
6B A 3.0 42.5 + - + +
3C G 3.2 38.2 + - - +
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Residues in contact with ASN 106 (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 THR* 3.3 0.6 + - - -
105A ASN* 1.3 85.6 + - - +
107A MET* 1.3 64.7 + - - +
109A GLU* 3.3 6.4 + - - +
110A PHE* 2.9 24.1 + - - +
133A SER* 4.3 5.2 + - - -
135A THR* 3.9 19.3 - - + -
136A ALA* 4.4 1.6 - - - +
139A TRP* 3.6 24.6 - - + -
6B A 4.6 3.1 + - - -
3C G 3.1 40.9 + - - -
4C T 2.9 39.4 + - - +
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Residues in contact with MET 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A THR* 3.0 30.9 + - - +
106A ASN* 1.3 75.4 - - - +
108A GLY* 1.3 59.3 + - - +
110A PHE* 3.2 5.0 + - - +
111A LEU* 2.8 34.4 + - - +
139A TRP* 4.1 7.0 - - + -
147A SER* 3.5 22.0 - - - +
149A LEU* 3.6 22.7 - - + -
158A ILE* 3.8 15.9 - - + -
159A TRP* 3.4 52.9 - - + +
162A VAL* 3.8 29.4 - - + -
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Residues in contact with GLY 108 (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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72A VAL* 3.6 23.8 - - - -
81A VAL* 3.7 15.2 - - - +
83A TYR* 4.0 6.9 - - - +
104A THR 3.1 10.7 + - - -
105A ASN 3.7 0.2 - - - -
106A ASN 3.2 0.2 - - - -
107A MET* 1.3 75.4 - - - +
109A GLU* 1.3 62.8 - - - +
111A LEU* 3.3 9.7 + - - +
112A ALA* 3.0 24.3 + - - +
158A ILE* 5.1 0.2 - - - +
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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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70A VAL* 4.9 0.7 - - - +
71A ASP* 3.0 17.2 - - - +
72A VAL* 3.2 25.3 + - + +
105A ASN 2.9 23.4 + - - +
106A ASN* 3.7 4.7 - - - +
108A GLY* 1.3 75.0 - - - +
110A PHE* 1.3 61.9 + - - +
112A ALA* 3.5 5.3 + - - +
113A ILE* 3.3 27.0 + - - +
131A SER* 4.6 4.9 + - - -
132A ASP* 3.2 2.1 - - - +
133A SER* 3.6 32.4 - - - +
136A ALA* 3.6 4.4 - - + +
401A MN 2.1 30.8 + - - -
6B A 2.7 20.8 + - - +
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Residues in contact with PHE 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 ASN 2.9 13.9 + - - +
107A MET* 3.2 8.5 - - - +
109A GLU* 1.3 75.1 - - - +
111A LEU* 1.3 75.6 + - + +
113A ILE* 3.1 5.7 + - - +
114A VAL* 3.1 34.5 + - + +
136A ALA* 3.5 9.1 - - + +
139A TRP* 3.6 44.6 - + + -
140A VAL* 3.7 29.4 - - + -
144A LYS 5.0 0.4 - - - -
145A ALA* 3.9 18.4 - - + -
162A VAL* 4.0 13.9 - - + -
165A ALA* 3.7 22.2 - - + -
166A GLU* 4.0 15.5 - - + -
169A LEU* 3.9 11.4 - - + -
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Residues in contact with LEU 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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83A TYR* 3.6 18.3 + - + -
100A ILE* 4.3 10.8 - - + -
107A MET 2.8 23.0 + - - +
108A GLY* 3.8 5.6 - - - +
110A PHE* 1.3 75.9 - - + +
112A ALA* 1.3 56.9 + - - +
114A VAL* 3.9 4.0 - - - +
115A HIS* 2.9 32.1 + - - +
158A ILE* 3.8 28.5 - - + -
161A LEU* 3.5 43.7 - - + +
162A VAL* 3.8 13.0 - - + -
165A ALA* 3.9 11.2 - - + -
502A CL 4.0 14.6 - - + -
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Residues in contact with ALA 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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70A VAL* 3.6 32.3 - - + +
71A ASP* 4.2 7.9 - - - +
83A TYR* 3.7 31.1 - - + -
95A PHE* 4.2 1.4 - - - -
108A GLY 3.0 17.3 + - - +
109A GLU* 3.5 9.6 - - - +
110A PHE 3.1 0.2 - - - -
111A LEU* 1.3 78.4 - - - +
113A ILE* 1.3 57.5 + - - +
115A HIS* 3.8 2.1 - - - +
116A GLY 3.0 21.5 + - - -
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Residues in contact with ILE 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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70A VAL* 3.9 9.6 - - + -
109A GLU 3.3 7.8 + - - +
110A PHE 3.1 6.8 + - - +
112A ALA* 1.3 75.4 - - - +
114A VAL* 1.3 60.6 + - - +
116A GLY* 3.0 3.4 + - - -
117A LEU* 2.9 28.3 + - + +
129A ILE* 3.8 9.0 - - + +
131A SER* 3.5 35.9 - - - +
136A ALA* 3.8 35.9 - - + +
137A ILE* 3.9 9.6 - - + +
140A VAL* 3.7 17.0 - - + -
178A ILE* 3.8 29.4 - - + -
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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 PHE* 3.1 32.2 + - + +
111A LEU* 4.0 3.1 - - - +
113A ILE* 1.3 74.4 - - - +
115A HIS* 1.3 64.6 + - - +
117A LEU* 3.1 9.6 + - - +
118A ARG* 3.0 37.9 + - - +
140A VAL* 4.2 5.6 - - + -
165A ALA* 3.9 33.9 - - + +
168A TRP* 4.3 2.7 - - + -
169A LEU* 3.8 36.6 - - + -
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Residues in contact with HIS 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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83A TYR* 3.3 28.0 + + + +
95A PHE* 3.4 43.4 - + - +
96A GLU 6.5 0.2 - - - -
111A LEU 2.9 18.9 + - - +
112A ALA 3.8 1.6 - - - +
114A VAL* 1.3 76.7 - - - +
116A GLY* 1.3 58.7 + - - +
118A ARG* 3.3 9.8 + - - +
119A TYR* 2.8 31.7 + - - +
501A MPD 3.7 36.5 + - + +
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Residues in contact with GLY 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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68A LEU* 3.7 21.1 - - - -
70A VAL* 4.6 0.7 - - - -
95A PHE* 3.8 8.3 - - - -
112A ALA 3.0 12.7 + - - -
113A ILE 3.0 8.1 + - - -
115A HIS* 1.3 78.0 - - - +
117A LEU* 1.3 60.4 + - - +
119A TYR* 3.3 0.9 + - - +
120A LEU* 3.0 30.7 + - - +
129A ILE* 3.5 9.9 - - - -
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Residues in contact with LEU 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 ILE 2.9 17.2 + - - +
114A VAL* 3.1 8.5 + - - +
116A GLY* 1.3 76.4 - - - +
118A ARG* 1.3 57.8 + - - +
120A LEU* 4.0 3.2 - - - +
121A LYS* 3.0 30.5 + - - +
129A ILE* 3.5 6.9 - - + +
140A VAL* 3.9 16.4 - - + -
168A TRP* 4.1 12.0 - - + -
169A LEU* 3.7 28.9 - - + -
174A TYR* 3.8 30.3 - - + +
176A THR* 3.4 40.0 + - + +
178A ILE* 4.2 10.5 - - + -
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Residues in contact with ARG 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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114A VAL* 3.0 24.5 + - - +
115A HIS* 3.7 11.0 - - - +
117A LEU* 1.3 73.0 - - - +
119A TYR* 1.3 66.3 + - - +
121A LYS* 3.9 1.5 - - - +
122A GLU* 3.0 26.2 + - - +
164A GLU* 4.7 8.9 + - - +
165A ALA* 5.2 4.0 - - - +
168A TRP* 3.3 71.3 - - + +
501A MPD 3.2 43.6 + - + +
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Residues in contact with TYR 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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68A LEU* 4.3 3.1 - - + -
94A LEU* 3.2 53.1 + - + +
95A PHE* 3.8 28.9 - + + -
115A HIS* 2.8 18.8 + - - +
116A GLY 3.5 3.4 - - - +
118A ARG* 1.3 78.6 - - - +
120A LEU* 1.3 77.8 + - + +
122A GLU* 3.5 3.6 + - - +
123A ARG* 3.4 71.7 + - - +
501A MPD 3.5 23.9 - - + +
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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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68A LEU* 3.9 19.1 - - + -
116A GLY 3.0 17.6 + - - +
117A LEU 4.0 2.5 - - - +
119A TYR* 1.3 93.3 - - + +
121A LYS* 1.3 64.5 + - - +
123A ARG* 3.2 6.6 + - - +
124A ASN 3.1 4.0 + - - -
125A SER* 2.9 57.1 + - - +
127A LYS* 3.4 33.4 - - + +
129A ILE* 3.5 29.8 - - + -
176A THR* 4.0 9.6 - - + +
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Residues in contact with LYS 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 LEU 3.0 19.1 + - - +
118A ARG* 3.9 4.3 - - - +
120A LEU* 1.3 76.1 - - - +
122A GLU* 1.3 63.6 + - - +
124A ASN* 3.1 22.4 + - - +
125A SER 5.0 1.8 - - - +
168A TRP* 3.8 22.9 - - + -
172A HIS* 4.6 18.4 - - - -
173A THR* 3.0 36.6 + - - +
174A TYR* 5.3 5.6 - - + -
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Residues in contact with GLU 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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118A ARG 3.0 17.9 + - - +
119A TYR 3.8 5.2 - - - +
120A LEU 3.3 0.2 - - - -
121A LYS* 1.3 77.2 - - - +
123A ARG* 1.3 59.7 + - + +
124A ASN* 3.4 6.1 + - - +
501A MPD 3.9 29.9 - - + +
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Residues in contact with ARG 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 TYR* 3.4 65.1 + - - +
120A LEU* 3.4 10.3 - - - +
121A LYS 3.2 0.2 - - - -
122A GLU* 1.3 77.9 - - + +
124A ASN* 1.3 73.8 + - - +
125A SER* 3.3 16.3 + - - -
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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