Contacts of the helix formed by residues 121 - 140 (chain A) in PDB entry 6G0P
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 ASN 121 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58A ARG* 3.8 14.8 - - - +
60A THR* 5.1 1.8 - - - -
63A LEU* 3.7 16.8 - - - +
119A TYR* 3.6 2.0 - - - +
120A TRP* 1.3 89.3 - - + +
122A ALA* 1.3 62.9 + - - +
123A GLN* 3.0 13.9 + - - +
124A GLU* 3.0 49.4 + - - +
125A CYS 3.7 0.7 + - - -
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Residues in contact with ALA 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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60A THR* 4.8 1.6 + - - -
62A GLN* 3.6 39.4 + - + +
63A LEU* 3.8 7.7 - - - +
66A LEU* 3.6 24.2 - - + +
121A ASN* 1.3 75.1 - - - +
123A GLN* 1.3 60.6 + - + +
125A CYS* 3.0 5.0 + - - +
126A ILE* 2.9 37.6 + - + +
164A LEU* 4.9 3.6 - - + -
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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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62A GLN* 5.7 0.3 - - - +
121A ASN* 3.0 12.1 + - - +
122A ALA* 1.3 77.8 - - + +
124A GLU* 1.3 56.9 + - - +
126A ILE* 3.6 36.5 - - - +
127A GLN* 2.9 30.3 + - - +
164A LEU* 4.4 10.0 - - - +
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Residues in contact with GLU 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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55A LYS* 2.8 31.4 + - - -
118A TYR* 5.0 0.7 - - - -
119A TYR* 3.6 15.6 - - + -
120A TRP* 2.7 35.0 + - - +
121A ASN* 3.0 31.0 + - - +
122A ALA 3.2 0.2 - - - -
123A GLN* 1.3 77.1 - - - +
125A CYS* 1.3 60.9 + - - +
127A GLN* 3.4 7.4 + - - +
128A ASP* 3.2 25.3 + - - +
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Residues in contact with CYS 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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63A LEU* 4.1 5.2 - - + -
66A LEU* 3.9 17.5 - - + -
110A ILE* 4.0 7.6 - - - -
114A LEU* 3.9 16.6 - - - -
119A TYR* 3.6 38.8 - - + -
121A ASN 3.7 0.6 + - - -
122A ALA 3.0 8.9 + - - +
124A GLU* 1.3 77.6 - - - +
126A ILE* 1.3 65.6 + - - +
128A ASP* 3.0 13.3 + - - +
129A PHE* 3.1 35.0 + - - -
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Residues in contact with ILE 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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66A LEU* 4.1 20.9 - - + -
122A ALA 2.9 19.1 + - - +
123A GLN* 3.6 37.5 - - - +
125A CYS* 1.3 75.5 - - - +
127A GLN* 1.3 62.7 + - - +
129A PHE* 3.2 4.5 + - - +
130A ASN* 2.9 38.0 + - - +
157A PHE* 4.1 20.0 - - + -
161A ILE* 4.1 22.4 - - + -
164A LEU* 4.1 20.6 - - + -
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Residues in contact with GLN 127 (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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123A GLN 2.9 18.2 + - - +
124A GLU* 3.5 9.2 - - - +
125A CYS 3.2 0.2 - - - -
126A ILE* 1.3 76.5 - - - +
128A ASP* 1.3 60.5 + - - +
130A ASN* 3.2 14.5 + - - +
131A THR* 2.8 46.5 + - - +
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Residues in contact with ASP 128 (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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105A MET* 3.3 33.5 - - + +
110A ILE* 3.8 8.1 - - + -
113A ARG* 2.8 31.6 + - - -
119A TYR* 2.6 29.7 + - - +
124A GLU 3.2 9.5 + - - +
125A CYS 3.0 10.1 + - - +
127A GLN* 1.3 79.2 - - - +
129A PHE* 1.3 64.3 + - - +
131A THR* 3.3 4.5 + - - -
132A MET* 3.0 18.9 + - - +
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Residues in contact with PHE 129 (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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66A LEU* 4.5 9.4 - - + -
70A VAL* 4.5 5.6 - - + -
71A LEU* 4.1 25.4 - - + -
74A LEU* 4.1 21.3 - - + -
107A MET* 4.1 14.4 - - + -
110A ILE* 3.7 36.3 - - + +
114A LEU* 5.2 0.2 - - + -
125A CYS* 3.1 36.8 + - - -
126A ILE* 3.2 2.2 + - - +
128A ASP* 1.3 75.8 - - - +
130A ASN* 1.3 64.8 + - - +
132A MET* 3.1 19.6 + - + +
133A PHE* 3.1 31.2 + + + -
157A PHE* 3.5 43.7 - + + -
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Residues in contact with ASN 130 (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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126A ILE* 2.9 37.7 + - - +
127A GLN* 3.7 17.0 - - - +
129A PHE* 1.3 76.8 - - - +
131A THR* 1.3 57.3 - - - +
133A PHE* 3.3 9.3 + - - +
134A THR* 2.8 37.1 + - - +
154A GLU* 5.0 5.7 - - - +
157A PHE* 3.7 18.0 - - - -
158A LEU* 5.1 5.8 - - - +
161A ILE* 5.8 0.4 - - - +
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Residues in contact with THR 131 (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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103A THR* 3.1 43.3 - - + +
105A MET* 3.9 10.8 - - + -
127A GLN* 2.8 35.5 + - - +
128A ASP* 3.6 9.1 + - - +
130A ASN* 1.3 75.9 - - - +
132A MET* 1.3 63.4 + - - +
134A THR* 3.8 5.3 - - - -
135A ASN* 2.9 36.5 + - - +
201A EDO 5.9 0.4 - - - -
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Residues in contact with MET 132 (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 PHE* 4.1 28.1 - - + -
105A MET* 3.5 27.8 - - + +
106A ASP* 3.8 3.1 - - - -
107A MET* 3.6 50.5 - - + -
110A ILE* 4.8 2.2 - - + -
128A ASP 3.0 13.4 + - - +
129A PHE* 3.1 18.6 + - + +
131A THR* 1.3 76.8 - - - +
133A PHE* 1.3 100.4 + - + +
135A ASN* 3.5 5.0 + - - +
136A CYS* 3.3 20.1 + - - +
153A LEU* 5.7 1.1 - - + -
117B ALY 6.0 0.7 - - + +
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Residues in contact with PHE 133 (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 LEU* 4.2 7.9 - - + -
83A PHE* 5.4 2.0 - + - -
129A PHE* 3.1 27.6 + + + -
130A ASN* 3.8 9.4 - - - +
132A MET* 1.3 98.3 - - + +
134A THR* 1.3 68.8 + - - +
136A CYS* 3.1 8.0 + - - +
137A TYR* 3.1 39.5 + - + -
150A ALA* 3.6 36.1 - - + -
153A LEU* 3.9 17.3 - - + -
154A GLU* 3.6 39.3 - - + +
157A PHE* 3.9 22.7 - + - -
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Residues in contact with THR 134 (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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130A ASN* 2.8 27.5 + - - +
131A THR* 3.8 6.7 - - - -
133A PHE* 1.3 71.9 - - - +
135A ASN* 1.3 65.1 + - - +
137A TYR* 3.1 12.5 + - + +
138A ILE* 2.9 42.5 + - + +
201A EDO 6.1 0.9 - - - -
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Residues in contact with ASN 135 (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 TYR* 4.1 14.0 + - - +
101A ILE* 3.6 21.4 - - + +
103A THR 2.8 24.4 + - - +
104A PRO* 3.5 14.6 - - - +
105A MET 3.6 9.0 + - - +
131A THR* 2.9 25.1 + - - +
132A MET* 3.7 5.5 - - - +
134A THR* 1.3 76.8 - - - +
136A CYS* 1.3 63.3 + - - +
138A ILE* 3.2 3.9 + - - +
139A TYR* 3.0 28.1 + - - +
201A EDO 2.8 26.5 + - - -
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Residues in contact with CYS 136 (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 PHE* 4.1 12.6 - - + -
97A TYR* 5.7 0.2 - - - -
132A MET 3.3 9.7 + - - +
133A PHE 3.1 10.8 + - - +
135A ASN* 1.3 80.4 - - - +
137A TYR* 1.3 58.3 + - - +
140A ASN* 2.9 52.1 + - - +
146A ILE* 3.8 37.7 - - - -
147A VAL* 4.3 4.8 - - - +
150A ALA* 3.8 16.8 - - + -
117B ALY 4.0 10.1 - - + +
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Residues in contact with TYR 137 (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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133A PHE* 3.1 29.6 + - + -
134A THR* 3.1 9.2 + - + +
136A CYS* 1.3 76.3 - - + +
138A ILE* 1.3 65.4 + - + +
140A ASN 3.3 13.9 - - - +
147A VAL* 4.1 19.7 - - + -
150A ALA* 3.4 25.7 + - + +
151A GLU* 3.3 40.4 + - + +
154A GLU* 2.8 32.0 + - - +
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Residues in contact with ILE 138 (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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100A ILE* 3.9 25.6 - - + +
101A ILE* 4.1 4.7 - - + -
134A THR* 2.9 40.1 + - + +
135A ASN* 3.7 5.2 - - - +
137A TYR* 1.3 79.7 - - + +
139A TYR* 1.3 62.6 + - - +
140A ASN 4.0 1.9 - - - +
141A LYS* 5.6 0.5 + - - -
201A EDO 4.4 24.5 - - - -
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Residues in contact with TYR 139 (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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94A LEU* 3.6 25.8 - - + +
96A ASP* 2.7 37.3 + - - -
97A TYR* 3.6 48.9 - + + -
100A ILE* 3.8 24.9 - - + -
101A ILE* 4.4 4.9 - - + -
135A ASN 3.0 16.1 + - - +
138A ILE* 1.3 81.6 - - - +
140A ASN* 1.3 83.3 + - - +
141A LYS* 3.8 14.4 + - - -
115B PRO* 3.2 28.2 + - - +
116B GLY* 4.8 2.1 - - - -
117B ALY 4.9 2.2 - - + -
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Residues in contact with ASN 140 (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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136A CYS* 2.9 27.4 + - - +
137A TYR* 3.3 17.5 - - - +
138A ILE 4.0 1.9 - - - +
139A TYR* 1.3 98.4 - - - +
141A LYS* 1.3 65.8 + - - +
142A PRO* 4.6 1.6 - - - +
144A ASP* 3.7 7.3 - - - +
146A ILE* 3.3 22.7 - - + +
147A VAL* 3.5 17.2 - - + +
116B GLY* 4.5 2.7 - - - -
117B ALY 2.9 46.0 + - - +
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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
------------------------------------------------------------
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