Contacts of the helix formed by residues 118 - 139 (chain A) in PDB entry 3G33
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 PRO 118 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115A PRO 5.4 0.9 - - - +
116A GLY 3.9 6.0 - - - +
117A LEU* 1.3 92.0 - - + +
119A ALA* 1.3 65.1 + - - +
120A GLU* 3.2 6.7 - - + +
121A THR* 3.2 25.6 + - + +
122A ILE* 3.2 17.8 + - - +
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Residues in contact with ALA 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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118A PRO* 1.3 74.1 - - - +
120A GLU* 1.3 61.8 + - + +
122A ILE* 4.3 3.6 - - - +
123A LYS* 3.0 38.9 + - - +
213A PHE* 5.5 7.2 - - + -
270A GLU* 4.2 26.5 - - - +
299A TYR* 4.5 7.3 + - - +
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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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118A PRO* 3.2 5.2 - - + +
119A ALA* 1.3 81.7 - - + +
121A THR* 1.3 59.9 + - - +
123A LYS* 3.3 35.9 + - - +
124A ASP* 2.9 29.1 + - - +
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Residues in contact with THR 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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108A TYR* 3.9 21.1 - - - +
117A LEU* 4.2 19.7 - - + -
118A PRO* 3.2 31.1 + - + +
120A GLU* 1.3 76.5 - - - +
122A ILE* 1.3 65.1 + - - +
124A ASP* 3.4 6.0 + - - +
125A LEU* 3.0 26.8 + - + +
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Residues in contact with ILE 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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117A LEU* 3.3 39.5 - - + +
118A PRO 3.2 7.7 + - - +
119A ALA 4.4 1.6 - - - +
121A THR* 1.3 74.0 - - - +
123A LYS* 1.3 66.6 + - - +
125A LEU* 3.3 7.3 + - - +
126A MET* 2.9 22.5 + - - +
209A PHE* 4.1 9.2 - - + -
212A MET* 3.4 50.0 - - + +
213A PHE* 3.6 46.2 - - + -
299A TYR* 4.8 1.3 - - - +
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Residues in contact with LYS 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 ALA* 3.0 34.0 + - - +
120A GLU* 3.3 37.6 + - - +
122A ILE* 1.3 79.9 - - - +
124A ASP* 1.3 57.1 + - - +
126A MET* 3.3 0.6 + - - -
127A ARG* 3.0 28.4 + - + +
270A GLU* 3.8 16.4 + - - -
299A TYR* 3.2 39.5 + - + +
300A LEU* 3.5 37.0 - - + +
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Residues in contact with ASP 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 2.9 17.4 + - - +
121A THR* 3.7 6.1 - - - +
123A LYS* 1.3 76.8 - - - +
125A LEU* 1.3 65.0 + - - +
127A ARG* 3.1 25.8 + - - +
128A GLN* 3.1 49.2 + - - +
157A GLY 4.8 4.2 - - - +
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Residues in contact with LEU 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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108A TYR* 4.6 18.6 - - + +
117A LEU* 4.9 4.0 - - + -
121A THR* 3.0 31.3 + - + +
122A ILE* 3.3 6.7 + - - +
124A ASP* 1.3 78.1 - - + +
126A MET* 1.3 58.8 + - - +
128A GLN* 3.6 1.1 + - - -
129A PHE* 3.0 27.9 + - - +
153A VAL* 6.2 3.6 - - + -
157A GLY 5.6 4.0 - - - +
159A VAL* 4.0 23.9 - - + +
212A MET* 4.2 19.4 - - + +
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Residues in contact with MET 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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122A ILE 2.9 19.5 + - - +
123A LYS* 3.7 4.3 - - - +
125A LEU* 1.3 74.3 - - - +
127A ARG* 1.3 64.4 + - - +
129A PHE* 3.5 12.1 - - + +
130A LEU* 3.1 41.8 + - + +
205A VAL* 3.7 28.0 - - + -
208A ILE* 5.9 0.7 - - - -
209A PHE* 3.3 53.2 - - + -
212A MET* 3.8 20.4 - - - +
276A LEU* 5.6 3.6 - - + -
280A MET* 4.1 5.4 - - + -
300A LEU* 4.4 15.3 - - + -
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Residues in contact with ARG 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 LYS 3.0 14.3 + - - +
124A ASP* 3.1 27.7 + - - +
126A MET* 1.3 77.8 - - - +
128A GLN* 1.3 65.2 + - - +
130A LEU 3.3 1.2 + - - -
131A ARG* 2.9 72.3 + - - +
295A LEU* 3.5 22.8 - - + +
300A LEU* 4.6 19.3 - - + +
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Residues in contact with GLN 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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75A ASN* 3.2 42.0 - - - +
124A ASP* 3.1 43.4 + - - +
125A LEU* 4.1 1.1 - - - +
127A ARG* 1.3 85.0 - - - +
129A PHE* 1.3 64.7 + - - +
131A ARG* 3.9 5.4 - - - +
132A GLY* 3.2 10.9 + - - -
157A GLY 3.7 9.6 + - - +
158A THR* 3.3 13.8 + - - +
159A VAL* 2.9 38.0 + - + +
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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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105A LEU* 5.4 3.4 - - + -
125A LEU 3.0 20.4 + - - +
126A MET* 3.5 16.8 - - - +
127A ARG 3.2 0.2 - - - -
128A GLN* 1.3 78.5 - - - +
130A LEU* 1.3 61.4 + - + +
133A LEU* 3.4 23.6 + - + +
146A LEU* 4.2 18.6 - - + -
151A ILE* 3.0 44.6 - - + -
159A VAL* 4.3 8.7 - - + +
161A LEU* 3.6 30.3 - - + +
205A VAL* 3.4 47.6 - - + -
208A ILE* 4.3 11.7 - - + -
212A MET* 5.8 2.5 - - + -
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Residues in contact with LEU 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 MET* 3.1 33.5 + - + +
127A ARG 4.0 2.7 - - - +
129A PHE* 1.3 75.9 - - + +
131A ARG* 1.3 61.5 + - - +
133A LEU* 3.8 5.0 - - + +
134A ASP* 3.0 30.5 + - - +
202A MET* 4.1 24.0 - - + -
205A VAL* 3.8 28.3 - - + -
276A LEU* 5.8 2.0 - - + -
280A MET* 5.4 1.3 - - - -
291A ALA* 4.0 16.4 - - + +
294A ALA* 3.9 21.5 - - + -
295A LEU* 4.0 11.3 - - + +
300A LEU* 3.8 24.7 - - + -
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Residues in contact with ARG 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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73A HIS* 3.5 14.4 + - + +
74A PRO* 5.5 9.7 - - - +
75A ASN* 3.2 17.2 + - - +
127A ARG* 2.9 66.0 + - - +
128A GLN* 3.4 7.2 + - - +
130A LEU* 1.3 79.2 - - - +
132A GLY* 1.3 62.0 + - - +
134A ASP* 3.9 3.5 - - - +
135A PHE* 3.2 21.5 + - - +
295A LEU* 3.8 25.5 - - + +
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Residues in contact with GLY 132 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73A HIS* 3.6 18.7 - - - -
75A ASN* 3.6 19.5 - - - -
76A VAL* 4.3 1.3 - - - -
128A GLN 3.2 8.6 + - - -
129A PHE 4.4 0.7 - - - -
131A ARG* 1.3 76.8 - - - +
133A LEU* 1.3 60.1 + - - +
135A PHE* 3.2 4.0 + - - +
136A LEU* 2.9 32.6 + - - +
161A LEU* 4.1 7.4 - - - -
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Residues in contact with LEU 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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129A PHE* 3.4 19.3 + - + +
130A LEU* 3.9 8.3 - - + +
131A ARG 3.4 0.4 - - - -
132A GLY* 1.3 74.3 - - - +
134A ASP* 1.3 63.8 + - - +
136A LEU* 3.0 13.9 + - + +
137A HIS* 2.9 55.5 + - + -
143A HIS* 4.9 1.3 - - + -
146A LEU* 3.9 23.1 - - + -
161A LEU* 3.9 16.2 - - + +
201A ASP* 4.0 11.4 - - + +
202A MET* 3.9 16.2 - - - -
205A VAL* 3.5 31.6 - - + -
291A ALA* 4.2 3.8 - - + -
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Residues in contact with ASP 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 LEU 3.0 20.3 + - - +
131A ARG* 3.9 5.4 - - - +
133A LEU* 1.3 76.8 - - - +
135A PHE* 1.3 57.1 + - - +
137A HIS* 3.4 7.6 + - - +
138A ALA* 2.9 30.0 + - - +
290A SER* 6.0 0.3 - - - -
291A ALA* 4.0 13.6 + - + +
292A PHE* 3.5 46.6 + - - +
295A LEU* 5.3 6.6 - - + +
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Residues in contact with PHE 135 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68A LEU* 3.9 25.4 - - + -
71A PHE* 3.7 39.9 - + + -
73A HIS* 3.4 43.1 - + + +
76A VAL* 4.2 8.1 - - + -
131A ARG 3.2 15.4 + - - +
132A GLY 3.3 8.1 - - - +
133A LEU 3.1 0.6 - - - -
134A ASP* 1.3 77.4 - - - +
136A LEU* 1.3 76.7 + - + +
138A ALA* 3.2 14.5 + - + +
139A ASN* 3.1 47.0 + - - -
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Residues in contact with LEU 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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68A LEU* 4.2 12.6 - - + -
76A VAL* 3.4 30.3 - - + -
132A GLY 2.9 7.5 + - - +
133A LEU* 3.3 12.6 - - + +
135A PHE* 1.3 89.1 - - + +
137A HIS* 1.3 61.4 + - + +
139A ASN* 3.2 9.6 + - - +
140A CYS 3.3 0.2 + - - -
141A ILE* 2.9 49.8 + - + +
143A HIS* 4.8 10.8 - - + +
161A LEU* 4.1 26.5 - - + -
164A PHE* 4.1 28.9 - - + -
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Residues in contact with HIS 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 LEU* 2.9 54.3 + - + +
134A ASP* 3.8 10.9 + - - +
136A LEU* 1.3 72.6 - - + +
138A ALA* 1.3 64.7 + - - +
140A CYS* 3.2 13.5 + - - +
141A ILE 4.0 12.5 + - - +
142A VAL* 4.3 0.9 - - + -
198A THR* 2.6 48.0 + - + +
201A ASP* 2.8 32.9 + - + -
202A MET* 5.5 4.3 - - + -
291A ALA* 4.6 6.8 + - + +
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Residues in contact with ALA 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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134A ASP* 2.9 18.9 + - - +
135A PHE* 3.2 11.6 + - + +
137A HIS* 1.3 78.3 - - - +
139A ASN* 1.3 62.1 - - - +
140A CYS* 3.3 7.9 + - - -
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Residues in contact with ASN 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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64A LEU* 4.8 10.5 - - + +
68A LEU* 4.1 22.1 - - + +
71A PHE* 4.0 21.1 - - - -
135A PHE* 3.1 55.8 + - - +
136A LEU* 3.2 6.7 + - - +
138A ALA* 1.3 80.2 - - - +
140A CYS* 1.3 72.5 + - - +
141A ILE* 3.3 11.7 + - + +
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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