Contacts of the helix formed by residues 133 - 148 (chain A) in PDB entry 2W9F
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 ARG 133 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125A CYS* 3.7 4.9 - - - -
130A ASN 5.4 2.7 - - - +
131A SER 5.7 0.2 - - - -
132A ILE* 1.3 84.3 - - - +
134A PRO* 1.3 59.8 - - + +
135A GLU* 2.7 29.2 + - + +
136A GLU* 2.5 50.9 + - + +
137A LEU 3.0 8.1 + - - -
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Residues in contact with PRO 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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121A ALA* 4.3 12.3 - - + -
122A GLU* 4.4 19.5 - - + +
125A CYS* 3.4 24.6 - - + -
132A ILE 4.4 0.4 - - - +
133A ARG* 1.3 85.2 - - + +
135A GLU* 1.3 64.9 + - - +
137A LEU* 3.4 5.8 + - + +
138A LEU* 2.8 44.7 + - + +
43B GLU 5.4 4.0 - - - +
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Residues in contact with GLU 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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133A ARG* 2.7 41.0 + - + +
134A PRO* 1.3 85.9 - - - +
136A GLU* 1.3 67.4 + - + +
138A LEU* 3.4 7.5 + - - +
139A GLN* 3.1 26.3 + - - +
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Residues in contact with GLU 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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98A ARG* 3.2 34.5 + - - +
101A LEU* 4.1 18.2 - - + +
131A SER 4.2 3.1 - - - +
132A ILE* 3.5 15.4 - - + +
133A ARG* 2.5 51.4 + - + +
135A GLU* 1.3 73.1 - - + +
137A LEU* 1.3 64.4 + - - +
139A GLN* 3.0 14.2 + - - +
140A MET* 3.0 22.2 + - - +
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Residues in contact with LEU 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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101A LEU* 3.9 12.4 - - + +
104A ALA* 3.7 15.3 - - + -
105A THR* 3.2 39.1 + - - +
108A PHE* 4.1 11.4 - - + -
121A ALA* 3.4 40.8 - - + +
124A LEU* 3.8 20.6 - - + -
125A CYS* 4.7 1.6 - - - -
132A ILE* 4.2 5.8 - - + +
133A ARG 3.0 5.3 + - - +
134A PRO* 3.4 12.1 - - + +
136A GLU* 1.3 79.0 - - - +
138A LEU* 1.3 58.5 + - - +
140A MET* 3.2 4.3 + - - +
141A GLU* 2.9 27.3 + - - +
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Residues in contact with LEU 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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108A PHE* 4.1 14.6 - - + -
121A ALA* 4.1 21.3 - - + -
134A PRO* 2.8 31.6 + - + +
135A GLU* 4.0 7.0 - - - +
136A GLU 3.3 0.2 - - - -
137A LEU* 1.3 73.0 - - + +
139A GLN* 1.3 62.0 + - - +
141A GLU* 3.5 9.2 + - - +
142A LEU* 3.5 24.0 + - - +
41B ASN* 4.7 4.7 - - - +
42B GLY 4.1 9.0 - - - +
43B GLU* 3.7 13.7 - - - +
44B GLU 4.1 1.1 - - - -
48B GLY* 3.3 40.6 - - - +
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Residues in contact with GLN 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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135A GLU 3.1 15.1 + - - +
136A GLU* 3.0 14.0 + - - +
138A LEU* 1.3 73.6 - - - +
140A MET* 1.3 65.7 + - - +
142A LEU* 3.2 16.7 + - - +
143A LEU* 3.2 23.3 + - + +
82B ARG* 3.9 28.6 + - - +
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Residues in contact with MET 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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88A PHE* 4.9 11.2 - - + -
94A VAL* 5.3 4.9 - - + -
98A ARG* 4.4 20.9 - - + +
101A LEU* 3.5 39.3 - - + +
102A LEU* 4.6 23.1 - - + -
105A THR* 2.9 25.4 - - + +
136A GLU 3.0 9.1 + - - +
137A LEU 3.2 4.2 + - - +
139A GLN* 1.3 76.8 - - - +
141A GLU* 1.3 51.6 + - - +
143A LEU* 2.9 28.1 + - + +
144A LEU* 2.7 36.6 + - - +
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Residues in contact with GLU 141 (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 THR* 3.3 15.7 - - + +
108A PHE* 3.5 14.4 - - + -
109A VAL* 3.9 18.2 - - + +
112A LYS* 2.5 36.2 + - - +
137A LEU 2.9 16.0 + - - +
138A LEU* 3.6 12.2 - - - +
139A GLN 3.2 0.2 - - - -
140A MET* 1.3 72.9 - - - +
142A LEU* 1.3 57.5 + - - +
144A LEU* 3.9 0.2 - - - +
145A VAL* 2.9 36.5 + - + +
48B GLY* 3.6 7.8 - - - -
49B LEU* 2.9 46.0 + - + +
54B VAL* 4.7 1.2 - - - +
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Residues in contact with LEU 142 (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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138A LEU 3.5 12.1 + - - +
139A GLN 3.2 8.2 + - - +
140A MET 3.1 0.6 - - - -
141A GLU* 1.3 75.9 - - - +
143A LEU* 1.3 66.1 + - + +
145A VAL* 4.9 0.7 - - + -
146A ASN* 2.5 40.0 + - - +
150A TRP* 5.2 0.4 - - + -
41B ASN* 6.0 1.8 - - - +
49B LEU* 3.8 29.6 - - + -
79B ALA* 3.7 31.2 - - + -
80B THR 5.1 1.1 - - - +
82B ARG* 3.1 45.8 - - + +
87B ILE* 4.4 14.1 - - + -
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Residues in contact with LEU 143 (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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88A PHE* 4.3 17.9 - - + -
92A GLU* 5.9 3.4 - - + +
139A GLN* 3.2 30.1 + - + +
140A MET* 2.9 28.8 + - + +
142A LEU* 1.3 80.0 - - + +
144A LEU* 1.3 56.7 + - - +
146A ASN* 3.2 4.0 + - - +
147A LYS* 2.8 36.6 + - + +
82B ARG* 4.8 11.4 - - - +
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Residues in contact with LEU 144 (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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84A TYR* 4.2 12.1 - - + +
88A PHE* 3.6 37.2 - - + -
102A LEU* 4.4 7.0 - - + -
105A THR* 4.0 13.9 - - + +
106A CYS* 3.2 45.1 - - - +
109A VAL* 4.7 3.4 - - + -
140A MET* 2.7 19.7 + - - +
141A GLU 3.9 2.7 - - - +
143A LEU* 1.3 73.8 - - - +
145A VAL* 1.3 62.2 + - + +
147A LYS* 3.4 1.2 + - - +
148A LEU* 3.0 56.5 + - + +
152A LEU* 6.0 0.2 - - + -
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Residues in contact with VAL 145 (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 VAL* 4.1 14.6 - - + -
141A GLU* 2.9 30.3 + - + +
142A LEU* 4.4 1.3 - - - +
144A LEU* 1.3 74.1 - - + +
146A ASN* 1.3 58.7 + - - +
148A LEU 3.4 0.9 + - - -
149A LYS 3.1 5.0 + - - -
150A TRP* 2.8 71.9 + - + +
152A LEU* 3.5 36.1 - - + -
49B LEU* 4.0 15.5 - - + -
54B VAL* 6.3 0.7 - - + -
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Residues in contact with ASN 146 (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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142A LEU* 2.5 39.7 + - - +
143A LEU* 3.8 3.5 - - - +
145A VAL* 1.3 75.6 - - - +
147A LYS* 1.3 59.5 + - - +
149A LYS* 3.0 23.7 + - - +
150A TRP* 3.3 14.0 + - - -
76B ASP* 5.1 0.5 - - - +
77B VAL 4.8 2.8 - - - +
78B CYS* 3.5 14.1 - - - -
79B ALA* 2.9 45.1 + - - +
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Residues in contact with LYS 147 (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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88A PHE* 3.7 34.5 - - + -
91A LEU* 2.9 50.8 + - + +
92A GLU* 2.3 36.9 + - + +
143A LEU* 2.8 20.6 + - + +
144A LEU 3.9 0.2 - - - +
146A ASN* 1.3 73.8 - - - +
148A LEU* 1.3 59.9 + - + +
149A LYS* 3.2 9.1 + - - +
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Residues in contact with LEU 148 (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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84A TYR* 3.8 24.2 - - + +
87A ARG* 3.6 56.1 + - + +
88A PHE* 4.5 1.8 - - - +
91A LEU* 5.3 2.7 - - + -
144A LEU* 3.0 48.5 + - + +
145A VAL 3.9 3.6 - - - +
146A ASN 3.1 0.4 - - - -
147A LYS* 1.3 79.7 - - + +
149A LYS* 1.3 69.4 + - - +
150A TRP 3.1 0.2 - - - -
151A ASN* 2.8 23.6 + - - +
152A LEU* 3.7 26.7 - - + -
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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