Contacts of the helix formed by residues 135 - 153 (chain A) in PDB entry 2W3C
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 ASP 135 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A SER* 3.4 20.3 - - - -
133A GLU* 3.3 14.8 - - + +
134A PHE* 1.3 75.9 - - - +
136A PHE* 1.3 66.1 + - - +
137A HIS* 3.7 25.1 - - + -
138A VAL* 3.1 16.6 + - + +
139A ARG* 3.0 21.8 + - - +
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Residues in contact with PHE 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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134A PHE 3.1 3.8 + - - -
135A ASP* 1.3 70.7 - - - +
137A HIS* 1.3 65.9 + - + +
138A VAL 3.1 0.9 + - - -
140A TRP* 3.1 67.4 + + + +
179A ARG* 3.6 42.6 - - + +
181A VAL* 4.1 25.6 - - + -
182A ILE* 3.8 23.8 - - + -
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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
----------------------------------------------------------
76A SER* 2.7 50.7 + - - -
77A GLU* 3.5 27.3 + - - -
80A GLY* 3.1 23.3 - - - +
135A ASP* 3.7 22.8 - - + +
136A PHE* 1.3 86.4 + - + +
138A VAL* 1.3 56.4 + - - +
140A TRP* 6.4 0.2 - - - -
141A PRO* 3.3 15.1 - - - +
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Residues in contact with VAL 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A SER* 3.9 28.9 - - - +
79A ILE* 4.0 16.6 - - + -
80A GLY* 4.5 0.4 - - - +
83A LEU* 3.2 27.4 - - + +
130A LEU* 3.5 25.1 - - + +
131A LEU* 5.0 0.3 - - - +
133A GLU* 3.8 15.0 - - + -
135A ASP* 3.1 25.7 + - + +
137A HIS* 1.3 81.8 - - + +
139A ARG* 1.3 65.2 + - - +
140A TRP 3.4 1.6 - - - -
141A PRO* 3.4 2.3 - - - +
142A GLY* 3.2 18.9 + - - -
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Residues in contact with ARG 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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130A LEU 4.9 0.7 - - - -
131A LEU* 3.2 34.9 + - + +
132A GLU* 4.0 8.9 + - - +
133A GLU 3.2 19.5 + - - +
134A PHE* 3.3 39.2 - - - -
135A ASP 3.0 10.9 + - - +
138A VAL* 1.3 75.8 - - - +
140A TRP* 1.3 60.2 + - - +
142A GLY* 3.5 0.5 - - - -
143A VAL* 2.8 35.7 + - + +
173A ASP* 4.6 15.6 + - - +
174A LEU* 3.9 20.4 - - + +
177A ASP* 2.5 44.3 + - - +
179A ARG* 3.9 4.0 - - - +
182A ILE* 3.8 24.7 - - + -
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Residues in contact with TRP 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 PHE* 3.1 50.7 + + + +
139A ARG* 1.3 72.8 - - - +
141A PRO* 1.4 70.4 - - + +
143A VAL* 3.1 7.3 + - + +
144A LYS* 3.1 52.1 + - + +
181A VAL* 3.8 28.5 - - + +
182A ILE* 4.1 14.7 - - + +
185A ASP* 2.7 31.4 + - + -
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Residues in contact with PRO 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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80A GLY 3.9 9.2 - - - +
83A LEU* 3.8 10.5 - - + +
84A ASP* 3.8 36.8 - - - +
87A TYR* 4.7 2.5 - - + +
136A PHE 4.0 0.2 - - - +
137A HIS* 3.3 28.7 - - - +
138A VAL* 3.4 11.9 - - - +
140A TRP* 1.4 97.7 - - + +
142A GLY* 1.3 48.8 + - - -
144A LYS* 3.7 13.1 - - - +
145A LEU* 2.7 37.6 + - - +
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Residues in contact with GLY 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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83A LEU* 4.2 7.3 - - - +
127A LEU* 4.4 15.9 - - - +
130A LEU* 6.3 0.2 - - - -
131A LEU* 3.6 20.6 - - - +
138A VAL 3.2 14.7 + - - -
139A ARG 3.5 3.8 - - - -
140A TRP 3.1 1.4 - - - -
141A PRO* 1.3 75.2 - - - +
143A VAL* 1.3 56.8 + - - +
145A LEU* 3.1 4.2 + - - +
146A LEU* 2.9 31.2 + - - +
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Residues in contact with VAL 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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131A LEU* 3.8 4.8 - - + +
139A ARG* 2.8 38.4 + - + +
140A TRP* 3.4 10.5 - - + +
142A GLY* 1.3 70.4 - - - +
144A LYS* 1.3 52.4 + - - +
146A LEU 3.3 1.0 + - - -
147A THR* 2.7 39.4 + - - +
174A LEU* 4.0 23.8 - - + -
182A ILE* 4.4 11.9 - - + +
185A ASP* 3.6 45.1 - - + +
186A GLY* 4.1 2.9 - - - +
189A LEU* 3.4 14.4 - - + +
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Residues in contact with LYS 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 ASP* 4.5 10.5 + - - -
87A TYR* 3.4 48.5 - - + +
140A TRP* 3.1 69.5 + - + +
141A PRO* 3.7 11.5 - - - +
143A VAL* 1.3 75.8 - - + +
145A LEU* 1.3 64.7 + - - +
147A THR* 3.8 7.2 - - - -
148A SER* 3.2 22.0 + - - -
185A ASP* 3.8 14.4 - - - +
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Residues in contact with LEU 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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69A LEU* 5.6 0.2 - - + -
83A LEU* 4.2 13.9 - - + +
86A LEU* 3.9 16.6 - - + -
87A TYR* 3.8 34.0 - - + +
90A ILE* 3.8 31.9 - - + -
117A PHE* 4.4 11.7 - - + -
127A LEU* 3.8 31.6 - - + -
141A PRO 2.7 22.2 + - - +
142A GLY 3.5 4.0 - - - +
144A LYS* 1.3 73.9 - - - +
146A LEU* 1.3 63.6 + - - +
148A SER* 3.0 4.7 + - - -
149A LEU* 2.9 29.7 + - + +
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Residues in contact with LEU 146 (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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124A VAL* 4.6 7.0 - - + -
127A LEU* 3.9 15.9 - - + -
128A LEU* 4.0 14.1 - - + -
131A LEU* 3.8 12.6 - - + -
142A GLY 2.9 16.6 + - - +
145A LEU* 1.3 78.5 - - - +
147A THR* 1.3 56.6 + - - +
149A LEU* 3.4 23.1 + - + -
150A LEU* 2.9 36.0 + - + +
157A VAL* 4.2 18.2 - - + -
161A ILE* 4.5 9.6 - - + -
171A LEU* 3.8 29.4 - - + -
189A LEU* 3.8 12.8 - - + -
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Residues in contact with THR 147 (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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143A VAL* 2.7 25.9 + - - +
144A LYS* 3.8 8.1 - - - -
146A LEU* 1.3 76.9 - - - +
148A SER* 1.3 51.4 + - - +
150A LEU* 3.1 9.3 + - - +
151A LYS* 2.8 59.4 + - + +
185A ASP 4.4 1.0 + - - -
188A LEU* 3.7 29.2 - - + +
189A LEU* 3.5 20.7 + - - +
192A ALA* 4.3 4.0 - - + -
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Residues in contact with SER 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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87A TYR* 4.3 9.4 - - - -
90A ILE* 4.0 13.5 - - - +
91A SER* 3.7 25.5 - - - -
144A LYS 3.2 14.6 + - - -
145A LEU* 3.0 11.7 + - - -
147A THR* 1.3 77.5 - - - +
149A LEU* 1.3 61.9 + - - +
151A LYS* 3.6 9.7 + - - +
152A GLN* 3.0 37.1 + - - +
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Residues in contact with LEU 149 (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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90A ILE* 4.3 18.8 - - + -
114A THR* 3.5 26.5 - - + +
117A PHE* 3.6 42.0 - - + -
118A ILE* 4.1 7.2 - - + -
124A VAL* 4.8 4.5 - - + -
127A LEU* 3.6 22.0 - - + -
145A LEU* 2.9 18.6 + - + +
146A LEU* 3.6 16.2 - - + +
147A THR 3.3 0.2 - - - -
148A SER* 1.3 74.8 - - - +
150A LEU* 1.3 56.5 + - - +
152A GLN* 4.0 0.5 - - - +
153A LEU* 3.0 26.5 + - - +
157A VAL* 3.7 23.5 - - + +
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Residues in contact with LEU 150 (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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146A LEU* 2.9 26.7 + - + +
147A THR* 3.1 5.4 + - - +
149A LEU* 1.3 75.4 - - - +
151A LYS* 1.3 63.3 + - - +
154A GLY* 3.0 28.3 - - - -
157A VAL* 3.4 36.1 - - + -
158A GLN* 4.3 6.7 - - + +
161A ILE* 3.9 13.0 - - + -
189A LEU* 3.9 37.9 - - + +
192A ALA* 3.6 28.0 - - + +
193A LEU* 4.1 13.9 - - + +
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Residues in contact with LYS 151 (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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147A THR* 2.8 42.7 + - + +
148A SER* 4.0 8.6 + - - +
150A LEU* 1.3 73.3 - - - +
152A GLN* 1.3 63.1 + - + +
154A GLY 4.8 1.0 + - - -
192A ALA* 4.3 11.6 - - + +
195A ARG* 5.8 2.1 + - - -
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Residues in contact with GLN 152 (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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90A ILE* 2.8 35.4 + - - +
91A SER* 4.7 1.4 + - - +
92A ASN* 5.0 5.2 + - - +
111A SER* 2.8 36.9 + - - +
114A THR* 3.3 25.1 + - + -
148A SER* 3.0 23.7 + - - +
149A LEU 4.0 2.0 - - - +
151A LYS* 1.3 83.8 - - + +
153A LEU* 1.3 69.2 + - + +
154A GLY 3.7 0.8 + - - -
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Residues in contact with LEU 153 (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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111A SER 5.7 1.3 - - - +
114A THR* 4.0 13.0 - - + +
115A GLU* 3.7 55.4 - - + +
118A ILE* 3.7 19.3 - - + -
149A LEU 3.0 13.6 + - - +
152A GLN* 1.3 83.3 - - + +
154A GLY* 1.3 62.3 + - - +
155A PRO* 3.6 4.5 - - - -
156A GLN* 3.3 28.6 + - - +
157A VAL* 3.0 29.2 + - + +
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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
------------------------------------------------------------
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