Contacts of the helix formed by residues 132 - 147 (chain A) in PDB entry 2WAL
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 132 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A GLU* 2.8 26.3 - - - +
29A LEU* 3.9 13.7 - - + -
32A SER* 2.7 26.4 + - - +
36A GLN* 5.6 1.6 - - - +
130A TRP* 3.4 25.0 + - + +
131A LYS* 1.3 79.6 - - - +
133A PRO* 1.3 70.1 - - - +
134A ALA* 2.7 35.9 + - - +
135A LEU* 3.2 23.5 + - + +
136A GLU* 3.9 2.3 + - - +
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Residues in contact with PRO 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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28A GLU* 5.1 0.4 - - - +
130A TRP* 3.9 19.5 - - + +
131A LYS 3.1 9.6 - - - +
132A ASP* 1.3 86.8 - - - +
134A ALA* 1.3 63.5 + - - +
135A LEU 3.1 2.0 - - - -
136A GLU* 3.0 21.5 + - + +
137A LYS* 3.0 23.3 + - - +
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Residues in contact with ALA 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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25A ALA* 3.3 38.3 - - - +
28A GLU* 3.9 10.1 - - - +
29A LEU* 4.3 4.5 - - + -
132A ASP* 2.7 31.6 + - - +
133A PRO* 1.3 73.1 - - - +
135A LEU* 1.3 60.1 - - - +
137A LYS* 3.4 3.5 + - - +
138A LEU* 3.0 30.9 + - - +
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Residues in contact with LEU 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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29A LEU* 4.2 27.8 - - + +
58A ALA* 3.8 26.5 - - + +
59A PHE* 4.2 32.5 - - + -
91A ASP* 5.8 0.2 - - - +
122A ILE* 5.3 2.9 - - + -
124A ASN* 4.5 2.7 - - - +
131A LYS* 4.1 28.0 - - - +
132A ASP* 3.2 17.2 + - + +
133A PRO 3.1 0.8 - - - -
134A ALA* 1.3 77.7 - - - +
136A GLU* 1.3 56.9 + - - +
138A LEU* 3.3 3.1 + - + +
139A SER* 2.9 29.8 + - - -
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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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131A LYS* 6.4 2.0 - - + -
132A ASP 3.9 0.9 + - - +
133A PRO* 3.0 24.3 + - + +
135A LEU* 1.3 77.7 - - - +
137A LYS* 1.3 61.4 + - - +
139A SER* 3.1 8.5 + - - -
140A LEU* 2.9 30.3 + - + +
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Residues in contact with LYS 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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17A ALA 4.6 0.8 + - - -
18A ARG* 3.4 31.3 + - - +
21A GLY* 3.8 8.3 - - - +
22A ALA* 3.5 27.0 - - - +
25A ALA* 3.8 22.4 - - + -
133A PRO 3.0 12.1 + - - +
134A ALA* 3.8 6.5 - - - +
136A GLU* 1.3 76.0 - - - +
138A LEU* 1.3 59.9 + - - +
140A LEU* 3.2 17.6 + - + +
141A PHE* 2.8 32.9 + - - +
144A GLU* 5.3 3.9 + - - -
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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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22A ALA* 3.4 33.0 - - + +
25A ALA* 3.9 5.8 - - + -
26A LEU* 3.7 28.0 - - + +
29A LEU* 3.8 23.8 - - + -
59A PHE* 3.8 23.8 - - + -
134A ALA 3.0 21.4 + - - +
135A LEU 3.7 4.5 - - - +
137A LYS* 1.3 72.2 - - - +
139A SER* 1.3 66.7 + - - +
141A PHE* 3.3 6.0 + - + +
142A CYS* 3.0 29.7 + - - -
155A ILE* 3.8 24.5 - - + -
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Residues in contact with SER 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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59A PHE* 4.9 0.8 - - - -
91A ASP* 2.7 28.3 + - - +
135A LEU* 2.9 17.2 + - - -
136A GLU* 3.1 12.8 + - - -
138A LEU* 1.3 77.0 - - - +
140A LEU* 1.3 56.2 + - - +
142A CYS* 3.2 5.2 + - - +
143A GLU* 2.9 38.4 + - - +
146A ARG* 4.6 0.5 + - - -
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Residues in contact with LEU 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 GLU* 2.9 14.9 + - + +
137A LYS* 3.3 20.9 - - + +
139A SER* 1.3 74.1 - - - +
141A PHE* 1.3 54.4 + - - +
143A GLU* 3.1 20.4 + - + +
144A GLU* 2.7 64.6 + - + +
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Residues in contact with PHE 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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18A ARG* 3.0 69.4 + - + -
19A MET* 4.1 13.7 - - + -
22A ALA* 3.4 27.1 - - + -
93A VAL* 4.5 0.4 - - + -
137A LYS* 2.8 17.8 + - - +
138A LEU* 3.4 11.9 - - + +
140A LEU* 1.3 75.2 - - - +
142A CYS* 1.3 67.4 + - - +
144A GLU* 3.1 13.8 + - - +
145A SER* 3.0 21.5 + - - -
153A PRO* 4.2 9.9 - - + -
154A SER 3.7 20.2 - - - -
155A ILE* 3.5 30.7 - - + -
14B GLU* 6.2 0.2 - - - -
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Residues in contact with CYS 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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59A PHE* 4.0 4.3 - - - -
91A ASP* 3.9 32.5 - - - +
92A ILE 4.3 3.1 - - - -
93A VAL* 3.6 31.6 - - - -
138A LEU 3.0 18.2 + - - +
139A SER 3.2 7.2 + - - +
141A PHE* 1.3 79.0 - - - +
143A GLU* 1.3 62.4 + - - +
145A SER* 3.3 7.6 + - - -
146A ARG* 3.1 36.7 + - - +
153A PRO* 4.3 9.7 - - + +
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Residues in contact with GLU 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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139A SER* 2.9 24.7 + - - +
140A LEU* 3.1 22.7 + - + +
142A CYS* 1.3 75.7 - - - +
144A GLU* 1.3 64.8 + - - +
145A SER 3.2 0.2 + - - -
146A ARG* 3.3 23.4 + - - +
147A SER* 3.1 24.2 + - - -
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Residues in contact with GLU 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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18A ARG* 3.2 30.9 + - - +
137A LYS* 5.3 4.5 + - - -
140A LEU* 2.7 41.4 + - + +
141A PHE* 3.3 23.0 + - - +
143A GLU* 1.3 73.1 - - - +
145A SER* 1.3 59.7 + - - +
147A SER* 2.8 21.5 + - - +
148A VAL* 3.7 3.3 + - - +
13B PRO* 3.5 33.0 - - + +
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Residues in contact with SER 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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18A ARG* 3.0 20.6 + - - +
141A PHE* 3.0 10.7 + - - -
142A CYS 3.5 8.1 - - - -
143A GLU 3.1 0.4 - - - -
144A GLU* 1.3 72.5 - - - +
146A ARG* 1.3 67.5 + - - +
147A SER 3.1 1.6 - - - -
148A VAL* 2.9 14.9 + - - -
149A ASN 3.2 0.2 + - - -
150A ASP* 3.0 39.5 + - - +
153A PRO* 3.4 27.0 - - - +
13B PRO* 5.3 0.4 - - - -
14B GLU* 3.8 10.8 + - - -
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Residues in contact with ARG 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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89A ASP* 5.4 4.9 + - - +
90A ILE 4.9 2.2 + - - -
91A ASP* 2.7 38.4 + - - +
92A ILE* 5.2 1.6 - - - +
139A SER 4.6 0.6 + - - -
142A CYS* 3.1 18.5 + - - +
143A GLU* 3.6 43.1 - - - +
145A SER* 1.3 76.3 - - - +
147A SER* 1.3 56.9 + - - +
148A VAL 3.0 0.2 - - - -
149A ASN* 2.9 17.5 + - - +
150A ASP 3.7 3.3 + - - +
151A TRP* 3.2 47.6 + - + +
66B GLU* 4.1 15.8 + - - +
69B GLU* 5.8 0.4 - - - +
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Residues in contact with SER 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 GLU 3.1 12.2 + - - -
144A GLU* 2.8 25.0 + - - +
145A SER 3.1 0.2 - - - -
146A ARG* 1.3 75.9 - - - +
148A VAL* 1.3 62.0 + - - +
149A ASN* 3.5 4.1 + - - +
13B PRO* 4.4 7.8 - - - +
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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