Contacts of the helix formed by residues 140 - 157 (chain A) in PDB entry 2WP9
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 140 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A ALA 3.9 4.3 - - - -
137A ALA* 2.8 14.5 + - - +
138A ALA* 4.7 0.6 - - + +
139A ASP* 1.3 83.3 - - - +
141A THR* 1.3 64.4 + - - +
142A GLY 3.2 3.1 - - - -
143A HIS* 3.1 19.1 + - + +
144A ALA* 2.9 20.3 + - - +
328A PRO* 3.4 33.6 - - - +
329A GLY* 4.3 8.1 - - - -
332A GLU* 3.1 35.6 + - - -
147B TYR* 3.8 24.9 + - + +
148B GLU* 3.7 37.8 + - - +
218B LYS* 5.2 9.3 - - - +
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Residues in contact with THR 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ALA 3.6 0.2 + - - -
50A GLN 3.2 19.2 + - - -
51A GLY 3.9 0.9 + - - -
52A GLY* 3.5 28.1 - - - -
53A ILE* 4.1 21.8 - - + -
104A LEU* 5.3 3.4 - - + -
106A PHE* 4.9 4.7 - - + -
135A ALA 4.2 2.7 - - - +
136A ALA* 3.5 2.8 - - - +
137A ALA* 2.9 36.5 + - + +
138A ALA 4.1 0.2 + - - -
140A ARG* 1.3 75.2 - - - +
142A GLY* 1.3 57.8 + - - +
144A ALA* 3.1 1.6 + - - +
145A LEU* 2.8 29.2 + - + +
405A LEU* 4.3 4.3 - - + -
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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
----------------------------------------------------------
46A THR* 3.1 26.1 - - - +
47A VAL* 4.0 0.2 - - - -
49A ALA* 2.7 30.4 + - - +
141A THR* 1.3 70.2 - - - +
143A HIS* 1.3 65.1 + - - +
145A LEU* 3.2 6.6 + - - +
146A LEU* 2.8 27.5 + - - +
405A LEU* 4.4 3.6 - - - +
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Residues in contact with HIS 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A VAL* 3.2 33.5 + - - +
49A ALA 4.0 0.2 + - - -
140A ARG* 3.1 21.0 + - + +
142A GLY* 1.3 76.0 - - - +
144A ALA* 1.3 69.1 + - - +
146A LEU* 4.0 0.2 - - - -
147A HIS* 3.1 56.4 + + + +
59B VAL* 4.6 11.4 + - + +
147B TYR* 2.7 38.5 + + - -
148B GLU* 3.6 15.8 - - - -
149B CYS 3.1 25.5 + - - -
150B ILE* 4.4 4.2 - - + +
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Residues in contact with ALA 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A LEU* 3.8 21.3 - - + -
105A PRO* 3.8 17.2 - - + +
137A ALA* 3.9 14.6 - - + -
140A ARG 2.9 12.6 + - - +
141A THR 3.1 7.1 + - - +
143A HIS* 1.3 82.6 - - - +
145A LEU* 1.3 58.7 + - - +
147A HIS* 4.2 2.0 - - - +
148A THR* 2.7 34.9 + - - -
147B TYR* 4.5 5.8 - - + -
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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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17A GLY* 5.1 0.9 - - - -
46A THR* 4.3 9.4 - - + -
53A ILE* 4.7 4.5 - - + -
99A LEU* 3.6 30.7 - - + -
104A LEU* 3.6 15.4 - - + +
141A THR* 2.8 22.6 + - + +
142A GLY 3.7 3.6 - - - +
144A ALA* 1.3 75.1 - - - +
146A LEU* 1.3 59.0 + - - +
148A THR* 3.3 2.5 + - - -
149A LEU* 3.0 50.2 + - + +
405A LEU* 3.7 39.7 - - + +
408A LEU* 4.9 4.5 - - + -
409A VAL* 4.3 11.9 - - + -
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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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15A ALA 4.0 0.2 - - - +
16A GLY* 3.8 27.1 - - - -
17A GLY* 3.8 5.8 - - - +
20A MET* 3.0 29.9 - - + +
41A PRO 3.5 13.7 - - - +
42A THR* 3.5 30.1 - - - +
44A SER* 3.9 7.2 - - - +
46A THR* 4.0 9.4 - - + -
47A VAL* 3.8 23.3 - - + +
142A GLY 2.8 17.0 + - - +
143A HIS 4.1 1.6 - - - +
145A LEU* 1.3 75.0 - - - +
147A HIS* 1.3 68.2 + - - +
149A LEU* 3.1 4.8 + - + +
150A TYR* 2.8 23.1 + - - +
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Residues in contact with HIS 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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42A THR* 3.5 37.9 + - + -
47A VAL* 4.3 11.1 - - + +
143A HIS* 3.1 59.4 + + - +
144A ALA* 4.2 2.5 - - - +
146A LEU* 1.3 75.4 - - - +
148A THR* 1.3 63.8 + - - +
150A TYR* 3.2 4.8 + + + +
151A GLN* 2.9 39.3 + - - +
114B TYR* 4.8 7.9 - - - -
147B TYR 5.8 0.7 - - - +
149B CYS 3.9 6.0 + - - -
150B ILE* 4.6 7.5 - - - -
151B LEU* 3.7 24.4 - - + +
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Residues in contact with THR 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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99A LEU* 4.2 2.7 - - + +
102A MET* 3.6 39.0 - - + +
103A GLY 4.3 1.1 - - - -
104A LEU* 3.3 37.0 - - + +
105A PRO* 3.9 4.5 - - - +
144A ALA 2.7 23.6 + - - -
145A LEU* 3.6 4.9 - - - -
146A LEU 3.2 0.4 - - - -
147A HIS* 1.3 77.4 - - - +
149A LEU* 1.3 59.4 + - + +
151A GLN* 3.3 15.2 + - - +
152A GLN* 3.0 27.3 + - + +
180B ARG* 5.5 0.7 + - - -
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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
----------------------------------------------------------
17A GLY* 3.7 35.7 - - - +
20A MET* 4.0 13.9 - - + -
21A ARG* 4.1 30.7 - - + +
24A LEU* 4.4 15.7 - - + -
99A LEU* 4.2 14.1 - - + -
102A MET* 4.4 7.0 - - - -
145A LEU* 3.0 39.2 + - + +
146A LEU* 3.1 5.1 + - - +
148A THR* 1.3 76.3 - - + +
150A TYR* 1.3 65.3 + - - +
152A GLN* 3.3 4.2 + - - +
153A ASN* 3.0 28.1 + - - -
409A VAL* 5.2 2.7 - - + -
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Residues in contact with TYR 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A MET* 3.7 13.6 - - - -
40A PHE* 3.2 33.8 - + - -
41A PRO* 3.8 35.2 - - + -
42A THR* 3.6 27.6 - - + -
146A LEU 2.8 12.4 + - - +
147A HIS* 3.7 4.3 - + - +
149A LEU* 1.3 75.7 - - - +
151A GLN* 1.3 64.9 + - + +
153A ASN* 2.9 5.1 + - + +
154A LEU* 2.8 59.4 + - + +
160A ILE* 3.9 20.1 - - + +
111B TYR* 5.2 3.3 - - - +
114B TYR* 4.4 18.4 - + - -
115B GLU* 4.7 5.4 + - - +
151B LEU* 5.2 1.3 - - + -
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Residues in contact with GLN 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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102A MET 5.0 3.0 - - - +
103A GLY 6.0 0.3 - - - -
147A HIS* 2.9 27.5 + - - +
148A THR* 3.4 20.5 + - - +
150A TYR* 1.3 77.7 - - + +
152A GLN* 1.3 58.0 + - - +
154A LEU* 3.2 11.2 + - - +
155A LYS 2.8 25.1 + - - -
114B TYR* 3.2 28.3 + - + +
119B PRO* 2.9 25.7 + - + +
120B TYR* 3.5 15.8 - - + -
180B ARG* 4.7 10.8 + - - +
181B PHE* 3.5 27.6 - - - -
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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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24A LEU* 3.6 20.3 - - + +
28A GLN* 5.5 2.8 - - - +
102A MET* 3.3 61.0 - - + +
148A THR 3.0 18.3 + - - +
149A LEU* 3.6 8.3 - - - +
151A GLN* 1.3 75.2 - - - +
153A ASN* 1.3 58.8 + - - +
155A LYS* 3.4 21.4 + - - +
156A ASN* 2.8 42.4 + - - +
120B TYR* 4.2 13.7 - - - +
121B LEU 4.5 3.3 + - - +
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Residues in contact with ASN 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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20A MET* 3.1 38.2 + - - +
23A ALA* 4.0 2.3 - - - +
24A LEU* 3.7 23.3 + - - +
35A LEU* 4.7 5.8 - - - -
149A LEU* 3.0 20.8 + - - +
150A TYR* 2.9 11.0 + - - +
152A GLN* 1.3 75.4 - - - +
154A LEU* 1.3 65.3 + - - +
156A ASN 3.3 0.2 + - - -
157A HIS 3.0 18.4 + - - -
158A THR* 2.5 48.1 + - - +
160A ILE* 4.5 13.5 - - + -
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Residues in contact with LEU 154 (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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150A TYR* 2.8 60.2 + - + +
151A GLN* 3.4 8.5 - - - +
153A ASN* 1.3 74.8 - - - +
155A LYS* 1.3 65.4 + - - +
157A HIS* 2.9 24.7 + - - +
160A ILE* 5.2 5.2 - - + -
114B TYR* 4.0 6.5 - - + -
115B GLU* 4.0 40.2 - - + +
119B PRO* 4.0 22.9 - - + -
120B TYR* 4.3 9.8 + - + -
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Residues in contact with LYS 155 (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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151A GLN 2.8 16.9 + - - +
152A GLN* 3.6 24.4 + - - +
153A ASN 3.3 0.2 - - - -
154A LEU* 1.3 76.7 - - - +
156A ASN* 1.3 70.1 + - - +
157A HIS* 3.5 13.8 + - - -
120B TYR* 3.7 46.8 - - + -
121B LEU 4.1 12.7 + - - +
122B LEU* 4.5 13.1 - - - +
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Residues in contact with ASN 156 (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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24A LEU* 2.6 36.5 - - + +
27A SER* 4.9 12.6 + - - +
28A GLN* 3.1 29.5 + - + +
152A GLN* 2.8 19.8 + - - +
153A ASN 3.3 2.2 + - - +
154A LEU 3.1 0.2 - - - -
155A LYS* 1.3 91.7 + - - +
157A HIS* 1.3 74.9 + - - +
158A THR* 3.2 5.9 + - - +
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Residues in contact with HIS 157 (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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153A ASN 3.0 1.5 + - - -
154A LEU* 2.9 22.1 + - - +
155A LYS* 3.9 12.1 + - - -
156A ASN* 1.3 79.8 - - - +
158A THR* 1.3 69.1 + - - +
159A THR* 3.4 5.4 + - - -
120B TYR* 5.7 4.3 - - - -
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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