Contacts of the helix formed by residues 132 - 148 (chain B) in PDB entry 6D6Q
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 GLY 132 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B ARG* 4.3 7.9 + - - -
42B GLN* 4.7 3.5 - - - +
45B THR* 4.0 4.5 + - - +
131B GLY* 1.3 76.4 - - - +
133B THR* 1.3 62.4 + - - +
134B TYR 3.6 2.2 - - - -
135B ALA* 4.5 8.7 - - - -
136B ALA* 3.9 18.4 + - - +
160B SER* 4.5 16.4 + - - -
171B ASP* 5.8 2.5 - - - -
172B LEU* 3.9 9.2 + - - +
177B GLU* 3.6 8.9 + - - -
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Residues in contact with THR 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B THR* 5.0 4.9 - - - +
75B TYR* 3.4 23.2 + - - +
77B SER* 5.5 1.8 - - - +
126B VAL* 4.0 24.4 - - + +
129B ALA* 3.7 22.0 - - + +
131B GLY* 4.2 9.9 + - - -
132B GLY* 1.3 74.4 - - - +
134B TYR* 1.3 60.5 + - - +
136B ALA* 4.4 2.5 - - - +
137B CYS* 3.2 24.3 + - - -
177B GLU* 5.4 4.0 + - - -
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Residues in contact with TYR 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B TYR* 5.5 4.3 - + - -
98B MET* 3.4 35.2 - - + +
101B GLN* 3.4 28.1 + - + +
102B LEU* 3.5 34.9 + - + +
105B THR* 3.9 2.8 - - - +
132B GLY 3.6 0.2 - - - -
133B THR* 1.3 78.8 - - - +
135B ALA* 1.3 62.3 + - + +
137B CYS* 3.1 9.2 + - + +
138B VAL* 2.9 45.4 + - + +
158B ALA* 5.3 2.2 - - + -
185B ALA* 5.1 17.5 - - + -
186B LEU 5.8 2.0 - - - -
187B ALA* 5.3 3.6 - - + -
197B LEU* 2.8 37.6 - - + +
199B GLU* 5.9 1.8 - - + -
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Residues in contact with ALA 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B GLN* 4.4 9.4 - - - +
132B GLY* 4.4 10.3 + - - +
134B TYR* 1.3 78.1 - - + +
136B ALA* 1.3 67.5 + - - +
138B VAL* 3.2 2.6 + - - +
139B ASN* 2.9 30.0 + - - -
158B ALA* 3.8 16.6 - - + +
159B CYS* 3.7 35.2 - - - +
160B SER* 4.9 2.9 - - - +
185B ALA* 6.1 2.2 - - + -
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Residues in contact with ALA 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B ILE* 3.7 13.0 - - + +
42B GLN* 3.4 23.3 + - + +
45B THR* 3.8 29.8 - - + -
47B ALA* 3.9 10.3 - - + -
132B GLY 3.9 8.9 + - - +
133B THR 4.5 3.1 - - - +
134B TYR 3.3 0.4 - - - -
135B ALA* 1.3 77.5 - - - +
137B CYS* 1.3 57.7 + - - +
139B ASN* 3.4 3.7 + - - +
140B ALA* 2.9 30.0 + - - +
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Residues in contact with CYS 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B ALA* 4.1 11.7 - - - -
75B TYR* 3.9 11.9 - - + -
102B LEU* 4.9 8.3 - - + -
124B VAL* 3.3 29.8 - - + +
126B VAL* 3.2 29.8 - - - -
133B THR 3.2 22.2 - - - -
134B TYR* 3.1 10.2 + - + +
135B ALA 3.1 0.2 - - - -
136B ALA* 1.3 77.1 - - - +
138B VAL* 1.3 67.3 + - - +
140B ALA* 3.8 1.1 - - - +
141B ALA* 2.9 26.2 + - - +
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Residues in contact with VAL 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B LEU* 3.8 12.8 - - + +
105B THR* 5.6 4.3 - - + +
106B PHE* 3.6 11.7 - - + -
134B TYR* 2.9 51.4 + - + +
135B ALA 3.5 5.8 - - - +
137B CYS* 1.3 76.9 - - - +
139B ASN* 1.3 58.3 + - - +
141B ALA 3.3 0.2 + - - -
142B THR* 2.9 29.5 + - - -
156B VAL* 3.6 30.7 - - + +
158B ALA* 3.8 18.8 - - + -
187B ALA* 4.4 8.1 - - + -
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Residues in contact with ASN 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B ILE* 3.9 17.5 - - + +
42B GLN* 4.2 10.7 + - - -
135B ALA 2.9 23.9 + - - +
136B ALA 3.9 3.1 - - - +
138B VAL* 1.3 72.6 - - - +
140B ALA* 1.3 67.0 + - - +
142B THR* 3.2 6.9 + - - -
143B LEU* 3.0 30.8 + - - +
156B VAL 3.9 2.8 - - - +
157B CYS* 3.6 10.6 - - - +
158B ALA 3.3 37.9 + - - -
223B VAL* 3.8 13.5 - - - +
227B LEU* 4.0 18.7 - - + +
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Residues in contact with ALA 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B ALA* 3.5 13.6 - - + +
39B TYR 5.2 0.2 - - - -
40B ILE* 3.8 23.6 - - + +
47B ALA* 4.1 11.4 - - + +
48B LEU* 4.6 1.6 - - - +
49B ALA* 3.4 25.6 - - + +
136B ALA 2.9 18.1 + - - +
137B CYS* 3.8 4.0 - - - +
139B ASN* 1.3 77.2 - - - +
141B ALA* 1.3 56.7 + - - +
143B LEU* 3.3 4.3 + - - -
144B ALA 2.9 22.3 + - - -
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Residues in contact with ALA 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B ALA* 3.5 13.6 - - + +
51B VAL* 4.5 0.4 - - - +
102B LEU* 5.8 1.1 - - + -
106B PHE* 3.5 26.9 - - + -
122B ILE* 4.2 20.9 - - + -
124B VAL* 4.5 5.6 - - + -
137B CYS 2.9 17.4 + - - +
140B ALA* 1.3 76.2 - - - +
142B THR* 1.3 57.2 + - - +
144B ALA* 3.3 2.9 + - - +
145B VAL* 2.9 35.9 + - + +
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Residues in contact with THR 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B PHE* 3.7 6.8 - - - -
138B VAL 2.9 15.5 + - - -
139B ASN* 3.2 11.2 + - - -
141B ALA* 1.3 73.5 - - - +
143B LEU* 1.3 70.2 + - + +
144B ALA 3.2 0.2 + - - -
145B VAL* 3.3 6.2 + - - +
146B LEU* 3.0 28.4 + - + +
152B MET* 4.1 18.4 - - + -
155B PHE* 4.1 25.4 - - + -
156B VAL* 3.2 36.9 + - - +
227B LEU* 5.2 2.9 - - + -
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Residues in contact with LEU 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B ALA* 4.1 25.4 - - + -
27B ARG 4.3 4.9 - - - +
28B MET* 3.5 43.5 - - + +
38B ALA* 3.7 11.7 - - + -
39B TYR 4.7 2.0 - - - +
40B ILE* 5.6 3.8 - - + -
139B ASN* 3.0 28.3 + - + +
140B ALA* 3.7 9.2 - - - +
142B THR* 1.3 77.4 - - + +
144B ALA* 1.3 62.8 + - - +
146B LEU* 3.3 6.1 + - + -
147B ASP* 2.9 19.6 + - - +
155B PHE* 5.5 0.9 - - + -
227B LEU* 3.4 36.1 - - + +
230B VAL* 5.0 5.6 - - + -
231B VAL* 4.8 7.6 - - + -
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Residues in contact with ALA 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B GLY* 4.1 0.8 - - - +
37B SER* 4.2 14.6 - - - +
38B ALA* 3.7 10.2 - - + +
49B ALA* 4.0 15.9 - - + -
51B VAL* 3.6 28.6 - - + +
140B ALA 2.9 13.8 + - - +
141B ALA 3.4 9.0 - - - +
142B THR 3.1 0.2 - - - -
143B LEU* 1.3 73.0 - - - +
145B VAL* 1.3 68.5 + - - +
147B ASP* 2.8 14.6 + - - +
148B ALA 2.9 9.7 + - - -
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Residues in contact with VAL 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B VAL* 4.0 19.5 - - + +
106B PHE* 4.7 12.3 - - + -
110B ILE* 3.2 35.2 - - + -
120B ILE* 6.0 0.7 - - + -
122B ILE* 4.8 8.1 - - + -
141B ALA 2.9 24.0 + - - +
142B THR* 3.5 8.1 - - - +
144B ALA* 1.3 70.6 - - - +
146B LEU* 1.3 63.9 + - - +
148B ALA* 2.9 14.1 + - - +
149B GLY 3.4 6.9 + - - -
150B ILE* 3.4 20.5 + - + +
152B MET* 3.2 22.7 - - + -
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Residues in contact with LEU 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B MET* 4.3 7.4 - - + -
142B THR* 3.0 23.7 + - + +
143B LEU* 3.6 8.7 - - - +
144B ALA 3.1 0.2 - - - -
145B VAL* 1.3 75.8 - - - +
147B ASP* 1.3 63.2 + - - +
149B GLY* 3.0 14.7 + - - -
150B ILE 5.1 3.6 - - - +
152B MET* 3.3 25.6 - - + -
155B PHE* 3.1 41.5 - - + +
231B VAL* 4.4 12.1 - - + -
29H PRO* 3.6 27.8 - - + -
55H SER 5.4 0.4 - - - +
56H VAL* 5.5 1.1 - - - +
57H ALA* 4.7 24.6 + - + +
72H LEU* 5.5 4.0 - - - +
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Residues in contact with ASP 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B MET* 4.1 13.1 - - + +
29B GLY* 3.5 21.1 + - - -
35B ASP 4.3 1.1 - - - -
36B GLY* 4.4 3.3 - - - -
37B SER* 3.3 30.8 + - - +
143B LEU 2.9 12.6 + - - +
144B ALA 2.8 9.9 + - - +
146B LEU* 1.3 76.1 - - - +
148B ALA* 1.3 56.1 + - - +
149B GLY 3.2 3.4 + - - -
234B HIS* 4.4 15.5 - - - -
72H LEU* 5.8 3.8 - - - +
73H LYS* 3.1 42.3 + - - +
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Residues in contact with ALA 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B ASP* 3.0 27.5 - - + +
51B VAL* 3.6 24.9 - - + +
53B GLY* 5.6 1.1 - - - -
54B PRO* 5.7 1.0 - - - +
144B ALA 2.9 2.8 + - - -
145B VAL 2.9 10.6 + - - +
147B ASP* 1.3 75.9 - - - +
149B GLY* 1.3 60.4 + - - +
150B ILE* 2.9 24.3 + - + +
73H LYS* 3.8 9.8 - - - +
74H THR* 4.7 4.7 - - - -
75H ARG* 6.1 0.5 - - - +
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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