Contacts of the helix formed by residues 132 - 146 (chain B) in PDB entry 6P7B
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7B ASP* 3.7 18.5 - - - +
12B ASN* 3.9 32.3 + - + +
14B ALA* 3.6 19.6 - - + +
34B LYS* 3.2 30.4 + - - +
129B LYS* 3.2 21.0 - - - +
130B LEU 2.7 1.9 + - - +
131B ASP* 1.3 73.3 - - - +
133B ILE* 1.3 70.5 + - - +
134B ALA 3.2 1.1 - - - -
135B ASN* 3.2 4.6 + - - +
136B SER* 2.9 25.3 + - - -
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Residues in contact with ILE 133 (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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14B ALA* 4.0 4.3 - - + -
32B ILE* 3.5 18.0 - - + +
33B GLU* 3.9 29.2 - - - +
34B LYS* 4.2 10.3 - - + -
109B PHE* 4.1 18.4 - - + -
123B ILE* 4.6 7.6 - - + -
127B TYR* 3.9 25.1 - - + -
130B LEU* 3.2 38.6 - - + +
132B ASP* 1.3 87.3 + - - +
134B ALA* 1.3 60.9 + - - +
136B SER* 2.7 21.7 + - - -
137B PHE* 2.9 19.1 + - - +
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Residues in contact with ALA 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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105B SER* 3.6 15.0 - - - +
106B ILE* 4.0 17.9 - - + -
109B PHE* 3.5 34.5 - - + -
130B LEU 2.8 17.8 + - - +
131B ASP* 4.3 1.8 - - - -
133B ILE* 1.3 79.8 - - - +
135B ASN* 1.3 55.7 - - - +
137B PHE* 3.3 1.9 + - - +
138B ASN* 2.9 34.7 + - - -
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Residues in contact with ASN 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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7B ASP* 2.3 36.1 + - - +
60B GLU* 2.6 32.0 + - - +
92B THR* 4.3 10.7 + - - -
93B PHE* 6.1 1.0 - - - -
101B ARG* 4.2 13.9 - - - +
105B SER* 3.7 12.1 + - - +
131B ASP 4.0 11.4 + - - +
132B ASP* 3.2 9.3 + - - +
134B ALA* 1.3 77.7 - - - +
136B SER* 1.3 58.9 + - - +
138B ASN* 3.3 2.9 + - - +
139B LEU* 2.9 30.7 + - - +
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Residues in contact with SER 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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5B SER* 2.6 44.3 + - - -
7B ASP* 3.9 19.2 - - - +
14B ALA 4.1 5.4 - - - -
15B TYR* 3.9 3.2 + - - -
16B ALA* 3.7 16.0 + - - +
32B ILE* 4.2 0.7 - - - +
132B ASP 2.9 11.2 + - - -
133B ILE* 2.7 28.2 + - - -
135B ASN* 1.3 75.2 - - - +
137B PHE* 1.3 56.1 + - - +
139B LEU* 4.4 4.0 - - - -
140B GLY 2.9 15.4 + - - -
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Residues in contact with PHE 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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16B ALA* 4.2 0.9 - - - -
18B PHE* 3.5 36.2 - + - -
29B LEU* 4.3 12.3 - - + -
32B ILE* 4.1 5.2 - - + -
109B PHE* 3.6 33.0 - + + -
112B LYS* 3.7 24.5 - - + -
113B ILE* 4.1 13.9 - - + -
116B TYR* 3.4 36.8 - + + -
117B THR* 6.1 0.2 - - + -
133B ILE 2.9 18.4 + - - +
134B ALA 3.7 0.2 - - - +
136B SER* 1.3 77.9 + - - +
138B ASN* 1.3 69.4 + - - +
140B GLY* 3.4 0.7 + - - -
141B LEU* 2.9 50.8 + - + +
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Residues in contact with ASN 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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92B THR* 4.0 15.6 - - - +
93B PHE* 3.5 11.0 - - + -
105B SER* 2.8 42.8 + - - -
108B VAL* 3.3 26.7 - - - +
109B PHE* 4.2 2.6 + - - -
134B ALA* 2.9 16.1 + - - +
135B ASN* 3.8 4.3 - - - +
136B SER 3.3 0.2 - - - -
137B PHE* 1.3 86.9 - - - +
139B LEU* 1.3 60.9 + - - +
141B LEU* 3.8 4.8 - - - +
142B SER* 2.8 32.4 + - - -
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Residues in contact with LEU 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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5B SER* 4.4 0.2 - - - -
6B VAL 3.5 29.4 - - - +
7B ASP* 5.4 0.7 - - - -
58B ILE* 3.5 19.2 - - + +
59B LEU 3.6 5.4 - - - -
60B GLU* 3.6 39.9 - - + +
89B ARG* 4.1 24.9 - - + -
90B ASN 4.4 0.4 - - - +
92B THR* 3.7 21.7 - - + +
135B ASN* 2.9 20.5 + - - +
136B SER* 3.6 5.2 - - - +
138B ASN* 1.3 76.4 - - - +
140B GLY* 1.3 61.4 + - - +
142B SER* 2.7 19.9 + - - -
143B TYR* 3.0 10.9 + - - +
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Residues in contact with GLY 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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3B ILE* 4.9 0.7 - - - -
5B SER* 3.4 21.9 + - - -
18B PHE* 3.8 16.4 - - - -
58B ILE* 3.9 9.3 - - - +
136B SER 2.9 12.1 + - - -
139B LEU* 1.3 75.8 - - - +
141B LEU* 1.3 56.9 + - - +
143B TYR* 3.2 4.3 + - - +
144B MET* 2.9 32.3 + - - +
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Residues in contact with LEU 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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18B PHE* 3.8 5.1 - - + -
27B ILE* 4.4 15.7 - - + -
108B VAL* 6.4 0.9 - - + -
112B LYS* 3.6 32.5 - - + -
116B TYR* 3.6 35.0 - - + +
137B PHE* 2.9 30.6 + - + +
138B ASN* 4.0 6.1 - - - +
140B GLY* 1.3 75.7 - - - +
142B SER* 1.3 57.4 + - - +
144B MET* 3.2 12.5 + - + +
145B GLU* 2.8 47.5 + - + +
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Residues in contact with SER 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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89B ARG* 3.5 15.3 + - - -
92B THR* 3.3 26.8 - - - +
138B ASN 2.8 15.3 + - - -
139B LEU 2.7 18.9 + - - -
141B LEU* 1.3 74.6 - - - +
143B TYR* 1.3 64.1 + - - +
145B GLU* 3.2 9.8 + - - +
146B SER* 2.9 23.6 + - - -
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Residues in contact with TYR 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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1B MET* 4.8 2.6 - - + +
3B ILE* 4.1 19.3 - - + -
56B VAL* 3.9 21.6 - - + +
58B ILE* 3.5 30.3 - - + -
87B ILE* 3.5 32.8 - - + +
89B ARG* 3.1 36.1 - - - +
139B LEU 3.0 6.2 + - - +
140B GLY 3.5 2.9 - - - +
142B SER* 1.3 80.9 + - - +
144B MET* 1.3 65.2 + - + +
146B SER* 3.2 5.9 + - - -
147B LEU* 3.1 54.8 + - + +
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Residues in contact with MET 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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3B ILE* 3.7 16.2 - - + -
18B PHE* 3.5 45.8 - - + -
20B TYR* 3.6 33.0 - - + +
27B ILE* 3.5 35.4 - - + -
140B GLY 2.9 15.5 + - - +
141B LEU* 3.6 13.7 - - + +
143B TYR* 1.3 76.8 - - + +
145B GLU* 1.3 66.4 + - - +
147B LEU* 3.0 33.1 + - + +
148B LEU* 3.6 13.3 - - - +
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Residues in contact with GLU 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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112B LYS* 5.6 2.8 - - - -
116B TYR* 4.7 5.2 + - - -
141B LEU* 2.8 44.7 + - + +
142B SER* 3.6 9.2 - - - +
144B MET* 1.3 77.2 - - - +
146B SER* 1.3 60.5 + - - +
147B LEU 3.1 1.3 + - - -
148B LEU* 3.7 17.5 + - - +
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Residues in contact with SER 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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89B ARG* 3.6 28.1 + - - -
142B SER 2.9 13.2 + - - -
143B TYR 3.2 10.3 + - - -
145B GLU* 1.3 75.3 - - - +
147B LEU* 1.3 61.6 + - - +
148B LEU* 3.5 3.1 - - - -
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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