Contacts of the helix formed by residues 134 - 152 (chain B) in PDB entry 5OND
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 134 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B LYS* 4.2 6.2 + - - +
132B GLU* 2.9 16.1 + - - +
133B PRO* 1.3 79.5 - - + +
135B GLY* 1.3 67.6 + - - +
136B GLU* 3.4 15.7 + - - +
137B ALA* 2.7 28.7 + - + +
138B ARG* 3.1 22.7 + - - +
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Residues in contact with GLY 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B LYS* 4.9 1.4 - - - +
48B GLU* 4.1 3.2 + - - -
52B PRO* 3.7 23.5 - - - +
133B PRO 3.7 4.0 + - - -
134B ASP* 1.3 74.6 + - - +
136B GLU* 1.3 62.2 + - - +
138B ARG* 2.9 39.1 + - - +
139B SER* 3.0 15.9 + - - -
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Residues in contact with GLU 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B TYR* 4.8 8.2 + - - -
52B PRO* 3.7 27.5 - - + +
53B ASN* 4.7 4.0 - - - +
54B TYR* 5.5 3.3 - - - -
134B ASP* 3.3 13.5 + - - +
135B GLY* 1.3 76.3 - - - +
137B ALA* 1.3 62.6 + - - +
139B SER* 3.5 11.8 + - - +
140B MET* 3.1 22.0 + - - +
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Residues in contact with ALA 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B GLU* 3.4 31.6 - - + +
134B ASP* 2.7 21.0 + - + +
136B GLU* 1.3 73.2 - - - +
138B ARG* 1.3 53.1 + - - +
140B MET* 3.1 12.2 + - + +
141B LEU* 2.7 42.3 + - + +
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Residues in contact with ARG 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ILE* 3.7 11.0 - - - +
35B LEU* 3.6 8.5 - - - +
48B GLU* 2.7 26.9 + - - +
49B PRO 2.8 24.7 + - - -
50B LEU* 2.7 39.2 + - - +
51B PHE* 3.4 16.0 - - + -
129B ILE* 3.3 24.4 - - + +
132B GLU* 2.9 40.6 + - + +
133B PRO 2.9 22.2 + - - -
134B ASP 3.1 8.1 + - - +
135B GLY* 2.9 19.3 + - - +
137B ALA* 1.3 77.0 - - - +
139B SER* 1.3 57.2 + - - +
141B LEU* 3.3 9.4 + - - +
142B LEU 2.8 22.5 + - - -
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Residues in contact with SER 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B PHE* 3.2 39.4 - - - +
52B PRO* 3.7 3.3 + - - +
54B TYR* 3.7 27.1 - - - -
135B GLY 3.0 9.9 + - - -
136B GLU* 3.9 13.7 + - - -
138B ARG* 1.3 72.3 - - - +
140B MET* 1.3 66.4 + - - +
142B LEU* 3.0 5.0 + - - +
143B LEU* 2.9 29.6 + - - +
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Residues in contact with MET 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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136B GLU 3.1 13.7 + - - +
137B ALA* 3.1 14.4 + - + +
139B SER* 1.3 76.7 - - - +
141B LEU* 1.3 80.5 + - + +
142B LEU 3.2 0.2 + - - -
143B LEU* 3.4 6.9 + - + +
144B ASN* 3.1 50.9 + - - +
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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
----------------------------------------------------------
125B GLY* 5.1 2.5 - - - +
128B ALA* 4.1 18.4 - - + +
129B ILE* 3.6 38.8 - - + +
132B GLU* 4.1 16.6 - - + +
137B ALA* 2.7 26.2 + - + +
138B ARG* 3.6 2.0 - - - +
140B MET* 1.3 87.5 - - + +
142B LEU* 1.3 57.8 + - - +
144B ASN* 3.5 6.9 + - + +
145B LEU* 2.9 30.3 + - - +
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Residues in contact with LEU 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B LEU* 3.6 28.3 - - + -
51B PHE* 3.6 50.7 - - + -
54B TYR* 5.4 1.8 - - + -
56B PHE* 3.8 12.6 - - + -
92B VAL* 4.6 3.4 - - + -
126B PHE* 4.6 11.9 - - + -
129B ILE* 3.8 11.0 - - + +
138B ARG 2.8 14.1 + - - +
139B SER* 3.0 9.4 + - - +
141B LEU* 1.3 78.1 - - - +
143B LEU* 1.3 59.3 + - + +
145B LEU* 3.2 5.2 + - + +
146B ILE* 2.9 48.6 + - + +
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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
----------------------------------------------------------
6B LEU* 3.7 19.7 - - + -
54B TYR* 3.7 24.2 - - + +
79B VAL* 3.6 39.7 - - + +
139B SER* 2.9 20.3 + - - +
140B MET* 4.0 6.3 - - + +
142B LEU* 1.3 77.2 - - + +
144B ASN* 1.3 60.5 + - - +
146B ILE* 3.3 4.9 + - + +
147B ASN* 2.9 31.0 + - - +
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Residues in contact with ASN 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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140B MET* 3.1 44.0 + - - +
141B LEU* 3.8 7.2 - - + +
143B LEU* 1.3 79.9 - - - +
145B LEU* 1.3 61.8 + - - +
147B ASN* 3.7 5.0 - - - +
148B LYS* 3.0 28.7 + - - +
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Residues in contact with LEU 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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92B VAL* 5.2 4.7 - - + -
121B GLY* 3.4 32.1 - - - +
122B ALA* 3.8 12.1 - - - +
125B GLY* 3.9 20.9 - - - -
126B PHE* 3.7 36.1 - - + -
129B ILE* 4.2 9.0 - - + -
141B LEU 2.9 18.1 + - - +
142B LEU* 3.2 6.9 + - + +
144B ASN* 1.3 76.3 - - - +
146B ILE* 1.3 60.2 + - + +
148B LYS* 3.6 15.9 + - - +
149B GLU* 3.0 38.0 + - + +
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Residues in contact with ILE 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B LEU* 3.8 22.0 - - + -
56B PHE* 4.7 1.6 - - + -
79B VAL* 5.1 7.2 - - + -
86B ALA* 4.5 13.0 - - + -
88B VAL* 4.3 23.6 - - + -
89B PRO* 5.0 3.4 - - + -
92B VAL* 4.3 17.5 - - + -
142B LEU* 2.9 46.7 + - + +
143B LEU* 3.7 6.5 - - + +
144B ASN 3.2 0.2 - - - -
145B LEU* 1.3 75.2 - - + +
147B ASN* 1.3 67.0 + - - +
149B GLU* 3.2 5.7 + - - +
150B ILE* 3.0 47.0 + - + +
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Residues in contact with ASN 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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80B ARG 5.1 6.3 + - - -
81B PHE* 3.5 28.2 - - - +
82B GLY 5.6 1.0 - - - +
143B LEU 2.9 17.1 + - - +
144B ASN* 3.7 7.0 - - - +
146B ILE* 1.3 79.0 - - - +
148B LYS* 1.3 63.6 + - - +
150B ILE* 3.2 1.6 + - - +
151B LYS* 2.9 55.3 + - - +
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Residues in contact with LYS 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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121B GLY* 3.2 32.7 + - - -
144B ASN* 3.0 16.4 + - - +
145B LEU* 3.8 14.5 - - - +
147B ASN* 1.3 81.9 + - - +
149B GLU* 1.3 70.9 + - - +
151B LYS* 3.5 8.8 + - - +
152B HIS* 3.2 24.5 + - + +
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Residues in contact with GLU 149 (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 PRO* 4.3 18.4 - - + +
92B VAL* 4.5 14.1 - - + -
119B THR* 2.9 37.0 + - - +
121B GLY* 3.7 10.4 + - - -
122B ALA* 3.7 18.1 - - + +
145B LEU* 3.0 24.3 + - + +
146B ILE* 3.2 4.7 + - - +
148B LYS* 1.3 93.9 + - - +
150B ILE* 1.3 62.4 + - - +
152B HIS* 3.6 12.4 + - - +
153B SER* 3.2 19.4 + - - -
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Residues in contact with ILE 150 (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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81B PHE* 3.5 38.8 - - + -
86B ALA* 3.9 16.6 - - + -
87B ILE 3.3 28.9 - - - +
89B PRO* 4.1 12.1 - - + -
146B ILE* 3.0 34.5 + - + +
147B ASN 3.7 2.7 - - - +
149B GLU* 1.3 72.8 - - - +
151B LYS* 1.3 69.1 + - - +
152B HIS 2.8 3.1 + - - -
153B SER* 2.8 27.7 + - - +
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Residues in contact with LYS 151 (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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81B PHE* 3.3 29.2 - - + -
147B ASN* 2.9 41.9 + - - +
148B LYS* 3.6 8.1 - - - +
150B ILE* 1.3 75.4 - - - +
152B HIS* 1.3 56.5 + - + +
153B SER 3.1 8.3 + - - +
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Residues in contact with HIS 152 (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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119B THR* 5.4 10.7 - - + +
148B LYS* 3.2 17.1 + - + +
149B GLU* 3.7 11.2 + - - +
150B ILE 2.8 4.2 + - - -
151B LYS* 1.3 71.3 - - + +
153B SER* 1.3 67.0 + - - +
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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