Contacts of the helix formed by residues 129 - 143 (chain B) in PDB entry 2OB1
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 TYR 129 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B TYR* 5.6 5.7 - - - -
128B ASP* 1.3 111.8 + - - +
130B ASN* 1.3 66.9 + - - +
131B GLU* 3.5 33.7 + - + +
132B SER* 3.1 39.0 + - - -
133B VAL* 3.1 8.7 + - - +
174B CYS 3.6 13.1 + - - +
175B ASP* 5.7 2.7 - - - -
176B LEU* 5.9 0.2 - - - +
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Residues in contact with ASN 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B ASP 3.7 0.6 + - - -
129B TYR* 1.3 74.1 - - - +
131B GLU* 1.3 59.7 + - - +
133B VAL* 3.2 1.6 - - - +
134B GLU* 2.9 57.0 + - - +
173B ALA* 3.7 27.2 - - + +
174B CYS 4.8 0.8 - - - +
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Residues in contact with GLU 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B TYR* 3.3 28.2 + - + -
130B ASN* 1.3 83.0 - - - +
132B SER* 1.3 62.9 + - - +
134B GLU* 3.9 5.7 - - - +
135B LEU* 3.3 22.1 + - + +
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Residues in contact with SER 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B TYR* 5.6 1.7 - - - -
107B GLY* 3.8 14.4 + - - -
128B ASP* 2.8 33.3 + - - +
129B TYR* 3.1 30.3 + - - -
131B GLU* 1.3 78.2 - - - +
133B VAL* 1.3 66.9 + - - +
135B LEU* 3.2 6.9 + - - +
136B LYS* 2.9 22.7 + - - +
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Residues in contact with VAL 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B CYS* 4.6 2.0 - - - -
128B ASP* 3.4 38.6 - - + +
129B TYR 3.1 5.6 + - - +
130B ASN 3.2 14.1 - - - +
132B SER* 1.3 76.3 - - - +
134B GLU* 1.3 56.9 + - + +
136B LYS* 4.3 5.8 - - - -
137B ASN* 2.8 31.7 + - - +
163B LEU* 3.5 13.4 - - + +
171B LEU* 3.5 31.4 - - + +
172B ALA 3.6 4.7 - - - +
173B ALA* 3.6 27.6 - - + +
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Residues in contact with GLU 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B ASN* 2.9 50.5 + - - +
131B GLU* 3.9 6.3 - - - +
132B SER 3.2 0.2 - - - -
133B VAL* 1.3 76.6 - - - +
135B LEU* 1.3 63.2 + - - +
137B ASN* 3.4 6.9 + - - +
138B SER* 3.0 27.4 + - - -
156B ASP* 5.4 1.4 - - - +
163B LEU* 3.6 33.9 - - + +
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Residues in contact with LEU 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B TYR* 5.4 1.3 - - - +
52B LEU* 3.8 22.4 - - + -
55B PHE* 3.8 33.0 - - + +
56B SER* 5.4 3.8 - - - -
59B ALA* 5.2 7.2 - - + -
131B GLU* 3.3 11.2 + - + +
132B SER* 3.2 8.8 + - - +
134B GLU* 1.3 76.4 - - - +
136B LYS* 1.3 65.8 + - - +
138B SER* 3.2 5.0 + - - -
139B ILE* 2.9 38.0 + - + +
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Residues in contact with LYS 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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48B TYR* 3.6 20.1 + - + +
106B CYS* 3.8 4.9 - - - +
107B GLY 3.1 27.5 + - - +
108B SER* 4.1 7.2 - - - +
109B ASP 2.7 29.9 + - - +
110B LEU* 4.5 4.5 - - - -
112B MET* 4.0 13.0 - - - -
126B ASP* 2.6 33.4 + - - +
132B SER 2.9 16.3 + - - +
133B VAL* 3.8 6.5 - - - +
135B LEU* 1.3 79.3 - - - +
137B ASN* 1.3 56.8 + - - +
139B ILE* 3.2 1.3 + - - +
140B LEU* 2.8 47.6 + - + +
169B TYR* 4.3 0.9 - - - +
171B LEU* 4.3 13.5 - - + -
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Residues in contact with ASN 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B VAL 2.8 22.4 + - - +
134B GLU* 3.5 8.3 + - - +
136B LYS* 1.3 73.9 - - - +
138B SER* 1.3 65.1 + - - +
140B LEU* 3.9 0.5 - - - +
141B ARG* 2.7 52.7 + - - +
156B ASP* 3.1 26.9 + - - +
163B LEU* 3.5 29.2 + - + +
164B ILE* 3.2 19.2 - - - +
171B LEU* 3.7 14.2 - - + +
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Residues in contact with SER 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B PHE* 3.7 34.8 - - - -
134B GLU* 3.0 16.9 + - - -
135B LEU* 3.4 11.4 - - - -
137B ASN* 1.3 79.4 + - - +
139B ILE* 1.3 58.6 + - - +
141B ARG* 3.5 3.3 + - - +
142B GLU* 2.9 32.2 + - - +
156B ASP* 5.5 1.7 + - - -
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Residues in contact with ILE 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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48B TYR* 3.4 55.9 - - + +
51B THR* 3.7 31.5 - - + +
52B LEU* 3.7 33.9 - - + +
55B PHE* 4.1 7.6 - - + -
135B LEU* 2.9 34.7 + - + +
136B LYS 3.8 2.9 - - - +
138B SER* 1.3 76.8 - - - +
140B LEU* 1.3 63.0 + - - +
142B GLU 3.2 0.2 + - - -
143B SER* 3.0 25.8 + - - -
146B LEU* 3.9 6.3 - - + -
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Residues in contact with LEU 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B TYR* 4.4 4.5 - - + -
110B LEU* 4.2 20.0 - - + -
112B MET* 4.1 5.4 - - + -
113B LEU* 5.1 0.9 - - + -
136B LYS* 2.8 41.7 + - + +
137B ASN 3.9 3.1 - - - +
139B ILE* 1.3 73.4 - - - +
141B ARG* 1.3 59.5 + - - +
143B SER 3.5 1.6 - - - +
146B LEU* 3.7 27.5 - - + -
147B ARG* 3.1 31.0 + - - +
150B LEU* 4.0 18.6 - - + -
152B LEU* 4.2 13.7 - - + +
164B ILE* 3.7 22.2 - - + -
169B TYR* 3.8 15.3 - - - +
171B LEU* 4.6 0.7 - - + -
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Residues in contact with ARG 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B ASN* 2.7 41.6 + - - +
138B SER* 4.1 3.6 - - - +
140B LEU* 1.3 74.9 - - + +
142B GLU* 1.3 60.4 + - - +
147B ARG* 2.9 31.5 + - - +
152B LEU* 3.9 24.2 - - + +
153B SER* 2.8 36.2 + - - +
154B LYS* 3.2 23.1 - - - +
155B GLU 3.8 5.5 + - - -
156B ASP* 3.7 30.5 - - - +
157B THR* 3.9 15.7 - - - +
158B ALA* 4.2 5.1 - - - +
163B LEU 2.9 22.2 + - - -
164B ILE* 3.5 17.4 - - - +
165B ASP 4.9 0.4 - - - +
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Residues in contact with GLU 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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51B THR* 3.7 12.8 - - + +
54B LYS* 3.7 32.3 + - + +
55B PHE* 3.5 27.3 - - + -
138B SER 2.9 19.1 + - - +
141B ARG* 1.3 78.2 - - - +
143B SER* 1.3 62.9 + - - +
144B GLU 3.4 1.7 + - - -
147B ARG* 3.3 9.7 + - - +
154B LYS* 3.1 31.9 + - - +
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Residues in contact with SER 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B SER* 2.6 28.4 + - - -
51B THR* 3.6 11.7 - - - -
139B ILE 3.0 17.1 + - - -
140B LEU 3.5 1.2 - - - +
142B GLU* 1.3 77.8 - - - +
144B GLU* 1.3 59.7 + - - +
145B ILE* 3.3 2.9 - - - +
146B LEU* 3.2 29.3 + - - +
147B ARG* 2.8 32.3 + - - +
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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
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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