Contacts of the helix formed by residues 120 - 139 (chain B) in PDB entry 1OCU
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 SER 120 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A SER* 4.7 2.2 - - - -
117B ASN* 3.2 24.2 + - - -
119B PHE* 1.3 79.7 - - - +
121B ASN* 1.3 67.5 + - - +
122B GLU* 3.6 13.2 + - - +
123B VAL* 3.3 12.6 + - - +
124B ILE* 3.0 24.7 + - - +
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Residues in contact with ASN 121 (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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51A MET* 5.0 9.0 - - - +
52A ASP* 3.4 34.9 + - - +
54A LYS* 6.4 1.1 - - + -
119B PHE 3.9 1.6 + - - -
120B SER* 1.3 73.5 + - - +
122B GLU* 1.3 72.5 + - + +
124B ILE* 3.1 6.6 + - - +
125B GLU* 3.0 26.5 + - - +
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Residues in contact with GLU 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B SER* 3.5 7.2 + - - +
121B ASN* 1.3 86.8 - - + +
123B VAL* 1.3 59.4 + - + +
125B GLU* 3.3 6.5 + - - +
126B GLU* 2.9 32.8 + - + +
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Residues in contact with VAL 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B ILE* 4.2 25.1 - - + -
117B ASN* 3.1 50.0 - - - +
118B ARG* 4.1 13.7 - - - +
120B SER* 3.3 12.1 + - - +
121B ASN 3.2 0.8 - - - -
122B GLU* 1.3 75.1 - - + +
124B ILE* 1.3 67.2 + - + +
126B GLU* 3.1 8.7 + - + +
127B ARG* 3.0 27.6 + - + +
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Residues in contact with ILE 124 (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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51A MET* 4.7 14.8 - - + +
52A ASP* 4.7 4.0 - - + -
43B PRO* 3.6 33.0 - - + -
45B THR* 4.7 0.7 - - - +
58B THR* 3.7 29.8 - - + +
60B TYR* 3.8 14.6 - - + +
118B ARG 3.0 25.4 - - - +
119B PHE* 4.3 5.8 - - - +
120B SER 3.0 23.2 + - - +
121B ASN* 3.6 7.0 - - - +
123B VAL* 1.3 75.7 - - + +
125B GLU* 1.3 57.6 + - - +
127B ARG* 3.5 4.8 + - - +
128B ARG* 2.8 27.5 + - - +
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Residues in contact with GLU 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B PRO* 5.5 1.4 - - - +
121B ASN* 3.0 18.3 + - - +
122B GLU* 3.5 11.2 - - - +
124B ILE* 1.3 76.2 - - - +
126B GLU* 1.3 67.0 + - - +
128B ARG* 3.1 40.4 + - - +
129B GLN* 2.9 45.1 + - - +
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Residues in contact with GLU 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B PRO* 6.2 0.2 - - - -
122B GLU* 2.9 16.3 + - + +
123B VAL* 3.2 14.4 - - + +
125B GLU* 1.3 76.8 - - - +
127B ARG* 1.3 64.7 + - - +
129B GLN* 3.2 13.5 + - - +
130B GLY* 3.0 18.7 + - - -
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Residues in contact with ARG 127 (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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60B TYR* 3.1 28.9 + - - +
82B TYR* 3.4 34.0 - - + +
110B PRO* 4.5 11.0 - - + +
111B GLY 3.1 24.9 + - - -
112B LYS* 4.0 1.4 - - - +
113B ILE* 3.4 17.9 - - + +
118B ARG* 5.0 8.3 + - - +
123B VAL* 3.0 15.3 + - + +
124B ILE* 3.7 5.3 - - - +
126B GLU* 1.3 76.1 - - - +
128B ARG* 1.3 61.2 + - - +
130B GLY* 3.0 3.3 + - - +
131B LEU* 2.8 48.2 + - + +
1164B PIB 2.8 47.3 + - - -
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Residues in contact with ARG 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B GLU* 4.8 4.8 + - - -
40B VAL* 3.0 28.9 + - + +
41B HIS* 3.8 19.8 - - - +
42B ASN 4.6 0.2 - - - +
43B PRO* 3.7 26.2 - - + -
60B TYR* 4.0 19.9 - - + -
124B ILE 2.8 21.8 + - - +
125B GLU* 3.1 39.5 + - - +
127B ARG* 1.3 71.7 - - - +
129B GLN* 1.3 78.4 + - - +
131B LEU* 3.2 5.1 + - - +
132B ASN* 2.8 45.8 + - - +
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Residues in contact with GLN 129 (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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125B GLU* 2.9 43.8 + - - +
126B GLU* 3.5 13.3 - - - +
128B ARG* 1.3 97.6 - - - +
130B GLY* 1.3 63.3 + - - +
132B ASN* 3.3 8.4 + - - +
133B THR* 3.0 27.6 + - - -
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Residues in contact with GLY 130 (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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110B PRO* 4.4 21.2 - - - +
126B GLU 3.0 13.6 + - - -
127B ARG 3.0 3.6 + - - -
129B GLN* 1.3 78.3 - - - +
131B LEU* 1.3 56.4 + - - +
133B THR* 3.4 5.1 + - - -
134B TRP* 2.9 30.2 + - - +
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Residues in contact with LEU 131 (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 VAL* 4.1 12.1 - - + -
60B TYR* 4.0 27.1 - - + -
82B TYR* 4.2 10.5 - - + -
85B PHE* 3.8 49.0 - - + -
109B LEU* 3.9 17.3 - - + -
110B PRO* 4.0 10.8 - - + -
127B ARG* 2.8 42.1 + - + +
128B ARG 3.6 3.1 - - - +
130B GLY* 1.3 70.3 - - - +
132B ASN* 1.3 61.8 + - - +
134B TRP* 3.7 3.3 - - - +
135B MET* 2.9 33.8 + - - +
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Residues in contact with ASN 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B ILE* 5.6 0.2 - - - +
39B GLU* 3.3 19.7 + - - +
40B VAL* 3.0 44.0 + - - +
128B ARG* 2.8 26.9 + - - +
129B GLN* 3.5 7.0 + - - +
131B LEU* 1.3 77.3 - - - +
133B THR* 1.3 64.1 + - - +
135B MET* 4.0 1.7 - - - +
136B GLN* 3.2 41.4 + - - +
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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
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129B GLN 3.0 17.2 + - - -
130B GLY* 3.8 5.8 - - - -
132B ASN* 1.3 77.6 + - - +
134B TRP* 1.3 65.9 + - - +
136B GLN* 3.2 11.7 + - - +
137B SER* 3.2 27.8 + - - +
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Residues in contact with TRP 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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85B PHE* 4.1 19.3 - + - -
88B PHE* 3.7 38.6 - + - -
89B ARG* 4.2 16.8 - - + -
92B LEU* 4.7 3.4 - - + -
106B VAL* 4.0 14.4 - - + -
107B PRO* 2.7 34.2 + - + +
108B HIS 3.3 25.8 + - - -
109B LEU* 3.4 26.0 - - + +
110B PRO* 4.8 2.5 - - + -
130B GLY 2.9 18.8 + - - +
131B LEU* 3.7 6.7 - - - +
133B THR* 1.3 78.0 - - - +
135B MET* 1.3 73.9 + - + +
137B SER* 3.3 6.9 + - - -
138B VAL* 3.1 47.8 + - + +
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Residues in contact with MET 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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38B ILE* 3.6 24.0 - - + +
39B GLU* 6.2 0.2 - - - -
40B VAL* 3.9 20.2 - - + -
62B ILE* 4.8 4.3 - - + -
85B PHE* 4.1 9.6 - - + -
88B PHE* 4.4 6.3 - - + -
131B LEU 2.9 21.6 + - - +
132B ASN 4.0 1.6 - - - +
134B TRP* 1.3 82.9 - - + +
136B GLN* 1.3 57.9 + - - +
138B VAL* 4.4 7.9 - - + -
139B ALA* 3.0 35.1 + - + +
151B LEU* 3.8 23.1 - - + -
154B PHE* 3.9 23.8 - - + -
155B ILE* 3.6 24.2 - - + -
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Residues in contact with GLN 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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38B ILE* 2.7 41.4 + - + +
39B GLU* 4.3 3.8 - - - +
132B ASN* 3.2 43.2 + - - +
133B THR* 3.2 9.0 + - - +
135B MET* 1.3 76.3 - - - +
137B SER* 1.3 59.1 + - - +
139B ALA* 4.7 0.2 - - - +
140B GLY* 3.2 22.5 + - - -
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Residues in contact with SER 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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107B PRO* 4.8 14.6 - - - -
133B THR* 3.2 17.0 + - - +
134B TRP* 3.3 9.1 + - - -
136B GLN* 1.3 75.1 - - - +
138B VAL* 1.3 68.6 + - - +
140B GLY* 3.3 8.6 + - - -
141B HIS* 3.3 13.3 + - - +
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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
----------------------------------------------------------
88B PHE* 4.5 3.8 - - + -
92B LEU* 3.7 27.1 - - + -
106B VAL* 4.7 1.8 - - + -
107B PRO* 4.6 14.6 - - + -
134B TRP* 3.1 51.1 + - + +
135B MET* 3.9 8.7 - - + +
137B SER* 1.3 79.2 - - - +
139B ALA* 1.3 61.8 + - - +
140B GLY 3.1 0.7 + - - -
141B HIS* 3.4 6.1 + - - +
144B LEU* 3.4 29.8 - - + +
151B LEU* 3.9 18.6 - - + -
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Residues in contact with ALA 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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36B LEU* 3.9 31.2 - - + +
38B ILE* 4.2 12.1 - - + -
135B MET* 3.0 31.7 + - + +
138B VAL* 1.3 75.7 - - - +
140B GLY* 1.3 56.9 + - - +
141B HIS 3.4 0.4 - - - -
145B GLN* 2.8 25.9 + - - +
151B LEU* 4.2 16.6 - - + +
155B ILE* 5.4 1.3 - - + -
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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