Contacts of the helix formed by residues 128 - 144 (chain B) in PDB entry 1OIZ
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 THR 128 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B TRP* 3.9 5.3 + - - -
126B VAL 5.4 2.0 - - - +
127B PHE* 1.3 77.5 - - - +
129B ALA* 1.3 65.6 + - - +
130B TYR* 3.3 21.1 + - - +
131B ASP* 2.9 32.9 + - - +
132B VAL* 3.2 13.2 + - - +
170B GLN* 3.0 13.9 - - - +
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Residues in contact with ALA 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B TRP* 3.7 5.0 - - + -
128B THR* 1.3 74.6 - - - +
130B TYR* 1.3 60.4 + - + +
132B VAL* 3.2 13.8 - - - +
133B PHE* 2.9 27.9 + - - +
170B GLN* 3.0 34.5 + - + +
171B ILE* 4.0 19.5 - - + -
175B VAL* 4.1 16.4 - - + -
1277B TRT 3.7 4.0 - - - +
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Residues in contact with TYR 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B GLU* 3.6 30.1 - - + +
83B ILE* 3.7 26.1 - - + +
128B THR* 3.1 11.8 + - - +
129B ALA* 1.3 78.1 - - + +
131B ASP* 1.3 61.2 + - - +
133B PHE* 3.5 8.1 - + - +
134B ARG* 2.9 34.2 + - - +
172B THR* 4.9 0.2 + - - -
174B SER* 3.7 14.4 - - - -
175B VAL* 3.7 32.0 - - + +
178B LYS* 3.1 42.9 + - + +
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Residues in contact with ASP 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B SER* 4.6 3.6 - - - +
92B ILE* 3.3 18.4 - - + +
95B LEU* 4.0 0.9 - - + -
126B VAL 4.1 2.8 - - - +
127B PHE* 3.2 30.7 - - + -
128B THR* 2.9 37.3 + - - +
130B TYR* 1.3 78.1 - - - +
132B VAL* 1.3 61.9 + - - +
134B ARG* 3.0 37.3 + - - +
135B VAL* 3.2 10.0 + - - +
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Residues in contact with VAL 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B LEU* 3.8 26.0 - - + -
100B TYR* 3.9 22.5 + - + +
122B TRP* 3.6 47.8 - - + +
127B PHE* 4.8 0.2 - - + -
128B THR 3.2 1.7 + - - +
129B ALA* 3.2 26.5 - - - +
131B ASP* 1.3 73.7 - - - +
133B PHE* 1.3 64.1 + - - +
135B VAL* 3.2 15.0 + - - +
136B SER* 3.3 13.5 + - - -
1277B TRT 3.7 22.6 - - - +
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Residues in contact with PHE 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B TRP* 3.7 23.1 - + - -
83B ILE* 3.8 24.0 - - + -
129B ALA 2.9 16.1 + - - +
130B TYR* 3.5 16.2 - + - +
131B ASP 3.2 0.2 - - - -
132B VAL* 1.3 73.9 - - - +
134B ARG* 1.3 67.2 + - - +
136B SER* 3.1 3.7 + - - -
137B LEU* 3.0 23.3 + - + +
175B VAL* 4.4 4.7 - - + -
178B LYS* 3.5 30.3 - - + -
179B ILE* 3.5 30.5 - - + -
182B VAL* 3.8 22.9 - - + -
1277B TRT 3.6 35.4 - + + -
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Residues in contact with ARG 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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82B GLU 2.7 26.7 + - - -
83B ILE* 3.8 27.8 + - + +
86B ASP* 3.3 25.7 + - - +
87B LEU* 4.5 3.8 - - + -
88B HIS 5.0 0.9 - - - -
91B SER* 2.9 30.9 + - - -
92B ILE* 3.7 14.6 - - + +
130B TYR* 2.9 18.4 + - - +
131B ASP* 3.0 38.2 + - - +
133B PHE* 1.3 75.9 - - - +
135B VAL* 1.3 62.5 + - - +
137B LEU* 3.2 2.6 + - - +
138B ILE* 2.9 40.3 + - + +
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Residues in contact with VAL 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B ILE* 3.8 22.4 - - + -
95B LEU* 3.7 28.7 - - + -
96B LEU* 4.1 10.3 - - + -
100B TYR* 4.1 10.8 - - + -
101B HIS* 3.5 37.9 - - + +
117B TYR* 4.8 0.4 - - + -
131B ASP 3.2 15.3 + - - +
132B VAL* 3.3 9.4 - - - +
133B PHE 3.2 0.4 - - - -
134B ARG* 1.3 76.6 - - - +
136B SER* 1.3 62.1 - - - +
138B ILE* 3.3 6.5 + - - +
139B THR* 3.1 23.4 + - - +
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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
----------------------------------------------------------
117B TYR* 2.7 37.2 + - - -
132B VAL 3.3 3.6 + - - -
133B PHE* 3.1 9.7 + - - -
135B VAL* 1.3 79.9 - - - +
137B LEU* 1.3 57.5 + - - +
139B THR* 3.5 3.0 + - - -
140B SER* 2.8 33.1 + - - -
1277B TRT 3.3 47.0 - - - +
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Residues in contact with LEU 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B TYR* 5.9 0.4 - - + -
76B TRP* 3.8 31.4 - - + -
77B ARG* 5.5 4.9 - - + +
83B ILE* 3.9 16.2 - - + +
84B SER* 4.1 7.4 - - - -
87B LEU* 3.9 25.4 - - + -
133B PHE* 3.0 17.8 + - + +
134B ARG* 3.6 9.6 - - - +
136B SER* 1.3 73.2 - - - +
138B ILE* 1.3 61.1 + - - +
140B SER* 3.2 3.0 + - - -
141B GLU* 2.9 43.6 + - + +
182B VAL* 5.9 2.9 - - + -
187B PHE* 3.7 32.5 - - + -
1277B TRT 5.8 3.1 - - + -
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Residues in contact with ILE 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B LEU* 3.4 42.0 - - + +
88B HIS 4.6 0.2 - - - -
89B PRO* 4.2 6.7 - - + -
92B ILE* 4.0 31.0 - - + -
134B ARG* 2.9 30.0 + - + +
135B VAL* 3.7 5.4 - - - +
137B LEU* 1.3 78.1 - - - +
139B THR* 1.3 62.8 + - - +
141B GLU* 3.3 4.3 + - - +
142B LEU* 3.1 22.7 + - + +
263B ILE* 3.7 29.6 - - + -
270B LEU* 3.8 22.7 - - + +
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Residues in contact with THR 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B HIS* 2.7 38.4 + - + -
103B VAL* 3.9 7.0 - - + -
115B LEU* 3.8 22.2 - - + -
135B VAL* 3.1 12.9 + - - +
136B SER* 3.7 5.4 - - - -
138B ILE* 1.3 78.1 - - - +
140B SER* 1.3 59.3 + - - +
142B LEU* 3.1 3.0 + - - +
143B ILE* 2.8 33.0 + - + +
259B TRP* 2.9 30.0 + - + -
263B ILE* 4.5 2.3 - - - +
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Residues in contact with SER 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B SER 2.8 23.9 + - - -
137B LEU* 3.5 8.3 - - - -
138B ILE 3.2 0.4 - - - -
139B THR* 1.3 77.1 - - - +
141B GLU* 1.3 57.4 + - - +
143B ILE* 3.7 10.3 - - - +
144B VAL* 3.0 34.3 + - - +
187B PHE* 3.6 27.8 - - - -
189B LEU* 3.8 2.8 - - - +
1277B TRT 3.2 32.8 - - - +
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Residues in contact with GLU 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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45B LEU* 6.4 0.2 - - - -
54B ARG* 3.8 18.7 + - - -
73B TYR* 2.5 36.5 + - - -
77B ARG* 4.3 9.7 + - - -
87B LEU* 4.2 10.9 - - + +
137B LEU* 2.9 26.2 + - + +
138B ILE* 3.9 4.5 - - - +
139B THR 3.3 0.2 - - - -
140B SER* 1.3 75.4 - - - +
142B LEU* 1.3 61.5 + - - +
144B VAL* 3.6 12.9 - - - +
145B GLN* 3.2 16.1 - - - +
187B PHE* 3.5 19.2 - - + -
188B PRO* 6.0 0.2 - - - +
269B TYR* 4.3 5.4 + - - +
270B LEU* 5.1 2.2 - - + -
273B ILE* 3.9 31.0 - - + +
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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
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138B ILE* 3.1 19.1 + - + +
139B THR 3.6 6.5 - - - +
141B GLU* 1.3 77.2 - - - +
143B ILE* 1.3 64.1 + - - +
144B VAL 3.3 0.2 - - - -
145B GLN* 3.2 35.1 + - - +
146B GLU* 4.6 2.4 + - - +
259B TRP* 4.4 5.8 - - + -
262B PHE* 3.8 32.4 - - + -
263B ILE* 3.2 36.1 - - + -
266B SER* 3.8 28.9 - - - +
269B TYR* 4.0 14.4 - - + -
270B LEU* 4.2 9.6 - - + -
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Residues in contact with ILE 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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103B VAL* 4.5 6.7 - - + -
113B LYS* 4.6 16.6 - - + -
115B LEU* 3.7 27.1 - - + -
139B THR* 2.8 29.6 + - + +
140B SER* 3.7 8.3 - - - +
142B LEU* 1.3 67.0 - - - +
144B VAL* 1.3 63.3 + - - +
145B GLN 3.0 7.4 + - - -
146B GLU* 3.1 18.7 + - - +
149B THR* 3.5 22.2 - - + +
154B ILE* 3.7 29.6 - - + -
189B LEU* 4.1 11.4 - - + -
259B TRP* 3.7 28.3 - - + -
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Residues in contact with VAL 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B ARG* 3.7 43.9 - - + +
140B SER 3.0 20.2 + - - +
141B GLU* 3.6 18.8 - - - +
143B ILE* 1.3 77.8 - - - +
145B GLN* 1.3 60.0 + - - +
146B GLU 3.2 0.2 - - - -
149B THR* 4.9 0.4 - - - -
150B GLN* 2.9 37.6 - - + +
187B PHE* 4.4 4.3 - - + -
188B PRO* 3.3 30.7 - - + +
189B LEU* 3.7 17.7 - - + -
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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