Contacts of the strand formed by residues 134 - 141 (chain B) in PDB entry 4IOP
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 PHE 134 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A MET* 3.2 28.9 - - + -
148A PHE* 3.7 26.9 - + - -
161A ILE* 3.2 47.3 - - + -
163A ILE* 4.5 7.9 - - + -
96B PHE* 5.0 0.9 - + - -
129B LEU* 4.1 5.5 - - - +
132B GLY 5.0 0.9 - - - -
133B HIS* 1.3 76.1 - - - +
135B GLY* 1.3 59.6 + - - +
174B VAL* 4.4 6.5 - - + -
175B ILE 3.0 26.0 - - - +
176B THR* 4.2 6.1 - - - +
189B PHE* 4.0 32.1 - + + -
190B LYS* 3.5 24.9 + - - +
192B ILE* 4.5 7.5 - - - +
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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
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134B PHE* 1.3 82.8 - - - +
136B TRP* 1.3 69.9 + - - +
174B VAL* 3.0 8.0 - - - +
175B ILE* 2.9 35.1 + - - +
189B PHE* 5.2 1.6 - - - -
190B LYS 3.0 13.9 - - - -
192B ILE* 3.7 12.6 - - - +
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Residues in contact with TRP 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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97B LYS 2.9 19.4 + - - -
99B TRP* 3.1 44.9 - + + -
102B SER* 3.8 12.6 - - - -
113B LEU* 4.0 16.8 - - + -
135B GLY* 1.3 80.9 - - - +
137B ILE* 1.3 71.0 + - - +
172B CYS* 3.7 15.3 - - + -
173B ALA 3.2 21.1 - - - -
174B VAL* 3.9 12.0 - - + +
183B GLU* 4.7 4.3 - - + -
184B ASP 3.8 7.6 - - - -
185B CYS* 3.7 21.3 - - - -
187B SER 2.8 29.4 - - - -
189B PHE* 3.1 40.8 + + + +
190B LYS 3.2 18.5 + - - -
191B GLY* 4.1 0.9 - - - -
192B ILE* 3.7 13.6 + - - +
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Residues in contact with ILE 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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99B TRP* 3.0 19.9 + - - -
113B LEU* 3.9 12.5 - - - +
114B LEU* 3.4 39.0 - - + +
115B VAL* 5.9 0.2 - - - -
116B ILE* 5.2 7.6 - - + +
135B GLY 4.1 3.8 - - - +
136B TRP* 1.3 85.7 - - - +
138B GLY* 1.3 54.4 + - - +
139B LEU* 2.6 32.4 + - + +
150B TRP* 5.6 2.5 - - - +
161B PHE* 5.1 4.9 - - + -
173B ALA* 3.2 41.5 + - + +
174B VAL* 4.0 5.4 - - - +
175B ILE* 4.5 11.0 - - + +
180B VAL* 4.0 17.0 - - + -
192B ILE* 4.8 0.2 - - + -
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Residues in contact with GLY 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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99B TRP* 4.7 6.3 - - - -
113B LEU* 4.2 7.4 - - - +
114B LEU 2.4 28.8 + - - -
137B ILE* 1.3 64.0 - - - +
139B LEU* 1.3 55.8 + - - +
140B TYR* 4.0 1.7 + - - -
149B MET 3.2 2.1 - - - +
150B TRP* 2.9 15.7 - - - -
151B ILE* 2.8 47.4 + - - +
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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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99B TRP* 4.1 0.4 + - - -
137B ILE* 2.6 20.2 + - + +
138B GLY* 1.3 73.4 - - - +
140B TYR* 1.3 60.6 + - - +
148B TRP* 3.7 21.3 - - + -
149B MET* 3.3 35.7 - - - +
150B TRP* 3.0 24.2 - - + +
156B LEU* 3.9 13.7 - - + -
161B PHE* 3.3 39.5 - - + -
172B CYS* 3.7 2.1 - - - +
173B ALA* 2.9 43.3 + - + -
180B VAL* 5.4 0.2 - - + -
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Residues in contact with TYR 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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99B TRP* 4.4 20.0 - + + -
138B GLY 4.2 3.6 - - - -
139B LEU* 1.3 74.8 - - - +
141B VAL* 1.3 75.6 + - - +
142B THR* 5.3 2.2 - - - -
148B TRP* 3.4 9.5 - - - -
149B MET* 2.7 92.2 + - + +
150B TRP 4.2 6.7 - - - -
151B ILE* 4.4 4.4 - - - -
153B GLU* 3.7 9.4 + - - -
171B SER 3.8 5.8 - - - +
172B CYS* 4.0 19.7 - - - +
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Residues in contact with VAL 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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140B TYR* 1.3 95.7 - - - +
142B THR* 1.3 74.1 + - - +
143B PHE 3.6 4.7 - - - +
146B ASN* 3.7 11.9 - - - +
147B LEU 2.8 14.6 - - - +
148B TRP* 3.7 27.1 - - + +
167B THR 4.1 8.1 - - - +
168B ASP 3.2 29.8 - - - +
169B ASP* 3.3 22.0 - - - +
170B ARG 4.7 0.9 - - - +
171B SER* 2.8 23.8 + - - +
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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