Contacts of the strand formed by residues 155 - 160 (chain G) in PDB entry 1IB1
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 ARG 155 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99G TRP* 5.1 1.4 - - - -
101G GLU 3.0 18.2 + - - -
102G GLU* 2.8 57.2 + - - +
117G HIS* 3.3 9.6 + - + +
118G SER* 3.3 25.0 + - - +
119G ALA 2.9 23.0 + - - -
153G VAL* 3.5 8.3 - - - +
154G ARG* 1.3 81.0 - - + +
156G ALA* 1.3 73.0 + - - +
157G VAL* 3.3 22.6 - - - +
192G HIS* 4.1 20.8 + - - -
193G CYS 3.2 21.1 - - - +
194G SER* 4.3 3.1 - - - +
195G LEU* 3.6 6.3 - - - +
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Residues in contact with ALA 156 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119G ALA* 3.3 13.5 - - + +
121G LEU* 4.2 4.9 - - + -
144G LEU* 3.9 22.9 - - + -
147G VAL* 5.7 0.4 - - + -
155G ARG* 1.3 75.1 - - - +
157G VAL* 1.3 67.9 + - - +
173G PHE* 3.9 19.3 - - + -
192G HIS* 3.5 0.9 - - - -
193G CYS* 2.8 37.2 + - + +
195G LEU* 4.4 7.0 - - + -
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Residues in contact with VAL 157 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99G TRP* 4.9 3.1 - - + -
102G GLU 4.8 0.4 - - - +
104G LEU* 4.0 22.7 - - + -
118G SER* 4.3 9.6 - - - -
119G ALA 2.9 6.1 + - - +
120G HIS* 3.4 27.1 - - + +
121G LEU* 2.8 28.6 + - - +
155G ARG* 3.3 33.2 - - - +
156G ALA* 1.3 79.9 - - - +
158G LEU* 1.3 63.6 + - - +
173G PHE* 4.5 0.2 - - - -
190G GLU* 5.2 0.7 - - - +
191G MET 3.4 5.6 - - - +
192G HIS* 3.3 23.1 - - + +
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Residues in contact with LEU 158 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104G LEU* 4.4 9.1 - - - +
120G HIS* 4.8 0.9 - - - -
121G LEU* 3.8 35.4 - - + +
124G LEU* 5.6 0.7 - - + -
157G VAL* 1.3 76.2 - - - +
159G MET* 1.3 74.6 + - - +
160G CYS* 4.2 0.2 - - + -
168G TYR* 3.8 40.8 - - + -
173G PHE* 3.6 34.1 - - + -
190G GLU* 3.7 3.3 - - - +
191G MET* 2.8 50.9 + - + +
402G COT 4.7 4.9 - - + -
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Residues in contact with MET 159 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104G LEU* 4.7 2.3 - - + +
109G LEU* 3.7 30.3 - - + -
120G HIS* 4.6 10.3 - - - +
121G LEU 4.8 3.6 + - - +
122G HIS* 5.3 4.5 - - - +
158G LEU* 1.3 77.5 - - - +
160G CYS* 1.3 64.8 + - - +
179G CYS* 3.8 28.9 - - - -
181G ILE* 3.8 21.8 - - + -
183G VAL* 5.0 1.1 - - + -
188G PHE* 3.6 31.2 - - + -
189G THR 3.2 10.8 - - - +
190G GLU* 4.7 0.2 - - - -
402G COT 3.0 53.9 + - + +
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Residues in contact with CYS 160 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159G MET* 1.3 77.1 - - - +
161G GLU* 1.3 74.0 + - - +
164G LEU* 4.0 2.5 - - + -
165G VAL* 3.9 21.1 - - - -
168G TYR* 3.6 29.4 - - + -
188G PHE* 3.2 10.8 - - - +
189G THR* 2.8 32.5 + - - +
191G MET* 3.9 13.9 - - - -
402G COT 3.6 22.9 - - - -
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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