Contacts of the strand formed by residues 156 - 161 (chain G) in PDB entry 5IC4
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 LYS 156 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114G PHE* 3.5 9.9 - - + +
143G PHE* 3.1 30.2 + - + +
145G GLY* 5.0 5.7 - - - +
151G LEU* 2.8 51.2 + - + -
152G THR* 4.3 2.6 - - - +
153G GLY 4.2 3.6 - - - +
154G LYS 2.9 14.9 + - - +
155G PRO* 1.3 71.7 - - - +
157G LEU* 1.3 64.0 + - - +
158G PHE* 3.8 14.6 - - + -
191H ALA 3.8 4.1 + - - -
192H ASP* 2.8 27.7 + - - +
193H PHE* 3.5 36.6 - - + -
194H LEU 2.9 24.1 + - - +
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Residues in contact with LEU 157 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78G PHE* 5.9 1.3 - - + -
83G TYR* 4.8 1.8 - - - +
113G SER* 5.5 2.7 - - - +
114G PHE* 2.8 16.2 + - - +
115G VAL* 3.4 25.2 - - + +
116G CYS 2.8 27.4 + - - +
155G PRO* 4.1 15.9 - - + +
156G LYS* 1.3 74.8 - - - +
158G PHE* 1.3 65.0 + - - +
159G ILE* 4.1 6.1 - - + -
194H LEU* 3.5 34.5 - - + +
232H PHE* 3.9 15.7 - - + -
269H LEU* 4.5 3.1 - - + -
273H LEU* 3.7 33.9 - - + -
275H PHE* 4.4 12.1 - - + -
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Residues in contact with PHE 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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100G MET* 4.3 2.7 - - + -
114G PHE* 4.0 9.0 - + - -
116G CYS* 3.3 35.4 - - + -
118G LEU* 5.2 6.7 - - + -
136G LEU* 6.5 0.4 - - + -
139G ILE* 4.1 15.7 - - + -
140G THR* 4.1 23.8 - - + -
143G PHE* 3.9 24.5 - + - -
156G LYS* 3.8 18.4 - - + -
157G LEU* 1.3 77.0 - - - +
159G ILE* 1.3 59.4 + - - +
160G ILE* 3.8 12.4 + - + +
193H PHE* 3.7 29.2 - + - -
194H LEU* 2.6 14.5 + - - +
195H TYR* 3.4 14.9 - + + -
196H ALA 2.8 30.7 + - - +
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Residues in contact with ILE 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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78G PHE* 3.9 26.0 - - + -
115G VAL* 4.4 7.6 - - + -
116G CYS 2.8 9.4 + - - +
117G VAL* 3.3 22.6 - - + +
118G LEU 2.8 26.5 + - - -
157G LEU* 5.1 5.8 - - + -
158G PHE* 1.3 75.0 - - - +
160G ILE* 1.3 61.0 + - - +
194H LEU* 5.9 0.4 - - + -
196H ALA* 3.6 14.4 - - + +
215H PHE* 3.6 27.1 - - + -
216H ILE* 4.1 12.1 - - + -
219H LEU* 3.6 29.4 - - + -
232H PHE* 5.1 10.3 - - + -
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Residues in contact with ILE 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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118G LEU* 3.7 14.6 - - + +
126G ILE 6.1 0.2 - - - +
127G ILE* 4.1 24.5 - - + -
136G LEU* 3.6 30.3 - - + -
140G THR* 6.4 1.3 - - + -
158G PHE* 4.0 20.9 - - + +
159G ILE* 1.3 78.8 - - - +
161G GLN* 1.3 60.0 + - - +
162G ALA* 3.8 10.7 + - + +
195H TYR* 5.0 6.1 - - + -
196H ALA 2.9 12.1 + - - +
197H TYR* 3.6 38.0 - - + +
198H SER* 3.0 30.2 + - - -
215H PHE* 4.3 3.2 - - - -
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Residues in contact with GLN 161 (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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64G ARG* 4.0 7.5 + - - +
70G ASP* 4.7 0.4 - - - +
118G LEU 2.9 8.7 + - - +
119G LEU* 3.6 23.3 - - + +
120G SER 3.0 24.8 + - - +
159G ILE 4.0 1.0 + - - -
160G ILE* 1.3 70.1 - - - +
162G ALA* 1.3 60.2 + - - +
198H SER* 3.1 17.7 - - - -
205H SER* 2.9 22.6 + - - -
206H TRP 3.6 6.1 + - - +
213H SER* 3.3 28.9 + - - +
215H PHE* 3.3 17.0 + - + +
216H ILE* 3.9 8.3 - - + -
4L MKE 3.2 33.3 + - - +
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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