Contacts of the helix formed by residues 149 - 156 (chain A) in PDB entry 5I1U
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 CYS 149 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145A TYR* 3.2 33.7 + - - +
146A TYR 3.9 4.9 - - - +
147A PHE 3.2 1.2 + - - -
148A ALA* 1.3 76.9 - - - +
150A HIS* 1.3 65.5 + - - +
151A PRO 3.4 0.7 - - - -
152A ALA* 3.3 7.0 + - - +
153A GLU* 3.2 17.0 + - - +
170A THR 5.3 2.2 - - - -
171A LEU* 3.6 18.6 - - + +
174A GLY* 3.7 22.0 - - - -
175A THR* 3.8 21.5 - - + +
199B HIS* 3.7 22.9 - - - -
204B ARG* 5.1 0.9 - - - -
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Residues in contact with HIS 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A PHE* 3.9 10.8 - + - -
80A ASP* 4.5 14.4 + - - +
83A PHE* 4.1 26.2 - + + -
94A VAL* 3.7 9.8 - - + +
98A CYS* 3.6 15.0 - - - -
146A TYR* 2.8 66.3 + + - -
147A PHE* 3.1 13.1 + - - +
149A CYS* 1.3 75.7 - - - +
151A PRO* 1.4 69.6 - - + +
153A GLU* 3.2 12.7 + - + +
154A ALA* 3.0 22.5 + - - +
175A THR* 4.7 15.9 - - + +
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Residues in contact with PRO 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A PRO* 3.7 18.5 - - - +
94A VAL* 4.0 9.2 - - + +
95A ALA* 3.5 31.2 - - - +
98A CYS* 4.5 3.1 - - + -
147A PHE 3.8 5.8 - - - +
148A ALA* 3.4 15.0 - - - +
150A HIS* 1.4 93.2 - - + +
152A ALA* 1.3 56.0 + - - +
154A ALA* 3.3 5.0 + - + +
155A ALA* 2.9 28.2 + - - +
195B GLN* 6.1 0.2 - - - +
196B HIS* 3.6 30.5 - - + -
279B MET* 4.1 9.0 - - + -
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Residues in contact with ALA 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A ALA 4.9 1.0 + - - +
149A CYS* 3.3 11.3 + - - +
150A HIS 3.3 0.4 - - - -
151A PRO* 1.3 79.1 - - - +
153A GLU* 1.3 63.0 + - - +
155A ALA* 3.2 5.9 + - - +
156A GLY* 3.0 20.1 + - - -
171A LEU* 4.2 7.1 - - + +
196B HIS 5.4 0.8 + - - +
200B HIS* 3.6 37.2 + - + +
201B PRO* 3.6 22.2 - - + -
279B MET* 4.1 4.2 - - - -
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Residues in contact with GLU 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A ASP* 5.4 5.9 - - - +
83A PHE* 6.6 0.2 - - + -
149A CYS 3.2 9.4 + - - +
150A HIS* 3.2 18.5 + - + +
152A ALA* 1.3 76.7 - - - +
154A ALA* 1.3 63.5 + - - +
156A GLY* 3.2 11.9 + - - +
157A ARG 3.3 14.6 + - - +
171A LEU* 3.3 28.2 - - + +
172A ARG* 5.8 0.9 + - - -
175A THR* 4.5 19.2 + - + +
233A ALA* 5.7 4.3 - - - +
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Residues in contact with ALA 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A PHE* 6.5 0.2 - - + -
88A GLY* 3.1 32.0 - - - +
89A ARG* 4.3 6.6 - - - -
91A PRO* 4.0 22.6 - - + +
94A VAL* 4.1 11.2 - - + -
150A HIS 3.0 12.9 + - - +
151A PRO 3.3 8.3 + - - +
153A GLU* 1.3 79.3 - - - +
155A ALA* 1.3 58.7 + - - +
157A ARG* 2.9 25.4 + - - +
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Residues in contact with ALA 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A PRO* 3.8 10.0 - - + +
151A PRO 2.9 13.5 + - - +
152A ALA* 3.6 9.0 - - - +
154A ALA* 1.3 76.2 - - - +
156A GLY* 1.3 58.2 + - - +
157A ARG* 2.9 28.3 + - - +
200B HIS* 5.7 1.8 - - - +
278B SER* 3.5 44.0 - - - +
279B MET* 4.2 5.2 - - + -
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Residues in contact with GLY 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A ALA 3.0 13.9 + - - -
153A GLU* 3.2 6.9 + - - -
154A ALA 3.2 0.6 - - - -
155A ALA* 1.3 74.4 - - - +
157A ARG* 1.3 69.5 + - - +
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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