Contacts of the strand formed by residues 161 - 167 (chain A) in PDB entry 5IXC
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 LEU 161 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159A ARG 3.5 2.1 + - - +
160A GLU* 1.3 83.3 - - - +
162A SER* 1.3 62.8 + - - +
210A HIS* 4.5 5.4 - - + -
211A TYR 3.7 17.0 - - - +
212A MET* 4.1 6.1 - - + +
213A ALA* 4.7 0.2 - - - -
273A GLY* 3.7 5.2 - - - -
274A CYS* 3.4 34.2 + - + -
507A PHE* 3.5 34.8 - - + -
508A MET* 3.8 21.5 - - + -
510A ARG* 3.3 51.8 - - - +
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Residues in contact with SER 162 (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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160A GLU* 4.2 1.7 + - - -
161A LEU* 1.3 73.4 - - - +
163A CYS* 1.3 60.6 + - - +
211A TYR* 2.9 63.2 + - - +
213A ALA* 3.8 17.1 - - - +
271A ALA* 5.4 2.2 - - - -
272A GLU 3.3 17.0 - - - -
273A GLY* 4.5 1.3 - - - -
274A CYS* 3.3 9.7 - - - -
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Residues in contact with CYS 163 (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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162A SER* 1.3 74.1 - - - +
164A LEU* 1.3 60.3 + - - +
165A ASP* 5.3 0.8 - - - +
208A ARG* 3.6 22.0 - - - +
209A PHE 3.1 2.9 - - - -
210A HIS* 3.2 24.5 - - - -
211A TYR* 4.0 3.1 - - - -
270A LYS 3.8 0.5 - - - +
271A ALA* 3.2 5.2 - - - +
272A GLU* 2.5 38.6 + - + +
273A GLY 4.7 0.4 - - - +
274A CYS* 2.1 51.8 - - - -
275A PRO* 4.0 7.0 - - + -
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Residues in contact with LEU 164 (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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163A CYS* 1.3 73.5 - - - +
165A ASP* 1.3 61.0 + - - +
166A VAL* 3.2 34.1 - - + -
189A LEU* 4.2 6.5 - - + -
207A PHE 3.7 0.9 - - - +
208A ARG* 3.4 7.5 - - - -
209A PHE* 2.7 44.8 + - + -
211A TYR* 3.7 20.1 - - + +
219A LEU* 4.0 27.1 - - + -
244A LEU* 4.8 14.8 - - + -
269A LEU* 4.4 10.1 - - + -
270A LYS 3.3 30.3 - - - +
271A ALA* 4.1 8.7 - - + +
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Residues in contact with ASP 165 (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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163A CYS* 5.3 1.1 - - - +
164A LEU* 1.3 74.3 - - - +
166A VAL* 1.3 72.0 + - - +
167A HIS* 4.8 5.2 - - + -
206A ALA* 5.0 2.6 - - - +
207A PHE 3.6 8.9 + - - +
208A ARG* 2.8 37.4 + - - +
268A GLN 3.3 1.8 - - - +
269A LEU* 3.2 7.8 - - - +
270A LYS* 2.8 43.8 + - + +
902A BA 3.1 24.3 - - - -
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Residues in contact with VAL 166 (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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164A LEU* 3.2 33.7 - - + +
165A ASP* 1.3 75.4 + - - +
167A HIS* 1.3 70.9 + - - +
187A LEU* 4.0 25.8 - - + -
206A ALA* 3.1 7.9 - - - +
207A PHE* 2.9 47.8 + - + +
209A PHE* 4.8 5.6 - - + -
219A LEU* 4.9 4.0 - - + -
267A LEU* 4.1 14.4 - - + -
268A GLN 3.2 2.2 - - - -
269A LEU* 4.1 20.9 - - + -
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Residues in contact with HIS 167 (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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165A ASP* 4.8 4.9 - - + -
166A VAL* 1.3 77.0 - - - +
168A LEU* 1.3 61.1 + - - +
169A ASP 3.8 1.8 - - - +
204A ALA 6.2 0.6 - - - -
205A SER 3.7 5.1 + - - -
206A ALA* 4.5 12.6 - - + +
207A PHE* 5.9 0.7 - - - -
267A LEU* 3.2 33.4 - - - +
268A GLN* 2.9 38.6 + - + +
902A BA 3.5 23.5 - - - -
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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