Contacts of the strand formed by residues 181 - 186 (chain A) in PDB entry 5MAJ
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 181 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120A LYS* 4.5 6.9 - - - +
150A ILE* 3.9 4.7 - - - +
171A GLY 3.4 12.1 - - - +
172A PHE* 4.2 7.4 - - + -
179A ASN* 3.5 6.8 - - - +
180A ASN* 1.3 94.1 - - - +
182A TYR* 1.3 62.8 + - - +
202A ALA* 3.8 5.2 - - - +
203A LYS* 3.0 42.7 + - + +
204A ASP* 2.9 39.3 + - - +
205A ARG* 5.7 0.9 - - - +
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Residues in contact with TYR 182 (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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150A ILE* 4.2 7.6 - - + -
170A TYR* 3.2 7.4 - - - +
171A GLY* 2.9 46.3 + - - +
172A PHE* 3.5 37.5 + - - -
173A GLU* 3.7 14.8 - - + -
180A ASN 4.1 1.6 - - - -
181A LYS* 1.3 77.1 - - - +
183A TRP* 1.3 67.6 - - - +
184A LEU* 4.0 15.7 - - + -
200A LYS* 3.5 52.6 + - + +
201A MET 3.0 15.0 - - - +
203A LYS* 3.5 10.2 - - - +
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Residues in contact with TRP 183 (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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119A GLU* 2.9 39.4 + - + -
122A LEU* 3.6 28.7 - - + -
123A MET* 3.5 34.8 - - - -
126A VAL* 4.2 5.2 - - + -
167A VAL* 3.8 17.5 - - + -
169A GLY 3.7 3.6 - - - +
170A TYR* 3.8 19.5 - + + -
182A TYR* 1.3 74.0 - - - +
184A LEU* 1.3 61.9 + - - +
185A VAL* 3.6 6.2 + - + +
199A VAL 3.4 2.6 - - - +
200A LYS* 3.5 2.9 - - - -
201A MET* 2.7 34.1 + - + +
202A ALA 3.7 13.2 - - - -
203A LYS* 3.5 37.4 - - + +
211A ILE* 3.6 36.2 - - + +
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Residues in contact with LEU 184 (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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5A VAL 5.1 0.9 - - - +
6A ASP* 3.7 18.4 - - + +
8A ARG* 3.3 30.5 - - - +
167A VAL* 3.5 4.0 - - - -
168A VAL* 2.8 52.6 + - + +
169A GLY* 2.9 24.2 + - - +
170A TYR 4.3 1.3 - - - +
182A TYR* 4.0 13.7 - - + -
183A TRP* 1.3 71.2 - - - +
185A VAL* 1.3 56.8 + - - +
198A TYR* 4.0 23.3 - - + -
199A VAL 4.0 1.1 - - - +
200A LYS* 4.5 18.6 - - + -
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Residues in contact with VAL 185 (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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136A ILE* 5.4 0.9 - - + -
165A VAL* 3.5 37.2 - - + -
166A LEU 3.3 4.7 - - - +
167A VAL* 4.1 10.5 - - + -
183A TRP* 3.9 6.3 - - + +
184A LEU* 1.3 79.4 - - - +
186A LYS* 1.3 63.3 + - - +
187A ASN 3.7 0.7 + - - +
198A TYR* 3.2 10.2 - - - -
199A VAL* 2.9 57.8 + - + +
201A MET* 3.7 23.6 - - + -
211A ILE* 4.0 18.2 - - + -
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Residues in contact with LYS 186 (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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13A VAL* 3.9 12.2 - - + +
14A THR* 2.9 46.6 + - - +
15A PRO 3.3 12.2 + - - -
16A VAL* 3.9 15.5 - - + +
17A LYS* 4.9 5.9 - - - +
32A GLY* 5.3 2.8 - - - -
35A GLU* 4.4 4.6 + - - -
165A VAL* 3.6 5.9 - - - +
166A LEU* 2.8 51.4 + - + +
168A VAL* 4.1 6.5 - - + +
184A LEU 4.2 0.2 + - - -
185A VAL* 1.3 71.0 - - - +
187A ASN* 1.4 71.0 + - - +
197A GLY 4.3 0.2 - - - -
198A TYR* 3.5 35.1 - - + +
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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