Contacts of the strand formed by residues 181 - 186 (chain A) in PDB entry 5A24
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 SER 181 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154A ILE* 4.6 0.5 - - - +
173A GLY 3.2 10.8 - - - -
174A THR* 2.7 22.5 + - - +
179A GLY 3.8 2.3 + - - -
180A ASN* 1.3 73.5 - - - +
182A TYR* 1.3 62.9 + - - +
202A GLN* 3.5 11.8 - - - +
203A MET* 2.9 32.0 + - - +
1225A PO4 3.2 27.8 + - - -
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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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154A ILE* 3.8 21.3 - - + -
172A TYR* 3.1 6.2 - - - +
173A GLY* 2.9 59.8 + - - -
174A THR 3.6 7.4 + - - -
175A ASP* 3.7 13.4 - - - -
180A ASN 3.9 1.8 - - - -
181A SER* 1.3 79.3 - - - +
183A TRP* 1.3 63.1 + - - +
184A ILE* 3.7 20.0 - - + +
200A TRP* 3.4 70.1 - + + -
201A MET 3.3 14.4 - - - +
202A GLN* 4.3 2.0 - - - -
203A MET* 3.6 8.7 - - - +
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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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124A GLU* 2.9 41.1 + - + -
127A LEU* 3.7 28.5 - - + -
128A GLN* 3.5 41.7 - - + -
131A ALA* 4.1 7.6 - - + -
169A VAL* 3.8 19.3 - - + -
171A GLY 3.7 8.3 - - - +
172A TYR* 4.0 19.5 - + + -
182A TYR* 1.3 72.4 - - - +
184A ILE* 1.3 60.2 + - - +
185A VAL* 4.0 16.7 - - + +
199A ILE 3.5 2.1 - - - +
200A TRP* 3.3 7.6 - - - -
201A MET* 2.8 47.3 + - + +
202A GLN 4.2 3.8 - - - -
203A MET* 3.5 21.6 - - + +
214A ILE* 3.8 24.0 - - + +
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Residues in contact with ILE 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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6A VAL 3.8 10.1 - - - +
7A ASP* 3.9 21.5 - - + +
9A ARG* 3.6 33.4 - - - +
169A VAL* 3.5 4.5 - - - -
170A VAL* 2.8 41.4 + - + +
171A GLY* 2.9 20.8 + - - +
172A TYR 3.8 20.2 - - - +
173A GLY* 5.2 0.4 - - - -
182A TYR* 3.7 27.6 - - + +
183A TRP* 1.3 69.5 - - - +
185A VAL* 1.3 61.9 + - - +
198A TYR* 4.1 5.4 - - + -
199A ILE 4.0 2.0 - - - -
200A TRP* 4.4 10.8 - - + +
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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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140A ILE* 5.8 0.2 - - + -
167A VAL* 3.4 37.7 - - + -
168A THR 3.4 4.5 - - - +
169A VAL* 4.2 7.0 - - + -
183A TRP* 4.0 24.2 - - + +
184A ILE* 1.3 79.4 - - - +
186A LYS* 1.3 64.1 + - - +
187A ASN* 3.6 0.9 + - - -
198A TYR* 3.3 10.1 - - - -
199A ILE* 2.9 54.8 + - + +
201A MET* 4.0 10.3 - - - -
214A ILE* 4.0 17.5 - - + -
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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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14A VAL* 3.8 16.4 - - + +
15A THR* 2.9 46.3 + - - +
16A PRO 3.3 11.8 + - - -
17A VAL* 3.9 13.9 - - + +
18A LYS* 4.8 7.0 - - - +
33A ALA* 4.4 20.4 - - + +
36A GLU* 4.1 6.1 + - - -
167A VAL* 3.7 5.5 - - - +
168A THR* 2.8 38.9 + - - +
170A VAL* 4.2 8.3 - - + +
184A ILE 4.2 0.4 + - - -
185A VAL* 1.3 70.1 - - - +
187A ASN* 1.3 67.7 + - - +
197A GLY 4.4 0.2 - - - -
198A TYR* 3.5 29.2 - - + +
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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