Contacts of the strand formed by residues 218 - 222 (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 ALA 218 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118A ASP* 3.7 4.7 - - - +
119A VAL* 2.8 48.6 + - + +
121A ALA* 6.3 0.2 - - - +
127A LEU* 3.8 22.4 - - + -
136A ILE* 3.9 0.4 - - + -
137A SER 3.2 10.3 - - - +
138A VAL* 3.9 7.2 - - + -
214A ILE 4.8 4.5 - - - +
215A ALA 5.3 4.5 + - - +
216A MET 4.1 0.8 - - - -
217A GLN* 1.3 76.4 - - - +
219A SER* 1.3 64.0 + - - +
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Residues in contact with SER 219 (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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71A PRO* 4.2 10.0 - - - +
72A ASP* 2.7 29.6 + - - -
75A PHE* 3.4 11.5 - - - -
116A TYR* 4.8 0.2 - - - -
117A GLN 3.2 16.2 - - - -
118A ASP* 3.6 7.6 - - - -
136A ILE* 3.5 2.7 - - - +
137A SER* 2.9 33.7 + - - +
218A ALA* 1.3 76.9 - - - +
220A TYR* 1.3 69.2 + - - +
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Residues in contact with TYR 220 (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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75A PHE* 3.9 6.5 - - - -
116A TYR* 3.3 0.9 - - - -
117A GLN* 2.8 83.7 + - + +
118A ASP 5.0 0.4 + - - -
119A VAL* 3.7 24.5 - - + -
130A ALA* 3.8 16.4 - - + +
133A THR* 5.1 3.6 - - - -
134A GLN* 3.3 33.4 - - + +
135A PRO 3.9 4.3 - - - +
136A ILE* 3.7 25.6 - - + -
219A SER* 1.3 80.1 - - - +
221A PRO* 1.3 76.3 - - + +
222A THR* 6.0 0.2 - - - -
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Residues in contact with PRO 221 (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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34A ALA* 3.6 43.5 - - + +
35A ILE* 3.9 9.0 - - + +
38A ALA* 3.8 6.3 - - + +
75A PHE* 3.6 15.0 - - + -
113A ILE* 3.8 31.4 - - + -
115A GLY 3.5 5.6 - - - +
116A TYR* 4.0 2.9 - - + -
134A GLN* 2.9 28.0 + - - +
220A TYR* 1.3 92.1 - - + +
222A THR* 1.3 59.9 - - - +
223A ALA 3.8 2.3 + - - -
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Residues in contact with THR 222 (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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113A ILE* 3.3 5.2 - - - +
114A THR* 2.9 43.0 + - - +
115A GLY* 2.8 24.5 + - - -
116A TYR* 3.9 5.4 + - - -
117A GLN* 4.0 22.1 + - - +
134A GLN* 5.8 0.4 - - - -
220A TYR* 6.0 0.2 - - - -
221A PRO* 1.3 70.1 - - - +
223A ALA* 1.3 65.0 + - - +
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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