Contacts of the strand formed by residues 1220 - 1224 (chain A) in PDB entry 2Y23
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 SER1220 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1142A LYS 3.8 8.9 + - - -
1143A GLU* 4.5 3.4 - - - -
1144A VAL* 3.9 22.5 - - - +
1158A PHE* 3.2 38.0 - - - -
1209A SER* 3.2 1.5 - - - -
1210A CYS 2.7 37.7 + - - -
1218A ILE* 4.3 2.1 + - - +
1219A ALA* 1.3 74.8 + - - +
1221A SER* 1.3 60.3 + - - +
2448A BME 5.4 2.8 - - - +
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Residues in contact with SER1221 (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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1143A GLU* 4.9 8.5 - - - +
1144A VAL* 4.8 8.4 + - - +
1175A TYR* 6.2 0.2 - - - -
1207A ILE* 3.8 21.6 - - - +
1208A TYR 3.0 10.8 - - - -
1209A SER* 3.6 15.0 - - - -
1219A ALA* 4.2 2.8 + - - -
1220A SER* 1.3 75.8 - - - +
1222A TYR* 1.3 65.0 + - - +
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Residues in contact with TYR1222 (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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1144A VAL* 3.7 37.7 - - + -
1145A VAL* 5.1 0.2 - - - -
1146A VAL* 3.3 35.5 - - + +
1156A LEU* 3.8 26.2 - - + -
1206A GLY 3.8 0.5 - - - +
1207A ILE* 3.7 4.1 - - - -
1208A TYR* 2.7 40.4 + - - +
1221A SER* 1.3 76.6 - - - +
1223A LEU* 1.3 80.0 + - - +
1224A ILE* 3.7 13.8 + - + -
1228A GLU* 3.0 28.7 + - - -
1231A ARG* 4.3 2.1 + - - -
1232A LEU* 5.4 1.3 - - + -
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Residues in contact with LEU1223 (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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1206A GLY* 3.9 14.4 - - - +
1207A ILE* 4.7 16.3 - - + +
1222A TYR* 1.3 87.3 - - - +
1224A ILE* 1.3 70.3 + - - +
1225A ASP* 4.0 27.8 + - + +
1228A GLU* 3.9 9.7 - - - +
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Residues in contact with ILE1224 (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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1156A LEU* 4.8 6.3 - - + -
1197A PHE* 3.8 34.5 - - + -
1200A LEU* 4.7 15.0 - - + -
1204A ASP 4.1 12.6 - - - +
1205A LEU* 3.5 13.3 - - + +
1206A GLY* 2.9 40.8 + - - +
1208A TYR* 4.0 16.2 - - + -
1222A TYR* 3.7 16.1 + - + -
1223A LEU* 1.3 76.7 - - - +
1225A ASP* 1.3 66.2 + - - +
1228A GLU* 4.4 7.4 - - + -
1229A LEU* 4.9 12.3 - - + +
1232A LEU* 4.8 11.7 - - + -
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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