Contacts of the strand formed by residues 1223 - 1228 (chain P) in PDB entry 1YYL
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 PHE1223 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1219P ALA* 3.6 9.4 - - - +
1220P PRO* 3.0 39.1 + - + +
1221P ALA 3.7 12.1 - - - -
1222P GLY* 1.3 83.1 + - - +
1224P ALA* 1.3 61.9 + - - +
1246P GLN* 5.6 0.7 + - - -
1488P VAL* 4.4 15.7 - - + -
1489P VAL 3.2 20.0 - - - +
1490P LYS* 3.5 32.5 - - + -
1491P ILE* 3.6 7.1 - - - +
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Residues in contact with ALA1224 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1219P ALA* 3.9 4.9 - - - -
1223P PHE* 1.3 72.7 - - - +
1225P ILE* 1.3 64.1 + - - +
1226P LEU* 3.9 5.6 - - + -
1244P THR* 4.5 13.9 - - - +
1245P VAL 5.3 0.4 - - - +
1488P VAL* 3.5 3.3 - - - +
1489P VAL* 2.8 43.8 + - + +
1491P ILE* 3.3 23.5 - - + +
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Residues in contact with ILE1225 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1100P MET* 4.9 7.6 - - - -
1217P TYR* 3.4 25.4 - - + +
1218P CYS 3.6 3.4 - - - +
1219P ALA* 3.3 35.4 - - + +
1224P ALA* 1.3 74.4 - - - +
1226P LEU* 1.3 63.1 + - - +
1244P THR* 3.5 5.5 + - - -
1245P VAL* 3.2 42.4 + - + +
1246P GLN 3.7 8.1 - - - +
1247P CYS* 4.3 1.1 - - - -
1248P THR* 4.4 7.0 - - + +
1486P TYR* 3.8 34.8 - - + -
1487P LYS 3.9 4.7 - - - +
1488P VAL* 4.4 11.2 - - + +
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Residues in contact with LEU1226 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1089P VAL* 6.2 5.8 - - + -
1091P GLU* 3.8 33.2 - - + +
1093P PHE* 4.4 9.0 - - + -
1224P ALA* 4.6 5.8 - - + -
1225P ILE* 1.3 82.0 - - - +
1227P LYS* 1.3 60.4 + - - +
1228P CYS 4.2 0.2 - - - -
1242P VAL* 4.1 19.1 - - + -
1243P SER 3.5 8.5 - - - +
1244P THR* 4.4 10.1 - - - -
1485P LYS 3.7 0.2 - - - +
1486P TYR* 3.3 7.8 - - - +
1487P LYS* 2.8 42.6 + - + +
1489P VAL* 3.5 34.3 - - + -
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Residues in contact with LYS1227 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1226P LEU* 1.3 75.5 - - - +
1228P CYS* 1.3 60.4 + - - +
1229P ASN* 3.2 19.1 + - - +
1242P VAL* 3.4 4.8 - - - +
1243P SER* 3.0 44.9 + - - +
1245P VAL* 3.9 24.2 - - + +
1249P HIS* 5.3 5.9 - - - +
1485P LYS* 3.4 38.1 - - - +
1486P TYR* 3.7 36.1 + - + -
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Residues in contact with CYS1228 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1093P PHE* 3.7 17.5 - - + -
1227P LYS* 1.3 72.3 - - - +
1229P ASN* 1.3 57.8 + - - +
1230P ASP* 3.4 8.7 - - - +
1233P PHE* 3.4 48.1 - - + +
1239P CYS* 2.0 48.7 - - - -
1485P LYS* 2.8 39.8 + - - +
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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