Contacts of the strand formed by residues 1465 - 1470 (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 THR1465 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1358P THR* 3.0 40.4 - - + +
1360P ILE* 5.6 6.5 - - + -
1463P ASN* 2.8 37.9 + - - +
1464P GLY* 1.3 82.5 + - - +
1466P GLU* 1.3 68.9 + - - +
1467P ILE* 4.2 8.1 + - - +
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Residues in contact with GLU1466 (chain P).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1353P PHE* 4.3 18.2 - - + +
1357P LYS* 3.1 37.6 + - + +
1358P THR 2.6 18.7 + - - +
1359P ILE* 3.7 4.1 - - + -
1360P ILE* 3.2 18.0 + - - +
1456P ARG* 3.1 36.4 + - - +
1457P ASP 4.4 4.7 - - - +
1458P GLY* 5.0 0.9 - - - -
1464P GLY 6.2 0.2 - - - -
1465P THR* 1.3 80.5 - - - +
1467P ILE* 1.3 63.7 + - - +
1468P PHE* 3.8 23.4 - - + -
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Residues in contact with ILE1467 (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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1360P ILE* 3.3 12.8 - - + +
1362P ASN* 3.3 37.2 - - + +
1456P ARG* 3.5 5.9 - - - +
1457P ASP* 3.0 58.4 + - + +
1463P ASN* 5.3 8.7 - - - +
1465P THR* 4.2 9.4 + - - +
1466P GLU* 1.3 80.1 + - - +
1468P PHE* 1.3 69.4 + - - +
1469P ARG* 4.6 5.6 - - - +
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Residues in contact with PHE1468 (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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1284P ILE* 3.8 15.0 - - + -
1349P LEU* 3.5 48.7 - - + -
1353P PHE* 3.8 12.6 - + - -
1359P ILE* 4.2 14.4 - - + -
1360P ILE 3.1 10.8 + - - -
1361P PHE* 3.4 25.0 - + + +
1362P ASN 2.9 24.9 + - - +
1391P PHE* 5.9 0.2 - - - -
1454P LEU* 4.3 11.2 - - + -
1455P THR 3.3 9.0 - - - +
1456P ARG* 3.4 42.2 - - + -
1466P GLU* 3.8 22.9 - - + -
1467P ILE* 1.3 74.8 - - - +
1469P ARG* 1.3 64.6 + - - +
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Residues in contact with ARG1469 (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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1362P ASN* 3.2 24.8 + - + +
1363P PRO* 2.8 44.1 + - - +
1364P SER* 4.2 5.4 + - - -
1365P SER* 2.9 34.2 + - - +
1391P PHE* 5.4 0.9 - - - -
1454P LEU* 3.4 10.9 - - - -
1455P THR* 3.0 34.2 + - - +
1457P ASP* 2.5 36.6 + - - +
1467P ILE* 4.6 9.8 - - + +
1468P PHE* 1.3 78.6 - - - +
1470P PRO* 1.3 75.7 - - + +
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Residues in contact with PRO1470 (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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1258P GLN* 3.1 41.4 + - + +
1362P ASN 3.3 14.4 - - - +
1363P PRO* 3.5 0.7 - - + -
1364P SER* 3.5 25.4 + - - +
1371P ILE 5.0 2.1 - - - +
1387P SER* 4.3 1.6 - - - +
1391P PHE* 3.2 39.9 - - + -
1453P LEU 3.8 4.7 - - - +
1454P LEU* 4.8 4.5 - - + -
1455P THR* 4.0 4.5 + - - -
1469P ARG* 1.3 90.5 - - + +
1471P GLY* 1.3 59.6 + - - +
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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