Contacts of the helix formed by residues 1368 - 1373 (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 ASP1368 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1367P GLY* 1.3 75.1 - - - +
1369P PRO* 1.3 75.6 - - + +
1370P GLU* 3.3 9.4 - - - +
1371P ILE* 3.0 7.2 + - + +
1372P VAL* 2.9 18.2 + - - +
1425P ASN* 3.6 22.8 + - - +
1009S ARG* 2.9 34.7 + - - +
1022S SER 5.0 0.9 - - - +
1023S BIF 4.0 13.6 - - + -
1024S CYS* 2.8 33.4 + - - +
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Residues in contact with PRO1369 (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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1367P GLY 3.8 1.3 - - - +
1368P ASP* 1.3 86.4 - - + +
1370P GLU* 1.3 66.7 + - - +
1372P VAL* 2.8 11.3 + - + +
1373P THR* 2.7 42.9 + - + +
1384P TYR* 4.1 4.5 - - + -
1421P LYS* 3.6 28.9 - - - +
1425P ASN* 3.6 9.9 - - - +
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Residues in contact with GLU1370 (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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1257P THR* 2.9 25.8 + - - -
1368P ASP* 3.5 4.9 - - - +
1369P PRO* 1.3 80.4 - - - +
1371P ILE* 1.3 58.1 + - - +
1373P THR* 2.9 9.2 - - - +
1375P SER* 3.0 17.5 + - - +
1384P TYR* 3.0 31.4 + - + +
1421P LYS* 5.4 0.5 + - - -
1424P ILE* 3.9 1.2 - - - -
1425P ASN* 2.6 58.1 + - - +
1023S BIF 3.4 39.8 - - + -
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Residues in contact with ILE1371 (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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1257P THR* 3.9 9.6 - - + -
1258P GLN* 3.3 17.0 + - - +
1364P SER* 3.9 9.5 + - - +
1366P GLY 3.8 22.7 - - - +
1368P ASP* 3.0 13.8 + - + +
1370P GLU* 1.3 77.6 - - - +
1372P VAL* 1.3 65.2 + - - +
1373P THR 4.1 0.4 - - - +
1470P PRO 5.0 2.8 - - - +
1471P GLY 5.0 3.6 - - - +
1472P GLY 3.5 13.7 - - - +
1473P GLY* 3.3 32.8 - - - +
1020S ALA* 4.4 8.1 - - + -
1023S BIF 3.3 29.8 - - + -
1024S CYS 4.1 13.2 - - - +
1025S ALA* 4.3 8.7 - - + -
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Residues in contact with VAL1372 (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* 2.9 13.5 + - - -
1364P SER* 4.0 17.8 + - - +
1366P GLY* 3.9 25.4 - - - -
1367P GLY 3.7 13.7 - - - +
1368P ASP 2.9 16.0 + - - +
1369P PRO* 2.8 11.2 + - + +
1371P ILE* 1.3 79.8 - - - +
1373P THR* 1.3 65.7 + - + +
1387P SER* 3.9 6.8 + - - -
1886P NAG 5.4 7.9 - - + -
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Residues in contact with THR1373 (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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1257P THR* 3.4 3.3 + - - -
1258P GLN* 3.6 7.7 + - - +
1369P PRO* 2.7 25.7 + - + +
1370P GLU 2.9 14.7 - - - +
1372P VAL* 1.3 82.0 - - + +
1374P HIS* 1.3 59.1 + - - +
1375P SER* 2.9 10.9 + - - -
1384P TYR* 3.6 30.9 - - + +
1385P CYS 3.1 24.7 - - - +
1386P ASN* 4.5 2.0 - - - +
1387P SER* 4.7 2.5 - - - +
1886P NAG 4.3 23.3 - - + -
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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