Contacts of the helix formed by residues 1305 - 1308 (chain B) in PDB entry 3PT6
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 GLY1305 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1303B GLN* 2.8 24.3 - - - +
1304B ALA* 1.3 73.0 - - - +
1306B GLN* 1.3 56.0 + - - -
1307B TYR 3.0 4.7 + - - -
1308B GLY 3.4 9.1 + - - -
1309B VAL 3.6 20.7 + - - +
1311B GLN 3.5 12.8 + - - -
1335B HIS* 4.1 8.1 - - - +
1337B PHE* 3.8 20.5 - - - -
1368B ILE 5.8 0.9 + - - -
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Residues in contact with GLN1306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1303B GLN* 2.9 31.0 + - + +
1304B ALA 2.8 3.2 + - - -
1305B GLY* 1.3 73.3 - - - +
1307B TYR* 1.3 63.5 + - + +
1308B GLY 3.6 0.7 - - - -
1333B PRO* 3.2 38.8 - - + +
1334B LEU 2.7 31.5 + - - -
1335B HIS 3.0 19.9 + - - +
1336B VAL* 5.8 0.4 - - - +
1337B PHE* 4.1 9.5 - - + +
1342B CYS* 3.7 26.9 - - - +
1344B LEU* 3.5 26.4 - - - +
1359B ARG 4.3 6.7 + - - -
1360B LEU 5.1 4.8 + - - -
1361B SER 6.0 0.4 + - - -
1362B SER 5.6 1.6 + - - -
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Residues in contact with TYR1307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1302B LEU* 3.4 22.7 - - + +
1303B GLN 3.2 25.4 - - - -
1304B ALA 2.7 16.9 + - - +
1306B GLN* 1.3 81.7 + - + +
1308B GLY* 1.3 56.2 + - - +
1331B PRO* 2.5 45.3 + - + +
1332B GLU 3.6 16.4 - - - -
1333B PRO* 3.8 11.1 - - + +
1334B LEU* 4.3 18.2 - - + +
1335B HIS* 3.7 8.5 + - - -
1357B ILE* 3.9 5.9 - - - +
1585B PRO* 3.5 36.5 - - - +
1586B LEU* 3.8 21.8 - - + +
1589B ALA* 3.6 17.5 - - + -
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Residues in contact with GLY1308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1305B GLY 3.4 1.6 + - - -
1307B TYR* 1.3 81.7 - - - +
1309B VAL* 1.3 66.0 + - - +
1335B HIS* 3.3 33.1 - - - -
1368B ILE* 3.9 7.0 - - - -
1398B TRP* 6.0 0.8 - - - -
1399B PHE* 3.3 25.3 - - - -
1585B PRO* 4.3 6.1 - - - +
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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