Contacts of the helix formed by residues 1549 - 1557 (chain A) in PDB entry 3PTA
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 SER1549 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1412A HIS* 3.2 25.8 + - - -
1413A ILE 3.5 19.7 - - - -
1414A CYS* 3.7 13.5 - - - +
1546A ARG* 4.3 4.5 - - - -
1547A VAL 3.5 0.2 + - - -
1548A VAL* 1.3 73.5 - - - +
1550A VAL* 1.3 60.2 + - - +
1551A ARG 3.9 0.5 + - - -
1552A GLU* 2.6 36.0 + - - +
1553A CYS* 2.9 30.5 + - - -
1573A HIS* 4.0 3.4 - - - -
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Residues in contact with VAL1550 (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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1411A ASP* 3.5 14.6 - - + +
1413A ILE* 3.1 19.4 + - + +
1549A SER* 1.3 73.9 - - - +
1551A ARG* 1.3 59.0 + - - +
1553A CYS* 3.0 5.9 + - + +
1554A ALA* 2.8 26.0 + - - +
1565A LEU* 3.6 32.1 - - + -
1569A ILE* 4.1 15.9 - - + +
1572A LYS* 3.9 15.7 - - + -
1573A HIS* 3.7 32.0 + - + +
1576A VAL* 4.4 9.0 - - + +
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Residues in contact with ARG1551 (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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1374A LEU* 4.6 7.4 - - + -
1409A LEU* 3.7 24.5 - - + -
1410A ARG* 3.1 30.0 + - - +
1411A ASP* 2.9 24.9 + - - +
1412A HIS* 3.8 17.9 - - - +
1549A SER* 3.3 0.4 + - - -
1550A VAL* 1.3 75.3 - - - +
1552A GLU* 1.3 58.1 + - - +
1554A ALA* 3.1 30.4 + - - +
1555A ARG* 2.9 32.7 + - - +
1559A PHE* 5.1 2.8 - - - +
1560A PRO 3.9 8.5 + - - -
1561A ASP* 3.2 51.3 + - - +
1563A TYR* 3.9 13.9 + - - +
1565A LEU* 4.4 17.2 - - - +
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Residues in contact with GLU1552 (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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1371A MET* 3.3 29.7 - - - +
1374A LEU* 3.4 26.2 - - + +
1412A HIS* 3.9 0.6 - - + -
1523A PHE* 4.1 8.6 - - + -
1541A HIS* 3.3 12.4 + - - -
1546A ARG* 2.9 33.6 + - - -
1548A VAL* 3.0 11.1 - - + -
1549A SER* 2.6 45.4 + - - +
1550A VAL 3.2 0.4 - - - -
1551A ARG* 1.3 76.8 - - - +
1553A CYS* 1.3 57.9 + - - +
1555A ARG* 3.2 12.1 + - - +
1556A SER* 2.9 24.4 + - - -
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Residues in contact with CYS1553 (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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1523A PHE* 5.2 2.0 - - - -
1526A THR* 4.7 12.6 - - + -
1527A VAL 5.8 0.9 - - - -
1530A PRO* 4.4 4.5 - - - -
1548A VAL* 3.5 21.3 - - - -
1549A SER 2.9 22.2 + - - -
1550A VAL* 3.0 10.1 + - + +
1552A GLU* 1.3 74.3 - - - +
1554A ALA* 1.3 65.7 + - - +
1556A SER* 2.4 29.1 + - - +
1557A GLN* 3.1 11.1 + - - +
1573A HIS* 3.4 28.0 - - + +
1576A VAL* 3.6 15.2 - - + +
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Residues in contact with ALA1554 (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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1550A VAL 2.8 10.4 + - - +
1551A ARG* 3.1 44.2 - - - +
1553A CYS* 1.3 76.8 - - - +
1555A ARG* 1.3 58.0 + - + +
1557A GLN* 2.9 24.9 + - - +
1559A PHE* 3.4 28.3 + - + +
1561A ASP* 5.7 0.2 - - - +
1576A VAL* 4.0 16.8 - - + +
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Residues in contact with ARG1555 (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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1307A ALA 5.8 0.3 + - - -
1370A THR* 2.9 49.2 + - + +
1371A MET* 4.1 3.8 - - + +
1373A ASP* 3.3 34.5 + - - -
1374A LEU* 3.8 21.9 - - + +
1388A TYR* 4.3 8.9 - - - -
1396A PHE* 3.6 11.4 - - - -
1397A GLN* 4.3 7.5 + - - +
1400A LEU* 3.7 28.2 - - + +
1401A ARG* 5.1 3.2 - - - +
1409A LEU* 5.1 0.2 - - - +
1551A ARG* 2.9 20.3 + - + +
1552A GLU* 3.3 12.8 - - - +
1553A CYS 3.1 0.2 - - - -
1554A ALA* 1.3 73.8 - - - +
1556A SER* 1.3 58.7 + - - +
1557A GLN 2.5 18.5 - - - +
1559A PHE 4.8 2.2 - - - -
1561A ASP* 3.1 38.2 + - - -
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Residues in contact with SER1556 (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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1306A VAL* 2.8 29.3 - - - +
1307A ALA 4.5 3.8 + - - -
1308A GLN* 3.4 6.2 + - - +
1370A THR* 4.2 8.1 - - - -
1523A PHE* 3.7 32.5 - - - -
1526A THR* 2.9 26.3 + - - +
1552A GLU 2.9 10.2 + - - -
1553A CYS* 2.4 27.3 + - - -
1555A ARG* 1.3 76.6 - - - +
1557A GLN* 1.3 60.5 + - - +
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Residues in contact with GLN1557 (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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1306A VAL* 4.5 4.9 - - - -
1308A GLN* 2.7 30.4 + - - +
1310A ARG* 3.7 15.4 - - - +
1396A PHE* 4.2 3.8 - - - -
1400A LEU* 4.7 0.2 - - - +
1526A THR* 4.4 5.4 - - + -
1553A CYS 3.1 12.7 + - - +
1554A ALA 2.9 12.0 - - - +
1555A ARG* 2.5 26.0 - - - +
1556A SER* 1.3 83.4 + - - +
1558A GLY* 1.3 61.6 + - - +
1559A PHE* 3.5 21.8 - - + -
1576A VAL* 3.1 34.1 + - + +
1577A GLY 4.3 0.8 + - - -
1579A ALA 3.5 21.8 + - - -
1581A PRO* 3.6 15.2 - - - +
1582A PRO* 4.8 0.9 - - + -
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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