Contacts of the helix formed by residues 1543 - 1551 (chain A) in PDB entry 2YIN
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 PHE1543 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1502A MET* 3.9 28.0 - - + -
1534A ILE 6.1 0.9 - - - -
1542A GLY* 1.3 69.2 - - - -
1544A ALA* 1.3 69.0 + - + +
1545A LYS 3.0 2.5 - - - -
1546A TYR* 2.9 21.7 + - + +
1547A GLU* 3.1 37.4 + - - +
1573A ILE* 3.5 41.5 - - + +
1576A GLN* 4.9 17.0 - - - -
1577A ILE* 4.8 4.9 - - + -
1609A LEU* 4.2 24.2 - - + -
1613A VAL* 3.5 21.1 - - + -
36C VAL* 3.4 6.0 - - + +
37C PHE* 4.4 5.9 - + + -
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Residues in contact with ALA1544 (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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1541A GLY 5.2 6.1 - - - +
1542A GLY* 3.0 3.3 - - - -
1543A PHE* 1.3 83.6 - - + +
1545A LYS* 1.3 62.8 + - + +
1547A GLU* 3.1 23.0 + - - +
1548A LYS* 3.0 22.8 + - - +
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Residues in contact with LYS1545 (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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1456A GLU* 3.0 30.2 - - - +
1457A ASN* 3.1 26.6 + - - +
1458A GLU* 5.9 0.2 - - - -
1459A PHE* 3.4 38.1 - - + -
1541A GLY* 3.1 34.8 - - - +
1542A GLY 3.4 6.7 + - - +
1543A PHE 3.0 0.8 - - - -
1544A ALA* 1.3 78.7 - - + +
1546A TYR* 1.3 57.5 + - - +
1548A LYS* 3.4 4.5 + - - -
1549A ALA* 2.8 25.9 + - - +
36C VAL* 4.4 2.2 - - + -
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Residues in contact with TYR1546 (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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1459A PHE* 4.1 29.9 - + + -
1494A PRO 5.2 0.7 - - - -
1497A ASN 5.1 0.2 - - - -
1498A ALA* 3.4 33.9 - - + -
1501A THR* 3.6 26.2 + - - +
1502A MET* 3.0 38.6 - - + -
1543A PHE* 2.9 15.9 + - + +
1545A LYS* 1.3 78.6 - - - +
1547A GLU* 1.3 58.7 + - - +
1549A ALA* 3.2 0.4 + - + -
1550A PHE* 3.0 53.7 + + + +
1551A PHE* 4.2 3.1 + - - -
1569A LEU* 4.3 15.3 - - + -
1573A ILE* 5.7 1.8 - - + -
35C THR* 5.4 0.3 - - - -
36C VAL* 3.7 27.0 + - + +
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Residues in contact with GLU1547 (chain A).
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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1543A PHE* 3.1 33.3 + - + +
1544A ALA* 3.1 25.3 + - - +
1546A TYR* 1.3 78.3 - - - +
1548A LYS* 1.3 59.2 + - - +
1551A PHE* 3.0 51.0 + - + +
1552A THR* 4.2 0.5 + - - +
1573A ILE* 4.7 1.1 - - + -
1613A VAL* 5.5 0.5 - - - +
1616A GLU* 5.6 0.3 - - - +
1617A TYR* 3.3 32.1 + - - +
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Residues in contact with LYS1548 (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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1457A ASN* 4.6 6.1 - - + +
1544A ALA 3.0 11.9 + - - +
1545A LYS* 3.7 7.9 - - - +
1547A GLU* 1.3 79.4 - - - +
1549A ALA* 1.3 60.1 + - - +
1552A THR* 3.5 20.4 - - - +
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Residues in contact with ALA1549 (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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1457A ASN* 3.8 6.7 - - - +
1460A ALA* 3.3 38.5 - - + +
1545A LYS 2.8 18.2 + - - +
1546A TYR* 3.9 3.6 - - + +
1547A GLU 3.2 0.4 - - - -
1548A LYS* 1.3 79.5 - - - +
1550A PHE* 1.3 76.4 + - + +
1552A THR* 4.7 4.0 - - - +
1555A TYR* 4.1 11.8 - - - +
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Residues in contact with PHE1550 (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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1459A PHE 4.5 5.2 - - - -
1460A ALA* 4.4 5.2 - - - -
1494A PRO* 3.6 42.2 - - + -
1495A LEU* 3.8 18.2 - - + -
1498A ALA* 3.9 9.0 - - + -
1546A TYR* 3.0 51.7 + + - +
1549A ALA* 1.3 93.7 - - + +
1551A PHE* 1.3 69.3 + - + +
1552A THR 3.4 4.8 - - - +
1555A TYR* 2.9 62.3 - + + +
1556A VAL* 4.4 3.6 - - - +
1566A LEU* 4.0 13.4 - - + +
1569A LEU* 4.1 6.1 - - + -
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Residues in contact with PHE1551 (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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1546A TYR 5.0 1.1 - - - -
1547A GLU* 3.0 41.3 + - + +
1550A PHE* 1.3 84.4 - - + +
1552A THR* 1.3 67.2 + - - +
1553A GLU 3.7 0.5 + - - -
1556A VAL* 4.6 5.5 - - - +
1566A LEU* 4.0 31.0 - - + -
1569A LEU* 4.3 23.6 - - + -
1570A LYS* 4.3 20.2 - - + -
1573A ILE* 4.3 6.3 - - + -
1617A TYR* 3.3 32.5 - + - -
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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