Contacts of the helix formed by residues 1568 - 1578 (chain A) in PDB entry 4YOC
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 ASN1568 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1567A GLY* 1.3 77.3 - - - +
1569A ILE* 1.3 66.9 + - + +
1570A LEU* 3.1 32.7 + - - +
1571A ASP* 2.5 37.7 + - - -
1572A LYS* 3.1 19.5 + - - +
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Residues in contact with ILE1569 (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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1381A ALA 5.2 0.4 - - - +
1413A ILE* 3.8 25.8 - - + +
1414A CYS* 3.4 44.4 - - - +
1415A LYS* 3.6 12.8 - - + +
1550A VAL* 3.8 9.8 - - + +
1568A ASN* 1.3 78.7 - - + +
1570A LEU* 1.3 71.9 + - + +
1572A LYS* 3.3 4.7 + - - +
1573A HIS* 2.9 41.0 + - + +
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Residues in contact with LEU1570 (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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1415A LYS* 4.1 24.2 - - + -
1528A THR 4.2 1.4 - - - +
1529A ASN* 3.4 35.4 - - + +
1568A ASN* 3.1 11.6 + - - +
1569A ILE* 1.3 84.7 - - + +
1571A ASP* 1.3 61.7 + - - +
1573A HIS* 3.6 7.1 - - + +
1574A ARG* 2.9 30.5 + - - +
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Residues in contact with ASP1571 (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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1170A TRP* 3.2 33.1 + - + -
1172A PRO* 4.1 11.6 - - + +
1566A PHE 3.5 13.9 - - - +
1567A GLY* 3.7 4.9 - - - -
1568A ASN* 2.5 44.5 + - - +
1570A LEU* 1.3 79.1 - - - +
1572A LYS* 1.3 57.3 + - - +
1574A ARG 3.2 1.4 + - - -
1575A GLN* 2.9 36.3 + - - +
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Residues in contact with LYS1572 (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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1384A LEU* 3.6 21.8 - - - +
1411A ASP* 2.3 48.7 + - + +
1413A ILE* 4.5 10.2 - - + +
1550A VAL* 3.8 14.1 - - + -
1565A LEU* 3.7 14.8 - - + +
1566A PHE* 3.7 22.4 - - - +
1567A GLY 3.4 20.7 + - - +
1568A ASN 3.1 10.8 + - - +
1569A ILE 3.7 5.8 - - - +
1571A ASP* 1.3 72.6 - - - +
1573A HIS* 1.3 67.2 + - - +
1575A GLN* 3.2 9.6 + - - +
1576A VAL* 2.9 30.8 + - - +
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Residues in contact with HIS1573 (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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1413A ILE 4.7 1.0 + - - -
1415A LYS* 4.3 16.7 + - + +
1527A VAL 3.9 3.8 + - - +
1528A THR* 3.1 20.8 - - - +
1529A ASN* 4.8 0.9 - - - -
1530A PRO* 3.5 36.1 - - + +
1548A VAL 3.8 17.8 + - - -
1550A VAL* 3.4 30.4 + - + +
1553A CYS* 3.8 20.6 - - - +
1569A ILE* 2.9 36.7 + - + +
1570A LEU* 3.6 8.1 - - + +
1572A LYS* 1.3 77.6 - - - +
1574A ARG* 1.3 55.6 + - - +
1576A VAL* 3.4 5.9 + - - +
1577A GLY* 2.9 24.6 + - - -
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Residues in contact with ARG1574 (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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1170A TRP* 3.5 61.3 - - + +
1528A THR* 3.2 22.6 + - + +
1570A LEU 2.9 19.0 + - - +
1571A ASP 3.5 4.7 - - - +
1573A HIS* 1.3 74.9 - - - +
1575A GLN* 1.3 64.7 + - - +
1577A GLY* 3.1 0.9 + - - -
1578A ASN* 3.0 45.1 + - - +
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Residues in contact with GLN1575 (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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1147A GLY* 5.9 0.7 - - - -
1148A CYS* 3.6 23.0 + - + +
1170A TRP* 3.7 15.3 - - + -
1172A PRO* 3.5 24.7 - - - +
1173A ALA* 4.3 9.2 - - + -
1176A ALA* 3.7 13.2 - - - +
1565A LEU* 3.4 16.7 - - + +
1566A PHE 2.5 49.2 + - - +
1571A ASP 2.9 16.3 + - - +
1572A LYS* 3.2 7.4 + - - +
1574A ARG* 1.3 75.6 - - - +
1576A VAL* 1.3 63.9 - - - +
1578A ASN* 3.7 3.5 + - - +
1579A ALA* 3.5 19.6 + - - +
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Residues in contact with VAL1576 (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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1148A CYS* 5.1 0.4 - - - -
1526A THR* 4.4 2.5 - - + -
1550A VAL* 4.3 8.3 - - + +
1553A CYS* 3.7 18.2 - - + +
1554A ALA* 3.6 38.6 - - + +
1557A GLN* 2.9 34.7 + - + +
1559A PHE* 4.5 10.1 - - + -
1565A LEU* 3.7 28.7 - - + -
1572A LYS 2.9 20.6 + - - +
1573A HIS* 3.7 5.6 - - - +
1575A GLN* 1.3 76.1 - - - +
1577A GLY* 1.3 58.3 + - - +
1579A ALA* 3.4 7.1 + - - +
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Residues in contact with GLY1577 (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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1310A ARG* 2.6 33.4 + - - -
1526A THR* 3.8 10.4 - - - +
1527A VAL 3.7 27.4 - - - -
1528A THR* 4.2 4.3 - - - -
1573A HIS 2.9 11.4 + - - -
1574A ARG 3.1 3.5 + - - -
1576A VAL* 1.3 79.8 - - - +
1578A ASN* 1.3 55.3 + - - +
1579A ALA 3.2 0.2 - - - -
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Residues in contact with ASN1578 (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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1147A GLY* 6.1 4.0 - - - -
1170A TRP* 5.6 2.0 - - - -
1266A GLU* 5.0 6.1 - - - +
1310A ARG* 4.3 3.4 + - - +
1312A ARG* 5.6 2.6 + - - -
1528A THR* 3.3 18.4 - - - +
1574A ARG* 3.0 43.6 + - - +
1575A GLN* 4.3 3.3 - - - +
1576A VAL 3.4 0.2 - - - -
1577A GLY* 1.3 75.5 - - - +
1579A ALA* 1.3 60.2 - - - +
1580A VAL* 3.9 1.6 + - - +
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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