Contacts of the helix formed by residues 1570 - 1581 (chain A) in PDB entry 4C6J
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 SER1570 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1568A LEU 3.5 1.4 - - - -
1569A ASP* 1.3 82.6 - - - +
1571A VAL* 1.3 59.3 + - - +
1572A VAL* 3.0 27.8 + - - +
1573A GLN* 2.9 33.8 + - - +
1574A TRP* 3.2 17.2 - - - +
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Residues in contact with VAL1571 (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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1570A SER* 1.3 72.4 + - - +
1572A VAL* 1.3 64.2 + - + +
1574A TRP* 3.0 38.1 + - + +
1575A MET* 2.9 23.9 + - + +
1598A ALA* 5.4 5.4 - - + +
1602A VAL* 3.6 27.6 - - + -
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Residues in contact with VAL1572 (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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1570A SER* 3.0 16.7 + - - +
1571A VAL* 1.3 79.6 - - + +
1573A GLN* 1.3 57.6 + - + +
1575A MET* 3.2 11.6 + - + +
1576A GLU* 2.9 45.4 + - + +
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Residues in contact with GLN1573 (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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1538A SER 5.6 0.2 - - - +
1539A SER* 3.4 29.9 + - - +
1568A LEU* 3.2 17.7 - - + +
1569A ASP* 2.4 50.9 + - - +
1570A SER* 2.9 20.1 + - - +
1572A VAL* 1.3 76.8 - - + +
1574A TRP* 1.3 64.2 + - - +
1576A GLU* 3.4 17.6 + - - +
1577A HIS* 3.1 31.3 + - + -
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Residues in contact with TRP1574 (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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1557A LEU* 4.5 12.1 - - + -
1559A LEU* 3.5 41.3 - - + +
1567A ARG* 6.1 0.4 - - - -
1568A LEU* 3.6 31.6 + - + +
1570A SER 3.2 20.1 + - - +
1571A VAL* 3.0 31.4 + - + +
1573A GLN* 1.3 76.7 - - - +
1575A MET* 1.3 63.8 + - - +
1577A HIS* 3.2 4.6 + - - +
1578A PHE* 3.0 27.7 + - + -
1595A THR* 3.9 16.8 - - + -
1598A ALA* 3.6 32.8 - - + -
1599A VAL* 3.7 17.7 - - + -
1602A VAL* 4.0 24.9 - - + -
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Residues in contact with MET1575 (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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1571A VAL* 2.9 20.3 + - + +
1572A VAL* 3.4 16.2 - - + +
1574A TRP* 1.3 78.2 - - - +
1576A GLU* 1.3 57.7 + - + +
1578A PHE* 3.2 3.0 + - - +
1579A GLU* 2.9 55.2 + - - +
1602A VAL* 3.6 29.1 - - + +
1605A LEU* 3.9 38.6 - - + +
1606A THR* 4.1 11.0 - - + -
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Residues in contact with GLU1576 (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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1542A ALA* 4.1 16.5 - - + +
1572A VAL* 2.9 35.8 + - + +
1573A GLN* 3.6 20.8 - - - +
1574A TRP 3.2 0.2 - - - -
1575A MET* 1.3 77.3 - - + +
1577A HIS* 1.3 59.7 + - - +
1579A GLU* 3.4 13.7 + - - +
1580A THR* 2.8 34.9 + - + +
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Residues in contact with HIS1577 (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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1537A ALA* 3.5 25.2 - - + +
1538A SER 2.9 24.5 + - - -
1541A ASN* 2.9 24.9 - - - -
1542A ALA* 3.4 25.5 - - + +
1545A LEU* 5.0 5.2 - - + +
1555A LEU* 3.9 21.1 - - + +
1557A LEU* 4.8 8.7 - - + -
1568A LEU* 4.4 9.6 - - + -
1573A GLN* 3.1 24.1 + - + +
1574A TRP* 3.2 8.3 + - - +
1576A GLU* 1.3 76.6 - - - +
1578A PHE* 1.3 58.1 + - + +
1580A THR* 3.7 3.9 + - - -
1581A TRP* 2.9 37.6 + - - +
1587A ILE* 5.0 1.3 - - - -
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Residues in contact with PHE1578 (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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1557A LEU* 3.8 25.4 - - + -
1574A TRP* 3.0 23.8 + - + +
1575A MET 3.7 6.3 - - - +
1577A HIS* 1.3 76.9 - - - +
1579A GLU* 1.3 59.9 + - - +
1580A THR 3.7 0.2 + - - -
1581A TRP 4.2 7.8 - - - +
1583A SER* 6.0 0.3 - - - -
1587A ILE* 3.9 23.4 - - + +
1599A VAL* 4.0 16.8 - - + -
1602A VAL* 3.7 12.1 - - + -
1603A ALA* 3.7 24.5 - - + -
1606A THR* 3.4 33.6 - - + +
1608A ARG* 3.6 26.7 - - + -
1609A SER 3.9 15.0 - - - -
1610A VAL* 3.9 23.3 - - + -
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Residues in contact with GLU1579 (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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1575A MET* 2.9 44.4 + - - +
1576A GLU* 3.7 18.3 + - - +
1578A PHE* 1.3 78.1 - - - +
1580A THR* 1.3 62.8 + - + +
1581A TRP 4.5 2.2 - - - +
1606A THR* 3.9 15.2 - - + +
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Residues in contact with THR1580 (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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1542A ALA* 3.8 4.0 - - + +
1543A GLY* 3.3 39.3 + - - +
1546A GLY* 5.9 1.6 - - - -
1576A GLU* 2.8 24.6 + - + +
1577A HIS* 3.5 7.4 + - - -
1579A GLU* 1.3 82.8 - - + +
1581A TRP* 1.3 69.3 + - - +
1582A PRO* 3.4 6.1 - - - +
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Residues in contact with TRP1581 (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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1535A LEU* 3.9 20.2 - - + -
1545A LEU* 4.1 20.9 - - + -
1549A ALA* 3.4 38.1 - - + -
1552A ALA* 4.6 0.2 - - + -
1554A GLY* 3.6 14.6 - - - -
1555A LEU* 3.5 46.9 - - + -
1577A HIS* 2.9 19.8 + - - +
1578A PHE 4.2 9.2 - - - +
1579A GLU 4.5 2.3 - - - +
1580A THR* 1.3 79.4 + - - +
1582A PRO* 1.3 93.9 - - + +
1583A SER* 3.2 4.0 + - - -
1585A LEU* 3.3 24.9 + - + +
1586A PRO 3.0 15.8 + - - -
1587A ILE* 3.4 24.9 - - + -
1608A ARG* 3.7 3.1 + - - -
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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