Contacts of the helix formed by residues 1593 - 1606 (chain A) in PDB entry 4C6I
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 GLN1593 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1592A GLU* 1.3 72.6 - - + +
1594A GLN* 1.3 67.4 + - + +
1595A THR 3.0 1.4 + - - -
1596A VAL* 3.0 19.6 + - - +
1597A ALA 4.0 0.9 + - - -
1617A ARG* 3.4 45.4 + - - +
1619A GLU* 3.1 31.9 + - - +
1620A GLU* 2.8 25.0 + - - +
1623A LEU* 4.7 3.5 - - - +
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Residues in contact with GLN1594 (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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1592A GLU 3.2 0.4 + - - +
1593A GLN* 1.3 81.0 - - + +
1595A THR* 1.3 70.0 + - - +
1597A ALA* 3.0 13.4 + - + +
1598A ALA* 3.0 21.2 + - + +
1619A GLU* 4.0 6.9 + - - +
1623A LEU* 5.8 0.7 - - - -
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Residues in contact with THR1595 (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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1559A LEU* 3.6 33.2 + - + +
1560A ASN* 2.9 22.8 + - - +
1574A TRP* 3.9 15.0 - - + -
1591A ALA* 3.8 10.8 - - + -
1592A GLU 2.9 19.6 + - - -
1594A GLN* 1.3 84.8 - - - +
1596A VAL* 1.3 55.6 + - - +
1598A ALA* 4.1 6.1 - - - -
1599A VAL* 2.9 29.5 + - - +
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Residues in contact with VAL1596 (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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1591A ALA* 2.8 33.2 - - - +
1593A GLN 3.0 12.7 + - - +
1595A THR* 1.3 77.6 - - - +
1597A ALA* 1.3 62.8 - - - +
1599A VAL* 3.5 3.3 - - - +
1600A LEU* 3.0 31.2 - - + -
1612A ILE* 4.3 20.6 - - + -
1620A GLU* 4.1 23.6 - - + +
1623A LEU* 3.7 16.8 - - + -
1624A ILE* 4.0 24.9 - - + -
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Residues in contact with ALA1597 (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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1594A GLN* 3.0 14.5 + - + +
1596A VAL* 1.3 79.9 + - - +
1598A ALA* 1.3 62.9 + - - +
1600A LEU* 3.4 7.7 + - - +
1601A MET* 3.0 22.7 + - - +
1623A LEU* 3.3 28.9 - - + +
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Residues in contact with ALA1598 (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* 5.4 4.6 - - + +
1574A TRP* 3.6 24.2 - - + -
1594A GLN* 3.0 13.4 + - + +
1595A THR* 3.3 8.0 + - - +
1597A ALA* 1.3 77.7 - - - +
1599A VAL* 1.3 62.9 + - - +
1601A MET* 3.1 9.8 + - - +
1602A VAL* 3.1 24.3 + - - +
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Residues in contact with VAL1599 (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* 4.9 1.3 - - + -
1559A LEU* 3.7 26.2 - - + -
1574A TRP* 3.7 10.9 - - + -
1578A PHE* 4.0 27.4 - - + -
1589A ALA* 4.4 10.1 - - + -
1591A ALA* 4.0 9.6 - - + -
1595A THR 2.9 16.1 + - - +
1596A VAL 3.5 10.1 - - - -
1598A ALA* 1.3 73.2 - - - +
1600A LEU* 1.3 64.4 + - - +
1602A VAL* 3.2 2.2 + - + +
1603A ALA* 2.9 28.6 + - - +
1610A VAL* 4.5 5.1 - - + +
1612A ILE* 3.8 25.8 - - + -
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Residues in contact with LEU1600 (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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1596A VAL* 3.0 38.7 - - + -
1597A ALA* 3.6 9.2 - - - +
1598A ALA 3.3 0.2 - - - -
1599A VAL* 1.3 79.7 - - + +
1601A MET* 1.3 61.5 + - - +
1603A ALA* 3.3 3.0 + - - -
1604A GLN* 2.9 44.8 + - + +
1610A VAL* 3.8 13.5 - - + -
1612A ILE* 5.1 0.7 - - + -
1623A LEU* 4.6 10.5 - - + -
1624A ILE* 5.1 2.5 - - + -
1627A ALA* 4.1 23.1 - - + -
1632A LEU* 5.4 4.5 - - + -
1633A PRO 5.3 0.4 - - - +
1634A VAL* 3.6 38.6 - - + -
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Residues in contact with MET1601 (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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1597A ALA 3.0 13.1 + - - +
1598A ALA* 3.1 12.1 + - - +
1600A LEU* 1.3 75.4 - - - +
1602A VAL* 1.3 60.0 - - + +
1604A GLN* 3.1 20.1 - - + +
1605A LEU* 2.9 62.2 - - + -
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Residues in contact with VAL1602 (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* 3.6 31.4 - - + -
1574A TRP* 4.0 11.4 - - + -
1575A MET* 3.7 37.5 - - + +
1578A PHE* 3.7 31.4 - - + -
1598A ALA 3.1 12.6 + - - +
1599A VAL* 3.2 10.1 + - + +
1601A MET* 1.3 77.9 + - + +
1603A ALA* 1.3 60.1 + - - +
1605A LEU* 3.2 4.8 + - + +
1606A THR* 2.9 27.5 + - - +
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Residues in contact with ALA1603 (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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1578A PHE* 3.7 20.0 - - + -
1599A VAL 2.9 13.8 + - - +
1600A LEU 3.5 8.3 - - - +
1602A VAL* 1.3 75.5 - - - +
1604A GLN* 1.3 64.9 + - - +
1606A THR* 3.3 7.2 + - - -
1607A GLN 2.9 22.5 + - - -
1608A ARG 3.0 28.6 + - - +
1610A VAL* 4.0 17.0 - - + -
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Residues in contact with GLN1604 (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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1600A LEU* 2.9 45.9 + - + +
1601A MET* 3.1 21.1 - - + +
1603A ALA* 1.3 84.6 - - - +
1605A LEU* 1.3 66.4 + - - +
1607A GLN* 3.1 17.8 + - - +
1608A ARG 4.6 3.9 + - - +
1632A LEU* 3.5 41.3 - - + +
1633A PRO* 4.0 14.7 + - - +
2829A FMT 5.6 4.7 - - - -
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Residues in contact with LEU1605 (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* 3.9 32.7 - - + +
1601A MET* 2.9 46.2 - - + -
1602A VAL* 3.6 7.0 - - + +
1604A GLN* 1.3 76.8 - - - +
1606A THR* 1.3 59.7 + - - +
1607A GLN* 3.4 7.7 + - - +
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Residues in contact with THR1606 (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* 4.1 18.2 - - + -
1578A PHE* 3.4 43.6 - - + +
1579A GLU* 4.0 23.8 - - + +
1602A VAL 2.9 20.8 + - - +
1603A ALA 3.4 5.0 + - - -
1605A LEU* 1.3 79.0 - - - +
1607A GLN* 1.3 72.0 + - - +
1608A ARG* 3.5 7.7 + - - +
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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