Contacts of the helix formed by residues 1595 - 1611 (chain E) in PDB entry 3SUA
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 ARG1595 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1591E VAL* 3.8 11.0 - - + -
1592E PRO* 3.2 8.4 + - + -
1594E SER* 1.4 82.2 + - - +
1596E ARG* 1.3 62.1 + - - +
1597E PRO 3.6 0.9 - - - -
1598E THR* 3.3 43.6 + - + +
1599E VAL* 3.3 23.5 - - + +
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Residues in contact with ARG1596 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1589E LEU* 5.7 5.4 - - + -
1591E VAL* 3.8 20.1 - - + +
1592E PRO 2.9 18.5 + - - +
1593E GLU* 3.4 30.5 + - - +
1595E ARG* 1.3 76.5 - - - +
1597E PRO* 1.4 81.6 - - - +
1599E VAL* 3.5 1.9 + - - +
1600E GLU* 2.8 70.9 + - + +
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Residues in contact with PRO1597 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1593E GLU 3.4 11.2 - - - +
1594E SER 3.5 10.1 - - - +
1596E ARG* 1.4 112.9 - - + +
1598E THR* 1.3 60.0 + - - +
1600E GLU* 3.4 11.6 + - + +
1601E GLN* 3.4 23.7 + - - +
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Residues in contact with THR1598 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1594E SER 5.0 1.6 - - - +
1595E ARG* 3.3 56.2 + - + +
1597E PRO* 1.3 78.0 - - - +
1599E VAL* 1.3 60.0 + - + +
1601E GLN* 4.0 15.1 + - - +
1602E GLY* 3.7 11.8 + - - -
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Residues in contact with VAL1599 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1589E LEU* 6.4 0.7 - - + -
1591E VAL* 4.3 26.2 - - + -
1595E ARG* 3.3 30.1 + - + +
1596E ARG 4.1 2.7 - - - +
1597E PRO 3.3 0.4 - - - -
1598E THR* 1.3 79.3 - - + +
1600E GLU* 1.4 56.1 + - - +
1601E GLN 3.1 1.6 - - - -
1602E GLY* 2.9 23.6 + - - -
1603E LEU* 3.1 29.6 + - + +
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Residues in contact with GLU1600 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1589E LEU* 4.5 21.6 - - + +
1596E ARG* 2.8 67.0 + - + +
1597E PRO* 3.4 9.9 - - + +
1599E VAL* 1.4 74.1 - - - +
1601E GLN* 1.3 59.9 + - - +
1603E LEU* 3.7 15.6 - - + +
1604E GLY* 3.7 11.8 + - - -
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Residues in contact with GLN1601 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1597E PRO 3.4 14.6 + - - +
1598E THR* 4.0 13.7 + - - +
1599E VAL 3.0 0.6 + - - -
1600E GLU* 1.3 76.5 - - - +
1602E GLY* 1.3 75.6 + - - +
1604E GLY* 3.0 13.9 + - - -
1605E GLN* 3.4 17.0 + - + +
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Residues in contact with GLY1602 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1598E THR 3.7 3.7 + - - -
1599E VAL* 2.9 12.7 + - - -
1601E GLN* 1.3 83.9 - - - +
1603E LEU* 1.3 57.2 + - - +
1605E GLN* 3.0 25.8 + - - +
1606E LEU* 3.1 10.2 + - - +
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Residues in contact with LEU1603 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1589E LEU* 4.4 23.1 - - + -
1599E VAL* 3.1 33.7 + - + +
1600E GLU* 3.7 22.2 - - + +
1601E GLN 3.3 0.2 - - - -
1602E GLY* 1.3 73.0 - - - +
1604E GLY* 1.3 61.2 + - - +
1606E LEU* 3.0 34.6 + - + +
1607E SER* 3.1 12.3 + - - -
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Residues in contact with GLY1604 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1600E GLU 3.7 5.4 + - - -
1601E GLN 3.0 11.0 + - - -
1603E LEU* 1.3 78.2 - - - +
1605E GLN* 1.3 57.4 + - - +
1607E SER* 3.0 22.9 + - - -
1608E ASN* 3.0 22.3 - - - +
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Residues in contact with GLN1605 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1601E GLN* 3.4 15.4 + - + +
1602E GLY* 3.0 13.0 + - - +
1604E GLY* 1.3 71.9 - - - +
1606E LEU* 1.4 59.2 + - - +
1608E ASN* 3.2 30.5 + - - +
1609E LEU* 3.0 27.6 + - - +
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Residues in contact with LEU1606 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1602E GLY 3.1 7.7 + - - +
1603E LEU* 3.0 34.1 + - + +
1605E GLN* 1.4 75.7 - - - +
1607E SER* 1.3 55.0 + - - +
1609E LEU* 3.2 26.4 - - + +
1610E LEU* 2.9 54.2 + - + +
1615E PHE* 5.2 2.9 - - + -
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Residues in contact with SER1607 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1603E LEU 3.1 8.8 + - - -
1604E GLY* 3.0 15.2 + - - -
1606E LEU* 1.3 76.5 - - - +
1608E ASN* 1.4 54.7 + - - +
1610E LEU* 3.2 15.8 + - - +
1611E ASN* 2.8 43.4 + - - +
1644E ALA 5.7 1.0 + - - -
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Residues in contact with ASN1608 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1604E GLY 3.0 15.4 + - - +
1605E GLN* 3.2 41.7 + - - +
1607E SER* 1.4 74.8 + - - +
1609E LEU* 1.3 63.5 + - - +
1611E ASN* 3.5 22.6 + - - +
1612E SER* 4.0 6.2 + - - -
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Residues in contact with LEU1609 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1605E GLN 3.0 13.6 + - - +
1606E LEU* 3.2 29.4 - - + +
1608E ASN* 1.3 76.3 - - - +
1610E LEU* 1.4 59.8 + - - +
1612E SER* 3.2 20.3 + - - -
1615E PHE* 3.2 64.6 - - + +
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Residues in contact with LEU1610 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1606E LEU* 2.9 45.8 + - + +
1607E SER* 3.2 13.0 + - - +
1609E LEU* 1.4 72.5 - - - +
1611E ASN* 1.3 48.7 + - - +
1612E SER 3.0 8.6 + - - +
1615E PHE* 3.7 14.1 - - + -
1616E LEU* 3.4 40.8 - - + +
1619E PHE* 4.9 6.5 - - + -
1641E LEU* 4.1 12.6 - - + -
1644E ALA* 4.9 17.3 - - + -
1645E LEU* 4.8 9.4 - - + -
1651E TYR* 2.5 27.3 + - - -
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Residues in contact with ASN1611 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1607E SER* 2.8 33.5 + - - +
1608E ASN* 3.5 16.7 + - - +
1609E LEU 3.3 0.8 - - - -
1610E LEU* 1.3 71.8 - - - +
1612E SER* 1.4 54.4 + - - +
1613E LYS 3.6 0.3 + - - -
1645E LEU* 3.7 17.7 - - - +
1648E LYS* 3.5 43.0 + - + +
1651E TYR* 3.2 26.4 - - - -
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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