Contacts of the helix formed by residues 1567 - 1577 (chain D) 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 ASP1567 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1565D PHE 4.2 5.6 - - - +
1566D LEU* 1.3 75.1 - - - +
1568D TYR* 1.3 67.5 + - - +
1569D LYS* 3.2 6.5 - - + +
1570D VAL* 3.1 14.8 + - + +
1571D TYR* 3.0 19.1 + - - +
1696D TYR* 3.5 4.7 - - - -
1700D ARG* 3.9 20.2 + - - +
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Residues in contact with TYR1568 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1567D ASP* 1.3 71.8 - - - +
1569D LYS* 1.3 62.8 + - - +
1571D TYR* 3.8 24.0 - + - -
1572D ALA* 2.9 40.8 + - + +
1576D PHE* 4.7 0.6 - + - -
1646D HIS* 2.8 28.5 + + - -
1693D ILE* 3.1 35.7 - - + +
1696D TYR* 3.3 36.0 + + + -
1700D ARG* 4.9 0.8 - - - +
2074D LEU* 4.7 7.0 - - + -
2077D ASN 4.5 7.0 - - - +
2078D TYR* 3.7 43.1 - + + -
2079D SER* 5.0 3.4 - - - +
2082D LEU* 5.3 1.3 - - + -
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Residues in contact with LYS1569 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1567D ASP* 3.2 5.5 + - + +
1568D TYR* 1.3 77.3 - - - +
1570D VAL* 1.3 64.5 + - + +
1573D GLU* 3.1 50.9 + - - +
1586D HIS* 3.8 16.5 - - - -
2079D SER* 6.0 6.6 - - - -
2080D GLY* 5.3 9.9 - - - +
2081D ASP 3.2 30.4 + - - +
2082D LEU* 3.8 21.4 - - + +
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Residues in contact with VAL1570 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1566D LEU* 3.1 27.4 - - + -
1567D ASP* 3.1 17.6 + - + +
1569D LYS* 1.3 74.4 - - + +
1571D TYR* 1.3 66.4 + - - +
1573D GLU* 3.2 13.6 + - - +
1574D ARG* 2.9 59.7 + - + +
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Residues in contact with TYR1571 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1566D LEU* 4.1 6.6 - - + +
1567D ASP 3.0 16.2 + - - +
1568D TYR* 3.7 14.6 - + - +
1570D VAL* 1.3 74.9 - - - +
1572D ALA* 1.4 60.7 + - - +
1574D ARG* 3.5 2.9 + - - +
1575D ILE* 3.0 54.2 + - + +
1692D SER* 3.0 43.9 + - - -
1696D TYR* 3.5 44.4 - + + -
1699D VAL* 4.4 6.9 - - + +
1985D PHE* 3.4 18.0 - - - -
1989D ILE* 4.7 4.0 - - + -
1995D PHE 3.2 29.4 - - - +
1996D VAL* 4.6 16.6 - - + -
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Residues in contact with ALA1572 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1568D TYR* 2.9 36.9 + - + +
1569D LYS 3.9 2.2 - - - +
1571D TYR* 1.4 74.9 - - - +
1573D GLU* 1.3 57.5 + - - +
1575D ILE* 3.0 5.3 + - - -
1576D PHE* 2.8 67.6 + - + -
1692D SER* 6.2 0.2 - - - -
2082D LEU* 4.3 10.8 - - + -
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Residues in contact with GLU1573 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1569D LYS* 3.1 41.3 + - - +
1570D VAL* 3.5 13.1 - - - +
1572D ALA* 1.3 76.4 - - - +
1574D ARG* 1.4 58.7 + - + +
1576D PHE* 4.4 2.0 - - - -
1577D PHE* 2.9 45.1 + - + +
1581D ARG 5.2 2.0 - - - +
1582D GLU* 5.3 1.7 - - - +
1583D SER* 3.7 29.1 + - - +
1586D HIS* 2.7 31.6 + - - +
2082D LEU* 4.3 12.7 - - + +
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Residues in contact with ARG1574 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1566D LEU* 3.5 16.9 - - - +
1570D VAL* 2.9 41.6 + - + +
1571D TYR* 3.7 5.2 - - - +
1573D GLU* 1.4 76.6 - - + +
1575D ILE* 1.3 59.5 + - - +
1577D PHE 4.7 0.9 - - - -
1578D PRO* 3.5 18.3 - - - +
1581D ARG 4.2 19.9 + - - +
1794D LEU* 5.3 5.1 - - - +
1795D THR* 5.2 1.8 + - - -
1994D GLN* 2.7 42.3 + - - +
1995D PHE* 3.2 30.2 - - + -
1997D PHE 3.6 9.3 + - - -
1998D ASP* 3.4 22.6 + - - +
1999D VAL 4.9 3.6 + - - +
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Residues in contact with ILE1575 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1571D TYR* 3.0 59.8 + - + +
1572D ALA* 3.0 7.4 + - - +
1574D ARG* 1.3 76.5 - - - +
1576D PHE* 1.4 66.5 + - + +
1578D PRO* 3.6 9.0 - - - +
1685D LYS* 3.3 17.5 + - - +
1688D THR* 4.8 6.7 - - + +
1689D ASN* 4.4 10.3 - - - +
1692D SER* 3.4 26.7 - - - +
1989D ILE* 4.2 8.5 - - + -
1995D PHE* 3.8 34.8 - - + -
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Residues in contact with PHE1576 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1568D TYR* 5.5 0.2 - + - -
1572D ALA* 2.8 49.7 + - + +
1573D GLU* 4.4 1.3 - - - -
1575D ILE* 1.4 78.0 - - + +
1577D PHE* 1.4 72.3 + + + +
1578D PRO* 3.5 7.5 - - - +
1635D ALA* 5.0 2.1 - - - +
1636D TYR* 5.9 0.2 - - - -
1639D SER* 2.6 33.4 + - - +
1642D THR* 3.6 27.8 - - + -
1643D VAL* 4.0 20.2 - - + -
1646D HIS* 4.5 3.4 - + - -
1685D LYS* 4.1 4.7 - - - +
1689D ASN* 3.1 44.4 - - + -
1692D SER* 5.0 2.9 - - - -
1693D ILE* 3.9 16.6 - - + -
2082D LEU* 4.3 15.9 - - + -
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Residues in contact with PHE1577 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1573D GLU* 2.9 25.9 + - + +
1576D PHE* 1.4 90.5 - + + +
1578D PRO* 1.3 66.5 - - - +
1579D GLY 3.8 1.1 + - - -
1580D HIS* 4.2 7.8 + - - +
1581D ARG 3.9 17.3 + - - +
1582D GLU 4.5 1.7 - - - +
1583D SER* 3.8 16.2 - - - -
1584D PRO* 3.6 22.7 - - + -
1585D LEU* 3.7 26.0 - - + -
1636D TYR* 3.5 37.9 - + - -
1639D SER* 3.6 35.2 - - - -
1640D LEU* 4.0 3.1 - - + -
1643D VAL* 3.7 20.4 - - + -
2082D LEU 5.9 0.2 - - - -
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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