Contacts of the helix formed by residues 160 - 179 (chain 1) in PDB entry 3SDI
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 THR 160 (chain 1).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71 TYR* 4.2 2.2 - - - -
81 ASP* 4.0 13.0 - - - +
1581 LYS 4.5 7.9 - - - +
1591 THR* 1.3 76.2 - - - +
1611 VAL* 1.3 65.0 + - - +
1621 GLN* 3.3 20.5 + - - +
1631 VAL* 3.1 27.6 + - + +
1641 ALA* 2.9 23.7 + - - +
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Residues in contact with VAL 161 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71 TYR* 3.6 45.5 - - + +
81 ASP* 4.9 2.5 - - - +
91 ASN* 5.5 2.7 - - + +
121 ILE* 4.1 1.9 - - + +
1601 THR* 1.3 72.5 - - - +
1621 GLN* 1.3 72.7 + - - +
1641 ALA* 4.5 1.6 - - - -
1651 GLU* 2.8 35.1 + - - +
1901 ILE* 4.2 26.0 - - + -
1921 ASP* 4.3 7.2 - - - +
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Residues in contact with GLN 162 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1601 THR* 3.0 23.2 + - - +
1611 VAL* 1.3 91.6 - - - +
1631 VAL* 1.3 66.4 - - + +
1651 GLU* 4.0 3.6 - - - +
1661 GLU* 3.1 24.8 + - - +
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Residues in contact with VAL 163 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1491 VAL* 3.7 31.2 - - + -
1591 THR* 4.0 6.1 - - + -
1601 THR* 3.1 23.5 + - + +
1621 GLN* 1.3 79.6 - - + +
1641 ALA* 1.3 57.2 + - - +
1661 GLU* 3.2 16.0 + - - +
1671 ALA* 3.0 27.4 + - - +
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Residues in contact with ALA 164 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51 MET* 3.8 22.2 - - + +
71 TYR* 3.8 21.8 - - + -
121 ILE* 3.7 19.1 - - + -
1591 THR* 4.0 5.8 - - + -
1601 THR 2.9 16.4 + - - +
1611 VAL 4.0 0.9 - - - +
1631 VAL* 1.3 75.7 - - - +
1651 GLU* 1.3 64.8 + - - +
1671 ALA* 3.3 3.9 + - - +
1681 ILE* 3.1 26.9 + - - +
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Residues in contact with GLU 165 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121 ILE* 3.5 12.9 - - + +
1611 VAL* 2.8 24.6 + - - +
1621 GLN* 4.1 4.3 - - - +
1641 ALA* 1.3 73.2 - - - +
1661 GLU* 1.3 57.0 + - - +
1681 ILE* 3.4 3.5 + - - +
1691 VAL* 3.0 44.1 + - + +
1881 LEU* 4.2 29.5 - - + +
1901 ILE* 3.9 10.7 - - + +
2001 LYS* 3.0 33.1 + - - +
2031 LEU* 5.5 2.6 - - - +
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Residues in contact with GLU 166 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1621 GLN 3.1 18.5 + - - +
1631 VAL* 3.4 14.8 - - - +
1641 ALA 3.2 0.2 - - - -
1651 GLU* 1.3 77.3 - - - +
1671 ALA* 1.3 57.8 + - - +
1691 VAL* 3.4 6.4 + - - +
1701 ASN* 2.9 32.0 + - + +
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Residues in contact with ALA 167 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51 MET* 4.3 4.5 - - - -
1451 LEU* 5.5 3.3 - - + +
1461 LEU* 3.6 21.1 - - + +
1491 VAL* 3.9 24.2 - - + -
1631 VAL 3.0 12.5 + - - +
1641 ALA* 3.6 8.3 - - - +
1661 GLU* 1.3 75.4 - - - +
1681 ILE* 1.3 58.5 + - - +
1701 ASN* 3.5 6.1 + - - +
1711 ALA* 3.0 29.6 + - - +
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Residues in contact with ILE 168 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31 ILE* 3.8 16.9 - - + +
41 SER* 4.2 11.4 - - - -
51 MET* 4.0 19.3 - - + -
121 ILE* 4.3 14.6 - - + +
141 ALA* 3.8 19.3 - - + -
1461 LEU* 3.7 30.5 - - + -
1641 ALA 3.1 20.5 + - - +
1651 GLU* 3.8 5.4 - - - +
1671 ALA* 1.3 73.6 - - - +
1691 VAL* 1.3 66.4 + - - +
1711 ALA* 3.4 2.8 + - - +
1721 MET* 3.0 24.6 + - + +
1881 LEU* 3.7 25.6 - - + -
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Residues in contact with VAL 169 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1651 GLU* 3.0 37.7 + - + +
1661 GLU* 3.8 5.8 - - - +
1681 ILE* 1.3 77.2 - - - +
1701 ASN* 1.3 61.2 + - - +
1721 MET* 3.3 9.3 + - - +
1731 ARG* 3.2 27.7 + - - +
1861 PHE* 4.6 17.0 - - + -
1881 LEU* 4.2 12.6 - - + -
2031 LEU* 5.8 2.5 - - + -
2041 GLN 5.8 2.9 - - - +
2051 VAL* 5.3 3.6 - - - +
2061 GLU 6.1 2.5 - - - +
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Residues in contact with ASN 170 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1451 LEU* 4.0 9.9 - - - +
1661 GLU* 2.9 18.8 + - + +
1671 ALA* 3.7 7.2 - - - +
1681 ILE 3.3 0.2 - - - -
1691 VAL* 1.3 74.7 - - - +
1711 ALA* 1.3 61.8 + - - +
1731 ARG* 2.9 58.6 + - - +
1741 VAL* 3.1 15.2 + - - +
139H GLU 5.6 0.4 + - - -
140H SER* 3.3 33.9 + - - +
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Residues in contact with ALA 171 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31 ILE* 3.8 16.6 - - + -
1421 ALA* 4.1 21.0 - - + -
1451 LEU* 4.2 17.7 - - + -
1461 LEU* 4.4 8.3 - - + -
1671 ALA 3.0 18.3 + - - +
1681 ILE 3.7 4.5 - - - +
1701 ASN* 1.3 76.4 + - - +
1721 MET* 1.3 57.0 + - - +
1741 VAL* 3.4 2.3 + - - +
1751 LEU* 3.0 35.5 + - - +
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Residues in contact with MET 172 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11 SER* 5.7 3.1 - - - +
31 ILE* 3.7 25.6 - - + -
141 ALA* 4.2 12.6 - - + +
151 ALA* 4.1 5.2 - - - -
161 ASP* 3.9 22.4 - - + +
1681 ILE 3.0 19.9 + - - +
1691 VAL 3.5 8.7 - - - +
1701 ASN 3.1 0.2 - - - -
1711 ALA* 1.3 77.0 - - - +
1731 ARG* 1.3 62.7 + - - +
1751 LEU* 3.5 14.2 + - + +
1761 TYR* 3.1 21.7 + - - +
1831 SER 5.5 2.6 - - - +
1861 PHE* 3.6 57.4 - - + -
2051 VAL* 3.8 7.1 - - + +
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Residues in contact with ARG 173 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1691 VAL* 3.2 16.4 + - - +
1701 ASN* 2.9 43.6 + - - +
1721 MET* 1.3 74.4 - - - +
1741 VAL* 1.3 67.2 + - + +
1761 TYR* 3.0 5.9 + - - +
1771 TYR* 2.9 56.6 + - + -
2051 VAL* 3.6 26.3 - - + +
2061 GLU 2.7 34.1 + - - +
2071 ASN* 3.8 24.7 + - - +
2081 MET* 4.6 0.9 - - - -
139H GLU 5.6 2.0 + - - -
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Residues in contact with VAL 174 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1411 MET* 3.7 35.4 - - + -
1451 LEU* 3.8 23.6 - - + -
1701 ASN* 3.1 16.8 + - - +
1711 ALA 3.6 6.7 - - - +
1731 ARG* 1.3 74.9 - - + +
1751 LEU* 1.3 63.8 + - - +
1771 TYR* 2.9 22.2 + - + +
1781 ARG* 3.0 13.2 + - + +
136H ALA* 4.0 17.7 - - + +
139H GLU* 4.1 17.5 - - + +
140H SER* 3.8 14.1 - - - +
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Residues in contact with LEU 175 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11 SER* 4.1 23.8 - - - +
31 ILE* 4.1 21.3 - - + -
1371 PHE* 4.0 26.7 - - + +
1381 GLY* 4.2 2.9 - - - +
1411 MET* 3.9 30.7 - - + -
1421 ALA* 4.4 6.7 - - + +
1711 ALA 3.0 23.4 + - - +
1721 MET* 3.8 15.3 - - + +
1731 ARG 3.2 0.2 - - - -
1741 VAL* 1.3 76.3 - - + +
1761 TYR* 1.3 57.6 + - - +
1781 ARG* 4.5 0.7 - - - +
1791 ASP* 2.9 41.5 + - + +
1821 SER* 3.1 7.3 + - - -
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Residues in contact with TYR 176 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1721 MET 3.1 13.3 + - - +
1731 ARG 3.0 9.0 + - - +
1751 LEU* 1.3 74.5 - - - +
1771 TYR* 1.3 67.4 + + - +
1791 ASP 4.4 3.3 - - - +
1821 SER* 3.2 23.9 + - - +
1831 SER* 3.6 21.5 - - - +
1841 ARG* 3.6 39.0 - - + +
2051 VAL* 4.4 11.4 - - + -
2081 MET* 4.0 29.6 - - + -
2101 TRP* 5.8 6.3 - + - -
19N ARG* 4.6 17.1 + - - -
187N GLU* 3.0 23.6 + - - -
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Residues in contact with TYR 177 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1731 ARG* 2.9 38.8 + - + -
1741 VAL* 2.9 16.7 + - + +
1761 TYR* 1.3 80.2 - + - +
1781 ARG* 1.3 65.9 + - + +
2071 ASN 4.2 0.5 + - - -
2081 MET* 3.4 29.2 - - + -
2091 LYS* 3.0 31.8 + - + +
2101 TRP* 4.3 11.3 - + - -
139H GLU* 3.7 45.1 - - + +
19N ARG* 5.1 0.9 + - - -
26N ILE* 3.2 21.8 - - - +
29N ARG* 3.7 42.4 - - - +
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Residues in contact with ARG 178 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1371 PHE* 4.9 0.9 - - - -
1411 MET* 3.6 42.2 - - + -
1741 VAL 3.0 11.0 + - - +
1771 TYR* 1.3 82.5 + - + +
1791 ASP* 1.3 60.1 + - - +
124H TYR* 4.4 5.1 + - - -
135H MET* 3.3 40.7 - - + +
139H GLU* 3.0 35.2 + - + -
25N TYR* 3.6 20.4 + - + -
26N ILE* 2.9 58.9 + - - +
27N ALA 3.1 21.2 + - - -
28N ASN* 4.0 4.4 - - - +
29N ARG* 4.3 13.1 - - - +
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Residues in contact with ASP 179 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
01 THR* 2.9 27.6 + - - +
11 SER* 4.1 3.1 + - - -
1371 PHE* 3.5 40.9 - - + +
1411 MET* 6.3 0.2 - - - -
1751 LEU* 2.9 24.5 + - + +
1761 TYR 4.4 1.4 - - - +
1781 ARG* 1.3 76.5 - - - +
1801 ALA* 1.3 58.7 + - - +
1811 ARG* 2.7 33.2 + - - +
1821 SER* 2.6 37.2 + - - +
19N ARG* 5.2 1.4 + - - -
24N ALA 3.8 2.8 - - - +
26N ILE* 3.7 5.9 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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