Contacts of the helix formed by residues 160 - 177 (chain 2) in PDB entry 5IY6
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 LEU 160 (chain 2).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1592 VAL* 1.3 101.0 - - + +
1612 HIS* 1.3 55.9 + - + +
1632 MET* 3.1 2.2 + - - -
1642 VAL* 2.6 44.0 + - + +
2032 PHE* 4.3 13.0 - - + +
2052 LEU* 5.9 0.9 - - + -
2062 LEU* 2.9 46.0 - - + +
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Residues in contact with HIS 161 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482 LEU 6.1 1.1 - - - -
492 PRO* 5.5 6.1 - - + +
502 SER* 3.8 22.3 + - - +
1592 VAL* 2.8 28.5 - - + +
1602 LEU* 1.3 81.5 - - + +
1622 PHE* 1.3 62.1 + - - +
1642 VAL* 3.2 9.8 + - - +
1652 GLY* 2.9 18.2 + - - -
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Residues in contact with PHE 162 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
872 THR* 6.2 1.6 - - + -
902 LEU* 4.1 4.3 - - + -
1402 LYS* 2.9 57.9 - - + +
1412 HIS* 3.3 53.2 - - + -
1592 VAL 3.0 25.2 + - - +
1612 HIS* 1.3 75.6 - - - +
1632 MET* 1.3 73.6 + - + +
1652 GLY* 2.9 4.3 + - - +
1662 SER* 2.8 42.9 + - - -
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Residues in contact with MET 163 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1412 HIS* 5.0 17.0 - - + +
1592 VAL 2.6 20.2 + - - +
1602 LEU* 3.5 2.0 - - - +
1622 PHE* 1.3 83.2 - - + +
1642 VAL* 1.3 65.4 + - + +
1662 SER 3.2 0.5 + - - -
1672 PRO* 2.8 36.4 - - + +
1922 GLU* 5.4 1.1 - - - +
1932 PRO* 6.4 1.1 - - + -
1962 ILE* 3.1 50.0 - - + -
2022 GLN* 4.4 3.4 - - + -
2062 LEU* 2.9 54.1 - - + +
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Residues in contact with VAL 164 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
942 ARG* 4.4 13.2 - - - +
1602 LEU* 2.6 34.7 + - + +
1612 HIS* 3.5 8.7 - - - +
1622 PHE 3.1 0.2 - - - -
1632 MET* 1.3 75.4 - - - +
1652 GLY* 1.3 57.8 + - - +
1672 PRO* 4.0 0.4 - - - +
1682 SER* 2.8 30.0 + - - -
2052 LEU* 4.5 7.2 - - + +
2062 LEU* 3.6 19.7 - - + -
2092 PRO* 3.3 37.2 - - + +
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Residues in contact with GLY 165 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
902 LEU* 4.7 13.2 - - - +
942 ARG* 3.9 17.6 + - - +
1612 HIS 2.9 10.5 + - - -
1622 PHE* 2.9 8.2 + - - -
1642 VAL* 1.3 77.6 - - - +
1662 SER* 1.3 62.1 + - - +
1682 SER* 3.8 0.7 - - - -
1692 ALA* 2.9 26.2 + - - +
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Residues in contact with SER 166 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
902 LEU* 4.5 9.2 - - - -
1372 GLY* 3.9 18.2 + - - -
1412 HIS* 4.9 0.7 - - - +
1622 PHE* 2.8 41.6 + - - -
1632 MET 3.2 0.4 + - - -
1652 GLY* 1.3 75.9 - - - +
1672 PRO* 1.3 78.0 - - - +
1692 ALA* 3.2 3.7 + - - +
1702 ALA* 2.9 21.6 + - - +
1892 GLU* 4.0 13.2 + - - +
1922 GLU* 4.5 7.6 + - - -
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Residues in contact with PRO 167 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1412 HIS* 5.9 0.2 - - - +
1632 MET* 2.8 32.0 - - + +
1642 VAL 4.4 1.1 - - - +
1662 SER* 1.3 89.5 - - - +
1682 SER* 1.3 60.7 + - - +
1702 ALA* 3.6 7.2 - - + +
1712 VAL* 2.7 35.4 + - - +
1892 GLU* 5.6 0.9 - - - +
1922 GLU* 4.6 7.0 - - - +
1932 PRO* 4.3 25.4 - - + -
1962 ILE* 5.5 2.5 - - + -
2092 PRO* 4.2 14.1 - - + +
2102 ALA* 4.8 4.0 - - - +
2132 TRP* 4.0 19.1 - - + -
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Residues in contact with SER 168 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
942 ARG* 2.7 50.2 + - - +
1642 VAL* 2.8 28.4 + - - -
1652 GLY 3.9 0.4 - - - -
1672 PRO* 1.3 72.0 - - - +
1692 ALA* 1.3 64.0 + - - +
1712 VAL* 3.2 9.1 + - - +
1722 SER* 3.0 23.7 + - - -
2092 PRO* 5.0 6.6 - - - +
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Residues in contact with ALA 169 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
902 LEU* 4.5 24.0 - - + +
932 LEU* 4.9 9.1 - - + +
942 ARG* 4.2 17.3 - - + +
972 HIS* 5.4 1.4 - - - -
1332 THR* 5.7 3.1 - - - +
1652 GLY 2.9 17.7 + - - +
1662 SER* 3.5 5.4 - - - +
1682 SER* 1.3 78.2 - - - +
1702 ALA* 1.3 62.7 + - - +
1722 SER* 3.1 4.3 + - - -
1732 GLN* 3.0 23.1 + - - +
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Residues in contact with ALA 170 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1662 SER 2.9 13.6 + - - +
1672 PRO* 3.6 7.0 - - + +
1692 ALA* 1.3 76.2 - - - +
1712 VAL* 1.3 64.0 + - - +
1732 GLN* 3.1 10.8 + - - +
1742 ASP* 2.9 20.4 + - - +
1792 LEU* 5.2 2.7 - - + -
1892 GLU* 3.8 20.0 - - - +
2132 TRP* 2.9 38.7 - - + -
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Residues in contact with VAL 171 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1672 PRO 2.7 35.2 + - - +
1682 SER* 3.4 8.3 - - - +
1702 ALA* 1.3 69.9 - - - +
1722 SER* 1.3 62.5 + - - +
1742 ASP* 3.0 11.3 + - - +
1752 LEU 3.0 0.7 + - - -
2092 PRO 4.3 3.4 - - - +
2122 LEU* 3.8 13.7 - - + +
2132 TRP* 2.9 42.7 - - + +
2162 MET* 2.9 59.4 - - + +
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Residues in contact with SER 172 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
942 ARG* 2.8 36.0 + - - -
972 HIS* 3.2 22.3 - - - +
982 THR* 3.5 10.6 + - - -
1682 SER 3.0 10.7 + - - -
1692 ALA 3.5 8.1 - - - -
1712 VAL* 1.3 78.2 - - - +
1732 GLN* 1.3 65.0 + - - +
1752 LEU* 2.7 28.5 + - - +
1762 ALA 3.4 4.7 + - - -
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Residues in contact with GLN 173 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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972 HIS* 3.7 31.3 + - + +
1302 SER* 2.8 38.5 - - - -
1332 THR* 3.0 26.2 + - - +
1342 SER* 4.7 3.2 - - - +
1692 ALA 3.0 13.3 + - - +
1702 ALA* 3.1 10.8 + - - +
1722 SER* 1.3 78.0 - - - +
1742 ASP* 1.3 64.5 + - - +
1762 ALA* 3.2 17.0 - - - +
1772 GLN 3.4 3.8 + - - -
1782 LEU* 3.8 9.4 + - + -
1792 LEU* 2.9 31.8 + - + +
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Residues in contact with ASP 174 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1702 ALA 2.9 4.1 + - - +
1712 VAL 3.2 8.7 - - - +
1732 GLN* 1.3 73.6 - - - +
1752 LEU* 1.4 65.1 + - - +
1772 GLN* 2.8 2.1 + - - -
1792 LEU* 2.7 32.8 - - - +
1842 LEU* 4.4 0.8 - - - +
2132 TRP* 2.7 34.2 - - - -
2162 MET* 3.6 18.4 - - + +
2172 LEU* 3.2 27.8 - - - +
2202 LEU* 2.7 38.9 - - + +
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Residues in contact with LEU 175 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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972 HIS* 5.4 2.9 - - + +
982 THR* 5.2 16.2 - - + +
1012 LEU* 6.2 4.7 - - + -
1712 VAL 3.0 8.5 + - - -
1722 SER* 2.7 49.4 - - - +
1742 ASP* 1.4 76.3 - - - +
1762 ALA* 1.3 62.7 + - - +
1772 GLN* 3.2 16.8 + - - +
2162 MET* 3.1 38.1 - - + +
2192 TYR* 5.1 11.6 - - + -
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Residues in contact with ALA 176 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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972 HIS* 3.3 28.5 - - + +
1002 LEU* 6.4 1.6 - - + -
1232 LEU* 4.1 12.8 - - + +
1722 SER 3.4 6.8 + - - +
1732 GLN 3.2 12.3 + - - +
1742 ASP 3.1 0.2 - - - -
1752 LEU* 1.3 79.7 - - - +
1772 GLN* 1.4 64.8 + - - +
1782 LEU* 2.9 33.2 - - + +
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Residues in contact with GLN 177 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1232 LEU* 5.3 2.9 - - + +
1272 LYS* 4.5 6.1 + - - +
1732 GLN 3.4 0.6 + - - -
1742 ASP 2.8 9.3 + - - -
1752 LEU 3.0 11.1 + - - +
1762 ALA* 1.4 78.7 - - - +
1782 LEU* 1.3 61.8 + - - +
1792 LEU 3.4 5.8 - - - +
2192 TYR* 3.7 24.6 + - + -
2202 LEU* 2.8 73.2 + - - +
2222 THR* 4.9 9.1 - - - +
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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
------------------------------------------------------------
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