Contacts of the helix formed by residues 129 - 141 (chain 2) in PDB entry 5IY8
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 TRP 129 (chain 2).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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762 LYS* 3.6 45.4 - - + +
782 GLU* 2.7 50.3 - - + +
792 PHE* 4.7 18.4 - + + +
1252 GLY* 2.8 37.9 - - - -
1262 GLY 3.1 5.7 + - - -
1282 ALA* 1.3 91.6 - - + +
1302 SER* 1.3 61.5 + - - +
1312 ASP* 3.1 2.5 - - - +
1322 ASP* 3.2 25.2 + - + +
1332 THR 3.4 4.9 + - - -
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Residues in contact with SER 130 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
782 GLU* 4.6 0.9 - - - -
972 HIS* 6.3 0.2 - - - -
1262 GLY 3.3 7.7 + - - -
1272 LYS* 3.2 18.4 + - - +
1282 ALA 3.3 0.2 - - - -
1292 TRP* 1.3 78.8 - - - +
1312 ASP* 1.3 61.2 + - - +
1332 THR* 2.7 25.1 - - - +
1342 SER* 2.9 10.2 + - - -
1732 GLN* 2.8 25.1 - - - +
1782 LEU* 3.9 18.4 + - - -
1792 LEU* 3.7 14.5 - - - +
1802 SER* 5.0 4.2 + - - -
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Residues in contact with ASP 131 (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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1282 ALA 4.5 5.3 + - - +
1292 TRP* 3.1 1.3 - - - +
1302 SER* 1.3 81.5 + - - +
1322 ASP* 1.3 53.8 + - - +
1342 SER* 2.9 11.7 + - - -
1352 GLN* 2.6 39.6 + - - +
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Residues in contact with ASP 132 (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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792 PHE* 4.5 19.1 - - - -
812 LYS* 4.6 9.1 + - - +
822 ALA* 4.0 23.5 - - - +
1292 TRP* 3.2 27.5 + - + +
1312 ASP* 1.3 78.0 - - - +
1332 THR* 1.3 61.6 + - - +
1352 GLN* 2.7 44.9 + - - +
1362 LEU* 2.9 8.5 + - - +
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Residues in contact with THR 133 (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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782 GLU* 4.2 11.8 + - - +
812 LYS* 4.8 6.1 - - - +
932 LEU* 3.3 32.0 - - - +
962 TRP* 6.1 0.4 - - - -
972 HIS* 5.5 2.9 - - - +
1292 TRP 3.4 2.4 + - - +
1302 SER* 2.7 27.6 + - - +
1322 ASP* 1.3 79.2 - - - +
1342 SER* 1.3 51.6 + - - +
1362 LEU* 3.0 8.6 + - - +
1372 GLY* 2.6 33.6 + - - -
1692 ALA* 5.7 3.3 - - - +
1732 GLN* 3.0 35.2 + - - +
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Residues in contact with SER 134 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1302 SER 2.9 9.5 + - - -
1312 ASP* 2.9 15.6 + - - -
1332 THR* 1.3 82.1 - - - +
1352 GLN* 1.3 66.7 + - - +
1372 GLY* 4.2 0.7 - - - +
1382 PRO* 2.8 30.8 - - - +
1732 GLN* 5.0 2.0 - - - +
1792 LEU* 4.9 11.2 - - - -
1842 LEU* 4.8 9.7 - - - +
1892 GLU* 3.9 12.9 + - - -
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Residues in contact with GLN 135 (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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1312 ASP* 2.6 24.2 + - - +
1322 ASP* 2.7 45.0 + - - +
1342 SER* 1.3 73.0 - - - +
1362 LEU* 1.3 54.2 + - - +
1382 PRO* 2.7 30.0 - - - +
1392 ASP* 3.7 14.1 - - - +
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Residues in contact with LEU 136 (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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812 LYS* 4.8 3.1 - - - -
822 ALA* 5.5 8.3 - - + +
862 SER* 4.3 16.2 - - - +
892 LEU* 4.1 19.3 - - + -
902 LEU* 3.6 30.3 - - + -
932 LEU* 3.8 20.2 - - + -
1322 ASP* 2.9 16.3 + - - +
1332 THR* 3.0 8.7 + - - +
1352 GLN* 1.3 74.9 - - + +
1372 GLY* 1.4 61.8 + - - +
1382 PRO 2.5 17.6 - - - +
1392 ASP* 4.4 2.4 - - + +
1402 LYS* 3.5 13.9 + - + +
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Residues in contact with GLY 137 (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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902 LEU* 5.4 7.9 - - - -
1332 THR 2.6 17.9 + - - -
1342 SER* 3.0 1.6 + - - -
1362 LEU* 1.4 71.8 - - - +
1382 PRO* 1.3 75.4 - - - +
1402 LYS* 3.3 16.4 + - - +
1412 HIS* 3.4 6.4 + - - +
1662 SER* 3.9 18.3 + - - -
1892 GLU* 4.7 2.9 - - - -
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Residues in contact with PRO 138 (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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1342 SER* 2.8 23.1 - - - +
1352 GLN* 2.7 13.6 - - - +
1362 LEU 2.5 19.9 - - - +
1372 GLY* 1.3 85.4 - - - +
1392 ASP* 1.3 64.3 + - - +
1412 HIS* 4.5 6.7 - - + +
1872 SER* 5.7 3.8 - - - -
1882 THR* 4.0 19.5 - - + +
1892 GLU* 3.0 45.3 - - + +
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Residues in contact with ASP 139 (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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1352 GLN* 3.7 12.5 - - - +
1362 LEU* 4.4 3.1 - - + +
1382 PRO* 1.3 77.9 - - - +
1402 LYS* 1.3 64.1 + - - +
1412 HIS* 3.2 10.4 - - - +
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Residues in contact with LYS 140 (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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862 SER* 2.9 36.1 - - - +
872 THR* 3.5 28.7 - - - +
902 LEU* 3.1 29.6 - - + +
1362 LEU* 3.5 11.6 + - + +
1372 GLY 3.4 9.9 - - - +
1382 PRO 2.8 6.7 + - - -
1392 ASP* 1.3 78.0 - - - +
1412 HIS* 1.3 61.4 + - - +
1622 PHE* 2.9 57.5 - - + +
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Residues in contact with HIS 141 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1372 GLY 3.4 9.2 + - - +
1382 PRO* 4.7 5.2 - - + -
1392 ASP* 3.2 10.3 - - - +
1402 LYS* 1.3 83.8 - - - +
1622 PHE* 3.3 27.0 - - + -
1632 MET* 5.0 17.7 - - + +
1662 SER* 4.9 2.0 - - - +
1882 THR* 5.1 6.5 - - + -
1892 GLU* 5.9 0.4 - - + -
1922 GLU* 2.7 57.7 + - + +
1952 CYS* 5.6 4.5 - - - -
1962 ILE* 5.9 0.7 - - + -
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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