Contacts of the helix formed by residues 68 - 73 (chain 0) 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 SER 68 (chain 0).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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660 ASP* 2.6 23.4 + - - -
670 GLY* 1.4 80.4 - - - +
690 ARG* 1.4 60.1 + - - +
700 THR* 3.2 18.4 - - - -
710 MET* 3.0 23.4 + - - +
1090 THR 3.5 0.8 + - - -
1390 CYS* 3.3 5.0 - - - +
1400 HIS 3.6 4.5 - - - -
1410 GLY 3.0 16.2 - - - -
1420 GLU* 3.4 3.3 - - - +
1430 PRO* 3.1 21.7 - - - +
1730 SER* 3.1 11.8 + - - -
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Residues in contact with ARG 69 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
680 SER* 1.4 67.8 - - - +
700 THR* 1.3 63.1 + - + +
720 GLU* 2.7 55.0 + - - +
730 ASP 4.4 0.7 + - - -
1390 CYS 4.3 3.1 - - - -
1400 HIS* 3.4 33.6 + - - +
1410 GLY* 2.8 23.3 + - - +
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Residues in contact with THR 70 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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660 ASP* 4.0 0.9 + - - -
680 SER* 3.5 17.3 - - - -
690 ARG* 1.3 75.3 - - + +
710 MET* 1.4 60.2 + - - -
730 ASP* 3.3 12.7 + - - +
800 ARG* 2.9 28.8 + - - +
1720 SER* 3.3 27.9 + - - +
1730 SER* 3.6 10.4 + - - +
1740 LEU* 6.1 5.4 - - + -
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Residues in contact with MET 71 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
650 VAL* 4.1 13.5 - - + -
660 ASP* 3.1 32.5 - - + +
680 SER 3.0 16.0 + - - +
700 THR* 1.4 76.3 + - - +
720 GLU* 1.3 63.1 + - - +
730 ASP 3.2 0.9 + - - -
800 ARG* 3.3 23.5 + - - +
810 LEU* 3.1 42.4 + - + +
840 THR* 3.3 32.3 - - + +
1390 CYS* 3.6 9.0 - - + -
1700 ILE* 4.2 13.5 - - + -
1720 SER* 3.6 25.8 + - - -
2010 LEU* 4.6 3.1 - - + -
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Residues in contact with GLU 72 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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690 ARG* 2.7 54.8 + - - +
710 MET* 1.3 75.0 - - - +
730 ASP* 1.4 57.6 + - - +
740 GLN* 3.7 0.9 + - - +
790 ASN* 3.0 25.7 - - + +
1380 THR* 5.1 6.3 + - - -
1390 CYS* 3.3 25.8 - - - +
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Residues in contact with ASP 73 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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690 ARG 4.4 0.6 + - - -
700 THR* 3.3 16.7 + - - +
710 MET 3.2 2.8 + - - -
720 GLU* 1.4 76.9 - - - +
740 GLN* 1.3 78.8 + - - +
750 ASP* 3.2 21.7 + - - +
800 ARG* 2.9 49.3 + - - +
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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