Contacts of the helix formed by residues 1467 - 1471 (chain A) in PDB entry 5IYB
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 GLY1467 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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872A MET* 3.9 4.2 - - - +
1084A GLY* 3.5 24.7 + - - -
1086A MET* 5.0 0.4 - - - -
1466A ALA* 1.3 71.1 - - - +
1468A THR* 1.3 59.2 + - - -
1469A GLY 3.1 0.2 - - - -
1470A CYS* 2.8 30.4 + - - +
1471A PHE* 4.3 1.6 - - - -
1098B GLY* 4.1 11.4 - - - -
60F TYR* 4.0 18.5 - - - +
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Residues in contact with THR1468 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514A GLU* 2.5 33.6 + - + +
518A LEU* 4.4 5.8 - - + -
1463A LEU* 4.8 1.3 - - - +
1466A ALA 3.9 0.2 + - - -
1467A GLY* 1.3 70.3 - - - -
1469A GLY* 1.3 59.7 + - - +
1470A CYS 3.0 1.1 + - - -
1471A PHE* 3.9 14.9 - - - +
1098B GLY 3.3 13.4 + - - +
1100B ALA* 3.3 17.8 + - - +
1101B GLN* 4.0 2.1 + - - +
60F TYR* 3.3 39.6 - - + +
63F ALA* 4.5 0.7 - - + -
64F ARG* 3.8 34.6 + - + +
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Residues in contact with GLY1469 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1463A LEU* 3.8 22.6 - - - +
1464A ALA 3.3 17.1 + - - +
1465A PRO* 3.4 18.9 - - - +
1467A GLY 3.1 2.2 - - - -
1468A THR* 1.3 79.6 + - - +
1470A CYS* 1.3 60.4 + - - +
1471A PHE 3.4 4.3 + - - +
1100B ALA* 3.4 13.2 - - - +
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Residues in contact with CYS1470 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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872A MET* 4.1 24.9 - - + -
873A VAL 5.3 1.6 - - - -
874A LYS* 5.5 6.3 - - - -
875A TYR* 3.7 27.3 - - - +
1084A GLY* 4.3 9.6 - - - -
1465A PRO* 4.3 12.5 - - - +
1467A GLY* 2.8 27.0 + - - +
1468A THR 3.0 0.8 - - - -
1469A GLY* 1.3 76.5 - - - +
1471A PHE* 1.3 63.9 + - + +
109F TYR* 4.2 13.2 - - - +
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Residues in contact with PHE1471 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
875A TYR* 3.1 30.5 - - + +
1463A LEU* 5.9 1.2 - - - +
1467A GLY 4.3 7.2 - - - -
1468A THR 3.9 17.6 - - - +
1469A GLY 3.4 4.2 - - - +
1470A CYS* 1.3 83.8 - - + +
1472A ASP* 1.3 63.7 + - - +
1473A LEU* 3.4 30.9 - - + +
60F TYR* 4.3 5.6 - - + -
61F GLU* 3.5 38.1 - - + -
64F ARG* 3.6 22.9 + - + -
65F VAL* 5.8 0.2 - - + -
106F ILE* 3.6 27.4 - - + -
107F ARG 3.2 17.3 - - - +
108F ARG* 4.5 2.2 - - - -
109F TYR* 4.5 6.7 - - - +
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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