Contacts of the helix formed by residues 1004 - 1009 (chain B) in PDB entry 2IUI
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 ASN1004 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1002B ASN 4.0 0.4 + - - -
1003B ASN* 1.3 72.5 - - - +
1005B MET* 1.3 61.4 + - - +
1006B SER 3.7 0.7 - - - -
1007B LEU* 4.1 22.4 - - + -
1008B GLN* 3.3 37.1 + - + +
1047B TYR* 5.1 5.1 + - - +
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Residues in contact with MET1005 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A LYS* 5.8 1.8 - - - -
76A THR* 3.4 41.1 - - - +
77A PHE* 4.9 5.8 - - + -
78A SER* 5.9 1.1 - - - -
82A GLU* 3.6 18.4 - - - +
1003B ASN* 2.8 19.1 + - + +
1004B ASN* 1.3 75.9 + - - +
1006B SER* 1.3 68.1 + - - +
1007B LEU 3.1 1.3 + - - -
1008B GLN* 3.2 11.6 + - - +
1009B ASN* 3.1 27.9 + - - +
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Residues in contact with SER1006 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A GLU* 4.9 13.1 - - - +
1003B ASN* 3.1 16.2 + - - -
1005B MET* 1.3 81.3 - - - +
1007B LEU* 1.3 66.1 + - - +
1009B ASN* 3.3 5.8 + - - +
1010B ALA* 3.2 20.3 + - - +
1079B SER* 4.9 5.5 - - - -
1081B VAL* 3.5 31.6 - - - +
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Residues in contact with LEU1007 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1003B ASN 5.4 1.3 - - - +
1004B ASN* 4.0 20.6 + - + +
1005B MET 3.1 0.6 - - - -
1006B SER* 1.3 82.6 + - - +
1008B GLN* 1.3 63.3 + - + +
1010B ALA* 3.1 18.0 + - - +
1012B TRP* 3.9 26.5 - - + -
1013B TYR* 3.5 33.5 - - + +
1047B TYR* 3.4 42.0 - - + +
1080B VAL* 4.1 21.1 - - + -
1081B VAL* 3.7 9.9 - - + +
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Residues in contact with GLN1008 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A HIS* 6.5 0.4 - - + -
1004B ASN* 3.3 33.1 + - + +
1005B MET* 3.2 6.7 + - - +
1007B LEU* 1.3 79.1 - - + +
1009B ASN* 1.3 62.3 + - - +
1013B TYR* 3.8 29.7 + - + -
1015B GLY* 5.7 1.0 - - - -
1109B LYS* 2.8 26.7 + - - -
1110B TYR* 4.5 0.3 + - - -
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Residues in contact with ASN1009 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A PHE* 4.3 5.3 - - - -
82A GLU* 3.8 42.1 + - + +
85A ASN* 4.2 7.3 + - + +
86A HIS* 2.8 38.4 + - - +
1005B MET* 3.1 31.8 + - - +
1006B SER 3.3 5.4 + - - +
1007B LEU 3.2 0.4 - - - -
1008B GLN* 1.3 78.6 - - - +
1010B ALA* 1.3 66.8 + - - +
1011B GLU 3.3 2.4 + - - -
1110B TYR* 3.1 23.6 + - - +
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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