Contacts of the helix formed by residues 82 - 88 (chain B) in PDB entry 2IAG
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 82 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B LEU* 4.1 20.2 - - - -
79B ASP* 2.5 32.2 + - - -
81B HIS* 1.3 74.0 - - - +
83B TYR* 1.3 65.9 + - - +
84B ASP 3.2 4.1 + - - -
85B ALA* 3.8 6.0 + - - +
86B VAL* 3.6 21.7 + - - +
368B PRO 4.6 3.4 - - - +
369B MET* 3.6 17.1 - - - +
370B ALA* 3.2 24.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 83 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B LEU* 3.4 31.2 + - + -
78B LEU* 3.5 16.4 - - - +
79B ASP 3.3 18.2 - - - -
80B PRO* 3.3 27.4 + - + +
82B SER* 1.3 76.7 - - - +
84B ASP* 1.3 64.6 + - - +
86B VAL* 3.4 2.0 + - - +
87B VAL* 3.0 30.9 + - + +
385B LEU* 3.5 29.8 - - + -
386B PHE 4.0 10.4 + - - -
387B PRO* 4.4 6.7 - - + -
390B SER 2.6 30.1 + - - -
391B PRO* 3.7 8.3 - - + -
429B ASN* 4.5 9.0 - - + +
432B MET* 3.5 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 84 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B PRO 4.5 0.6 + - - +
81B HIS 4.3 8.9 + - - +
82B SER 3.2 1.0 - - - -
83B TYR* 1.3 77.5 - - - +
85B ALA* 1.3 67.7 + - - +
87B VAL* 3.4 7.4 - - - +
88B TRP* 3.0 40.1 + - - -
428B LYS* 2.7 43.3 + - + +
429B ASN* 3.3 15.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 85 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B HIS 5.6 0.2 + - - -
82B SER* 3.8 6.9 + - - +
84B ASP* 1.3 81.5 - - - +
86B VAL* 1.3 64.2 + - + +
88B TRP* 3.2 12.7 + - - +
89B GLU* 3.3 18.1 + - - +
368B PRO* 4.6 23.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 86 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B LEU* 4.2 9.0 - - + -
82B SER 3.6 14.6 + - - +
83B TYR 3.6 8.5 - - - +
84B ASP 3.2 0.8 - - - -
85B ALA* 1.3 80.1 - - + +
87B VAL* 1.3 63.2 + - + +
89B GLU* 3.2 27.4 + - - +
94B LEU* 3.6 8.7 - - + +
359B ARG* 4.8 7.1 + - + -
367B MET* 3.6 37.0 - - + -
368B PRO* 4.4 7.4 - - + +
383B LEU* 3.7 26.0 - - + -
385B LEU* 4.5 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 87 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B TYR* 3.0 28.2 + - + +
84B ASP* 3.4 13.0 - - - +
86B VAL* 1.3 72.8 - - + +
88B TRP* 1.3 67.5 + - + +
89B GLU 3.4 2.2 + - - +
357B ILE* 4.0 18.4 - - + -
359B ARG* 3.2 26.1 + - + +
385B LEU* 3.7 24.5 - - + -
429B ASN* 5.9 1.6 - - - +
432B MET* 5.6 0.2 - - + -
436B ALA* 3.8 26.2 - - + +
437B GLY* 3.8 26.6 - - - +
438B HIS* 3.8 7.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 88 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A TRP* 5.9 0.2 - + - -
84B ASP* 3.0 38.4 + - - +
85B ALA* 3.2 9.5 + - - +
87B VAL* 1.3 81.9 - - + +
89B GLU* 1.3 68.2 + - - +
90B PRO* 3.4 4.0 - - - +
428B LYS* 4.4 16.4 - - - +
437B GLY* 3.5 40.8 - - - -
438B HIS* 3.5 45.4 - + - -
440B HIS* 4.5 11.9 - + - -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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