Contacts of the helix formed by residues 80 - 84 (chain C) in PDB entry 4IL6
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 PRO 80 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C GLU 4.3 3.6 - - - +
79C LYS* 1.3 81.9 - - + +
81C MET* 1.3 65.8 + - - +
82C TYR* 3.5 33.7 - - + +
83C GLU* 3.1 39.5 + - + +
84C GLN* 3.1 14.4 + - - +
300C GLU 5.4 0.4 - - - +
394C GLU* 3.9 19.1 - - - +
526C DMS 4.1 22.4 - - + -
103V LYS* 4.3 9.6 - - + -
203V DMS 5.2 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 81 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C PHE* 4.1 16.8 - - + -
79C LYS 3.4 1.8 + - - +
80C PRO* 1.3 72.4 - - - +
82C TYR* 1.3 58.0 + - - +
84C GLN* 2.8 27.1 + - - +
85C GLY 3.7 2.3 + - - -
86C LEU* 3.7 25.4 + - + +
89C ILE* 3.9 19.7 - - + -
90C PRO* 3.9 25.8 - - + -
93C ALA* 3.8 16.6 - - + -
99C VAL* 4.3 1.6 - - + -
103C GLY 4.8 1.6 - - - +
105C VAL* 3.9 25.8 - - + -
111C PHE* 4.6 1.1 - - + -
300C GLU 4.9 3.0 + - - +
301C PHE* 3.6 46.0 - - + +
422C PRO* 5.3 0.4 - - - -
526C DMS 5.2 2.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 82 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C PRO* 3.5 18.7 - - + +
81C MET* 1.3 79.1 - - - +
83C GLU* 1.3 60.0 + - - +
84C GLN 3.2 1.3 + - - -
85C GLY 4.4 1.7 + - - -
299C SER 3.4 11.9 - - - -
300C GLU* 3.4 27.6 - - - -
301C PHE 3.7 5.6 - - - +
302C TYR 3.7 0.2 - - - -
303C GLY* 3.3 35.7 - - - +
304C PRO* 4.9 0.4 - - + -
394C GLU* 2.6 41.0 + - + +
395C TYR* 4.0 8.3 - + - -
398C HIS* 3.7 30.5 - + + -
419C PHE* 3.1 23.3 - + + -
422C PRO* 3.7 30.0 - - + +
516C DGD 4.4 4.2 + - - -
526C DMS 5.1 3.1 + - - -
203V DMS 5.1 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 83 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C LYS* 3.6 25.9 + - - -
80C PRO* 3.1 33.3 + - + +
82C TYR* 1.3 76.4 - - + +
84C GLN* 1.3 59.6 + - - +
394C GLU* 4.4 0.7 - - - +
398C HIS* 2.6 41.9 + - + +
418C ASN 4.6 3.7 - - - +
419C PHE* 4.4 6.7 - - + -
516C DGD 2.9 21.3 + - - -
35V TYR 4.7 0.2 - - - +
39V SER* 5.1 1.4 + - - -
103V LYS* 3.1 41.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 84 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C HIS* 3.8 6.6 - - - +
75C PHE* 3.3 21.2 - - - -
76C ILE* 2.7 51.4 + - - +
79C LYS* 2.9 41.1 + - + +
80C PRO 3.1 10.9 + - - +
81C MET 2.8 9.5 + - - +
83C GLU* 1.3 82.3 - - - +
85C GLY* 1.3 62.6 + - - +
86C LEU* 3.3 19.4 - - + +
504C CLA 3.5 10.9 - - - +
516C DGD 3.1 12.1 + - - +
518C LMG 3.7 6.4 + - - -
----------------------------------------------------------
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