Contacts of the helix formed by residues 76 - 87 (chain D) in PDB entry 1IRI
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 GLY 76 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72D ALA 3.1 0.2 + - - -
73D LYS 3.0 14.8 + - - -
74D SER 3.2 1.7 - - - -
75D ARG* 1.3 79.9 - - - +
77D VAL* 1.3 65.8 + - - +
78D GLU 3.3 2.9 + - - -
79D ALA* 3.3 11.6 + - - +
80D ALA* 3.0 24.3 + - - +
83D ARG* 5.0 1.6 + - - -
503D ILE* 4.2 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 77 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72D ALA* 3.0 41.5 + - + +
73D LYS* 5.1 0.4 - - - +
75D ARG* 4.9 0.2 - - + -
76D GLY* 1.3 76.4 - - - +
78D GLU* 1.3 60.0 + - + +
80D ALA* 3.4 2.9 + - - +
81D ARG* 2.9 27.1 + - + +
307D PHE* 5.1 7.0 - - + -
312D LEU* 4.5 19.1 - - + -
318D VAL* 4.7 4.3 - - + -
499D PHE* 4.5 3.2 - - + -
500D VAL* 4.1 32.1 - - + -
503D ILE* 4.1 14.6 - - + -
504D ILE* 4.0 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 78 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73D LYS* 4.5 11.4 - - - +
76D GLY 3.3 0.6 - - - -
77D VAL* 1.3 73.6 - - - +
79D ALA* 1.3 62.1 + - - +
81D ARG* 3.2 35.9 + - - +
82D GLU* 3.0 32.7 + - - +
310D THR 5.3 1.7 - - - +
311D PRO* 5.5 1.7 - - - +
312D LEU* 3.7 46.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 79 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76D GLY* 3.3 12.8 + - - +
78D GLU* 1.3 75.6 - - - +
80D ALA* 1.3 66.6 + - - +
82D GLU* 3.1 8.8 + - - +
83D ARG* 2.9 41.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 80 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76D GLY 3.0 16.4 + - - +
77D VAL 3.7 1.6 - - - +
79D ALA* 1.3 76.0 - - - +
81D ARG* 1.3 64.3 + - - +
83D ARG* 3.1 29.0 + - - +
84D MET 2.9 18.5 + - - -
90D ILE* 5.0 2.5 - - + +
499D PHE* 3.6 7.7 - - - -
503D ILE* 3.4 40.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 81 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77D VAL* 2.9 16.9 + - + +
78D GLU* 3.2 48.2 + - - +
80D ALA* 1.3 76.7 - - - +
82D GLU* 1.3 76.4 + - - +
84D MET* 3.1 4.6 + - - +
85D PHE* 2.9 42.4 + - + -
307D PHE* 2.9 49.4 + - + -
308D ARG* 3.1 40.3 + - - +
310D THR 4.5 5.1 + - - -
312D LEU* 4.8 4.0 - - - +
315D ASN* 4.3 3.8 + - - -
499D PHE* 3.7 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 82 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78D GLU 3.0 16.9 + - - +
79D ALA* 3.6 9.4 - - - +
81D ARG* 1.3 102.8 + - - +
83D ARG* 1.3 56.0 + - - +
85D PHE* 4.3 2.2 - - - +
86D ASN* 2.5 51.8 + - - +
308D ARG* 2.5 46.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 83 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76D GLY 5.0 1.6 + - - -
79D ALA* 2.9 39.0 + - - +
80D ALA* 3.1 32.0 + - - +
82D GLU* 1.3 75.3 - - - +
84D MET* 1.3 61.9 + - - +
86D ASN* 3.2 1.0 + - - -
87D GLY 3.1 17.8 + - - -
88D GLU* 3.1 45.6 + - - +
90D ILE* 3.6 23.9 - - + +
366D LYS* 5.3 12.2 - - - +
503D ILE* 5.3 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 84 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80D ALA 2.9 11.0 + - - +
81D ARG 3.4 5.2 - - - +
83D ARG* 1.3 78.9 - - - +
85D PHE* 1.3 86.9 + - + +
87D GLY* 3.2 2.9 + - - -
88D GLU 5.3 0.4 - - - +
90D ILE* 3.6 22.1 - - + +
98D VAL* 3.2 27.4 + - - +
99D LEU* 3.0 27.6 - - + +
100D HIS* 4.2 22.2 - - - +
101D VAL* 4.7 6.5 - - + -
307D PHE* 4.4 0.9 - - + -
496D HIS* 4.0 22.9 - - + +
499D PHE* 4.2 36.3 - - + -
510D PHE* 4.4 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 85 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81D ARG* 2.9 38.3 + - + +
82D GLU* 3.9 1.8 - - - +
84D MET* 1.3 102.6 - - + +
86D ASN* 1.3 64.4 + - - +
87D GLY 3.3 0.4 + - - -
99D LEU* 4.6 3.4 - - - +
101D VAL* 3.6 34.9 - - + +
111D ILE* 4.2 22.5 - - + +
304D ASP* 3.9 34.1 - - + -
305D GLN* 6.0 0.4 - - - -
307D PHE* 4.2 6.1 - + - -
308D ARG* 3.6 49.2 + - + +
496D HIS* 4.4 2.5 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 86 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82D GLU* 2.5 40.1 + - - +
83D ARG* 4.0 4.7 - - - +
84D MET 3.2 0.2 - - - -
85D PHE* 1.3 74.6 + - - +
87D GLY* 1.3 60.3 + - - +
88D GLU* 3.5 13.1 + - + +
111D ILE* 4.8 3.5 - - - -
112D LEU* 3.7 14.6 + - - +
308D ARG* 3.6 18.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 87 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83D ARG 3.1 3.2 + - - -
84D MET 3.2 10.9 + - - -
85D PHE 3.3 1.6 + - - -
86D ASN* 1.3 78.5 - - - +
88D GLU* 1.3 67.8 + - - +
89D LYS* 4.4 4.2 - - - +
97D ALA* 3.2 14.8 - - - +
98D VAL 5.8 0.2 - - - -
99D LEU* 4.0 21.5 - - - -
111D ILE* 4.7 1.3 - - - -
112D LEU 4.0 13.7 - - - +
113D VAL* 4.6 5.0 - - - +
----------------------------------------------------------
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