Contacts of the helix formed by residues 72 - 86 (chain K) in PDB entry 2AAZ
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 PHE 72 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70K ARG 4.0 2.0 + - - -
71K VAL* 1.3 69.7 - - - +
73K LEU* 1.3 66.6 + - - +
74K ARG* 3.7 31.2 - - + -
75K GLY* 3.0 37.5 + - - -
76K VAL* 3.1 17.2 + - - +
97K GLY 3.8 8.7 - - - -
98K VAL* 4.2 11.7 - - + -
99K GLY 5.3 1.1 - - - -
100K ILE* 5.0 6.7 - - + -
226K PHE* 3.8 19.3 - + + -
70N ARG* 3.3 52.0 - - - +
310N LYS* 6.3 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 73 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63K LEU* 4.6 7.4 - - + -
65K LEU* 4.1 30.1 - - + -
71K VAL 2.7 13.9 + - - +
72K PHE* 1.3 71.4 - - - +
74K ARG* 1.3 65.8 + - - +
76K VAL* 2.9 21.7 + - + +
77K ILE* 3.0 35.0 + - + +
233K LEU* 4.7 7.9 - - + -
300K PHE 5.9 0.4 - - - +
302K VAL* 3.5 41.5 - - + -
305K TYR* 5.4 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 74 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72K PHE* 3.4 16.6 - - + -
73K LEU* 1.3 79.9 - - - +
75K GLY* 1.3 57.7 + - - +
77K ILE* 3.8 8.9 - - - +
78K ALA* 2.9 30.6 + - + +
96K GLN* 2.8 30.6 + - - +
97K GLY* 4.2 3.8 + - - -
98K VAL* 4.0 11.8 - - + +
297K VAL* 4.4 20.8 - - + +
70N ARG* 2.8 39.2 - - - +
305N TYR* 5.7 2.9 - - - -
307N PRO* 4.2 17.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 75 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72K PHE* 3.0 35.3 + - - -
74K ARG* 1.3 78.4 - - - +
76K VAL* 1.3 63.2 + - - +
78K ALA* 3.8 1.0 - - - +
79K GLU* 3.0 26.2 + - - +
98K VAL* 4.0 17.5 - - - +
100K ILE* 4.4 0.2 - - - +
226K PHE* 3.9 8.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 76 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65K LEU* 5.3 0.4 - - + -
71K VAL* 4.3 7.6 - - + -
72K PHE 3.1 16.6 + - - +
73K LEU* 2.9 11.8 + - + +
75K GLY* 1.3 77.8 - - - +
77K ILE* 1.3 63.2 + - - +
79K GLU* 3.4 5.6 + - - +
80K LEU* 3.0 23.1 + - + +
226K PHE* 3.5 41.7 - - + +
229K ALA* 4.0 8.1 - - + -
230K SER* 3.6 37.3 + - - +
233K LEU* 3.9 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 77 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73K LEU* 3.0 35.1 + - + +
74K ARG* 3.8 8.7 - - - +
76K VAL* 1.3 75.3 - - - +
78K ALA* 1.3 64.1 + - - +
80K LEU* 3.1 7.9 + - - +
81K LEU* 3.0 32.2 + - + +
233K LEU* 4.0 20.9 - - + -
297K VAL* 4.1 19.7 - - + +
300K PHE* 3.6 58.3 - - + +
302K VAL* 5.3 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 78 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74K ARG* 2.9 19.5 + - + +
75K GLY 3.8 3.6 - - - +
77K ILE* 1.3 77.7 - - - +
79K GLU* 1.3 63.1 + - - +
81K LEU* 3.4 4.3 + - - +
82K TRP* 3.0 22.9 + - - +
93K LEU* 3.7 6.1 - - + +
96K GLN* 3.7 31.2 - - - +
98K VAL* 3.8 18.2 - - + -
297K VAL* 4.8 8.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 79 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75K GLY 3.0 18.1 + - - +
76K VAL* 3.7 4.6 - - - +
77K ILE 3.3 0.2 - - - -
78K ALA* 1.3 77.0 - - - +
80K LEU* 1.3 57.5 + - - +
82K TRP* 3.0 15.3 - - + +
83K PHE* 2.9 59.0 + - + -
93K LEU* 4.0 7.5 - - + +
100K ILE* 3.6 23.1 - - + +
101K TRP* 2.9 27.7 + - + +
188K HIS* 5.4 1.1 + - - -
226K PHE* 4.2 16.5 - - - +
227K ASN* 6.0 0.5 + - - -
230K SER* 4.8 7.8 + - - -
450K UMP 5.5 2.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 80 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76K VAL 3.0 17.9 + - - +
77K ILE* 3.1 5.4 + - - +
79K GLU* 1.3 73.3 - - - +
81K LEU* 1.3 66.0 + - + +
82K TRP 3.0 1.6 - - - -
83K PHE* 3.0 18.7 + - + +
84K VAL* 3.0 30.4 + - + +
131K TRP* 4.5 7.0 - - + -
230K SER* 3.6 35.6 + - - +
233K LEU* 3.6 19.7 - - + -
234K LEU* 3.7 26.7 - - + +
237K MET* 3.6 30.5 - - - -
300K PHE* 5.1 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 81 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77K ILE* 3.0 23.2 + - + +
78K ALA* 4.0 3.6 - - - +
80K LEU* 1.3 76.6 - - + +
82K TRP* 1.3 56.7 + - - +
84K VAL* 3.5 6.6 + - + +
85K SER* 3.0 28.9 + - - -
237K MET* 3.8 29.8 - - + -
292K ILE 5.9 0.2 - - - +
295K PHE* 3.8 20.6 - - + +
296K LYS* 3.7 11.0 - - - -
297K VAL* 3.5 43.5 - - + +
300K PHE* 4.1 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 82 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78K ALA 3.0 14.8 + - - +
79K GLU* 3.0 14.8 - - + +
81K LEU* 1.3 76.3 - - - +
83K PHE* 1.3 99.7 + + - +
85K SER* 2.6 22.5 + - - -
86K GLY 3.4 2.9 + - - -
87K CYS* 3.4 43.6 + - + +
88K THR* 3.7 22.7 - - - -
89K ASP 3.2 25.9 + - - -
90K ALA* 4.0 5.4 - - - -
92K MET* 4.0 12.3 - - + +
93K LEU* 3.7 25.1 - - + +
96K GLN* 5.9 0.4 - - - +
101K TRP* 3.7 23.1 - + - -
123K LEU* 3.5 25.4 - - + -
126K VAL* 4.7 8.1 - - + -
127K TYR* 5.4 0.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 83 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79K GLU* 2.9 50.5 + - + -
80K LEU* 3.3 15.7 - - + +
82K TRP* 1.3 101.0 - + - +
84K VAL* 1.3 55.6 + - - +
86K GLY* 2.8 22.9 + - - -
87K CYS 5.1 0.4 - - - -
101K TRP* 4.7 0.2 - - - -
127K TYR* 3.4 43.7 - + + -
128K GLY* 3.1 22.1 - - - +
131K TRP* 3.5 35.1 - + + -
132K ARG* 4.5 0.7 - - - +
188K HIS* 3.8 21.5 - + - -
230K SER* 4.5 9.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 84 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80K LEU* 3.0 24.2 + - + +
81K LEU* 3.7 10.8 - - + +
83K PHE* 1.3 80.8 - - - +
85K SER* 1.3 60.4 + - - +
86K GLY 3.1 1.2 + - - -
131K TRP* 4.7 5.4 - - + -
132K ARG* 2.6 32.5 + - - +
153K LEU* 3.8 27.6 - - + -
234K LEU* 4.6 7.4 - - + -
237K MET* 4.3 18.6 - - + -
292K ILE* 3.4 25.8 - - + +
293K ASP* 3.8 12.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 85 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81K LEU 3.0 14.5 + - - -
82K TRP* 2.6 24.1 + - - -
84K VAL* 1.3 76.5 - - - +
86K GLY* 1.3 59.0 + - - +
87K CYS* 3.1 18.6 + - - +
132K ARG* 4.6 2.4 - - - +
133K HIS* 5.2 3.6 + - - -
293K ASP* 4.7 5.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 86 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83K PHE 2.8 10.6 + - - -
84K VAL 3.0 1.2 - - - -
85K SER* 1.3 79.3 + - - +
87K CYS* 1.3 62.7 + - - +
88K THR* 3.8 3.3 + - - +
128K GLY 3.3 25.6 - - - -
129K PHE* 3.7 18.0 + - - +
132K ARG* 4.0 9.4 - - - -
133K HIS* 4.7 9.6 - - - -
145K TYR* 5.9 1.9 - - - -
----------------------------------------------------------
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