Contacts of the helix formed by residues 77 - 88 (chain A) in PDB entry 2AY5
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 77 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A GLY 4.0 4.7 - - - +
76A GLU* 1.3 94.8 - - + +
78A GLU* 1.3 64.3 + - - +
79A PHE 3.0 0.2 + - - -
80A GLN* 3.1 14.8 + - + +
81A LYS* 2.9 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A GLU* 3.3 7.6 - - + +
77A PRO* 1.3 78.4 - - - +
79A PHE* 1.3 57.0 - - - +
81A LYS* 4.2 3.2 - - - +
82A ALA* 3.2 28.2 + - - +
304A LYS* 2.9 28.6 + - - +
307A SER* 3.5 35.7 + - - +
308A THR* 4.1 4.3 + - - -
311A THR* 3.6 22.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A GLU* 2.9 19.6 + - + +
78A GLU* 1.3 75.8 - - - +
80A GLN* 1.3 65.5 + - + +
81A LYS 3.2 1.3 - - - -
82A ALA* 3.2 2.6 + - + +
83A MET* 2.9 59.6 + - + +
104A ALA* 4.2 19.7 - - + -
256A CYS* 4.6 0.7 - - - -
267A THR* 3.8 20.2 - - + -
268A GLY 3.8 21.1 - - - -
269A CYS* 4.0 11.0 - - + -
303A ALA* 3.3 40.8 - - + +
306A VAL* 3.8 26.5 - - + -
307A SER* 3.9 8.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A SER* 3.0 37.3 + - - +
75A GLY 4.0 4.8 + - - +
76A GLU 3.0 15.4 + - - +
77A PRO* 3.4 26.1 - - + +
79A PHE* 1.3 82.6 - - + +
81A LYS* 1.3 57.6 + - - +
83A MET* 4.1 2.2 - - - +
84A GLY* 3.0 24.9 + - - -
95A LEU* 5.5 0.5 - - - +
102A THR* 3.4 53.9 + - + +
104A ALA 5.2 0.7 - - - +
284A GLN* 4.5 4.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A PRO 2.9 16.4 + - - +
78A GLU* 4.2 4.3 - - - +
80A GLN* 1.3 75.3 - - - +
82A ALA* 1.3 67.2 + - - +
84A GLY* 3.3 2.2 + - - -
85A GLU* 3.0 56.2 + - - +
95A LEU* 3.0 34.3 - - - +
97A SER* 3.9 17.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A GLU 3.2 18.1 + - - +
79A PHE* 3.2 6.8 + - + +
81A LYS* 1.3 81.0 - - - +
83A MET* 1.3 57.8 + - + +
85A GLU* 3.3 8.8 + - - +
86A LEU* 3.0 28.8 + - - +
307A SER* 4.6 7.4 - - - -
310A LEU* 3.7 35.0 - - + +
311A THR* 4.9 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A PHE* 2.9 45.4 + - + +
80A GLN* 4.1 3.4 - - - +
82A ALA* 1.3 73.0 - - + +
84A GLY* 1.3 66.4 + - - +
86A LEU* 3.1 26.3 + - + +
87A ILE* 3.0 38.0 + - + +
102A THR* 5.8 0.2 - - + -
254A ALA* 4.0 25.8 - - + -
255A SER 5.2 1.6 - - - +
256A CYS* 3.8 30.5 - - - -
259A ASN* 6.3 0.9 - - - +
269A CYS* 3.9 19.5 - - - +
271A LEU* 5.1 0.2 - - - -
306A VAL* 4.0 16.2 - - + -
310A LEU* 4.5 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A GLN 3.0 16.3 + - - -
81A LYS 3.3 3.3 + - - -
83A MET* 1.3 77.2 - - - +
85A GLU* 1.3 55.7 + - - +
88A LEU* 2.8 35.6 + - - +
95A LEU* 3.6 19.3 - - - +
102A THR* 5.9 0.2 - - - -
271A LEU* 4.3 21.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A LYS* 3.0 58.1 + - - +
82A ALA* 3.8 6.7 - - - +
84A GLY* 1.3 74.3 - - - +
86A LEU* 1.3 62.9 + - - +
89A GLY* 2.8 38.8 + - - +
95A LEU* 3.8 6.5 - - + -
241A ARG* 4.5 0.5 + - - -
316A ARG* 5.8 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A ALA 3.0 17.1 + - - +
83A MET* 3.1 30.5 + - + +
85A GLU* 1.3 76.2 - - - +
87A ILE* 1.3 61.3 + - - +
226A GLN* 3.1 39.8 + - - +
233A LEU* 4.4 20.6 - - + -
234A GLU* 5.0 1.0 - - - +
241A ARG* 3.4 9.5 + - - -
259A ASN* 4.7 7.0 - - - +
260A PHE* 4.3 19.3 - - + -
310A LEU* 4.3 13.9 - - + -
316A ARG* 4.7 17.5 - - - +
319A TRP* 4.4 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A MET* 3.0 29.2 + - + +
84A GLY 4.2 1.3 - - - +
86A LEU* 1.3 78.8 - - + +
88A LEU* 1.3 61.8 + - + +
223A LEU* 3.7 27.1 - - + -
226A GLN* 3.9 11.0 - - - +
237A ALA* 3.5 6.5 - - + +
240A THR* 4.2 20.6 - - + -
241A ARG* 2.8 26.5 + - - +
252A ILE* 4.2 15.0 - - + -
254A ALA* 3.5 32.1 - - + -
269A CYS* 4.9 0.2 - - - -
271A LEU* 3.9 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A GLY 2.8 17.6 + - - +
87A ILE* 1.3 82.5 - - + +
89A GLY* 1.3 63.4 + - - +
90A ASP 3.5 0.3 + - - -
91A GLY* 3.2 17.1 + - - +
95A LEU* 3.9 38.4 - - + +
96A LYS 5.3 0.4 - - - +
100A THR* 4.8 2.5 - - + +
240A THR* 4.7 2.5 - - + -
241A ARG* 3.8 25.3 + - + +
244A ALA* 3.9 26.7 - - + -
252A ILE* 4.2 16.2 - - + -
271A LEU* 4.6 9.9 - - + -
273A LEU* 4.3 25.6 - - + -
----------------------------------------------------------
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