Contacts of the helix formed by residues 71 - 82 (chain A) in PDB entry 5E2Q
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 ASP 71 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A PHE* 3.9 8.4 + - - +
70A GLN* 1.3 74.8 - - - +
72A PRO* 1.3 71.5 - - + +
73A ASP* 3.1 7.1 + - - +
74A GLN* 2.6 59.7 + - - +
75A LEU* 2.8 25.8 + - - +
698A ARG* 3.8 22.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A PHE* 4.0 17.3 - - + -
71A ASP* 1.3 88.4 - - + +
73A ASP* 1.3 57.7 + - - +
76A ARG* 3.0 16.6 + - - +
89A TYR* 2.4 35.3 + - - +
93A LEU* 4.2 9.6 - - + -
694A ALA* 3.7 41.1 - - + +
697A ILE* 4.1 16.2 - - + -
698A ARG* 3.9 20.6 - - + +
701A SER* 5.8 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ASP* 3.1 7.9 + - - +
72A PRO* 1.3 75.1 - - - +
74A GLN* 1.3 65.4 + - + +
76A ARG* 3.2 35.5 + - - +
77A GLN* 3.6 16.0 + - - +
694A ALA* 5.8 0.4 - - - +
698A ARG* 2.5 33.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A ALA 4.0 5.8 + - - +
70A GLN* 3.3 29.5 + - + +
71A ASP* 2.6 53.3 + - - +
73A ASP* 1.3 72.3 - - + +
75A LEU* 1.3 64.8 + - - +
77A GLN* 3.2 24.8 + - - +
78A HIS* 3.5 7.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A LEU* 4.8 15.9 - - + +
67A PHE* 3.7 28.0 - - + -
70A GLN* 3.6 32.2 - - + +
71A ASP 2.8 17.7 + - - +
74A GLN* 1.3 70.1 - - - +
76A ARG* 1.3 59.8 + - - +
78A HIS* 3.4 9.9 + - + +
79A ALA* 2.9 27.9 + - - +
89A TYR* 3.5 17.5 - - + +
92A PHE* 3.9 21.3 - - + -
126A VAL* 4.0 22.4 - - + -
130A SER* 4.5 7.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A PRO* 3.0 23.9 + - - +
73A ASP* 3.2 38.7 + - - +
75A LEU* 1.3 77.4 - - - +
77A GLN* 1.3 62.0 + - + +
79A ALA 3.3 0.2 + - - -
80A LEU* 2.9 49.1 + - + +
86A GLU* 3.1 37.6 + - - +
89A TYR* 3.1 28.5 + - + -
90A GLN* 3.7 15.0 - - - +
93A LEU* 4.2 4.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ASP 3.6 15.1 + - - +
74A GLN* 3.2 14.3 + - - +
76A ARG* 1.3 81.4 - - + +
78A HIS* 1.3 60.5 + - - +
80A LEU* 4.3 3.5 - - - +
81A ALA* 3.3 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A GLN* 4.2 19.1 - - - +
74A GLN 3.5 2.4 + - - +
75A LEU* 3.4 13.1 + - + +
76A ARG 3.2 0.6 - - - -
77A GLN* 1.3 78.3 - - - +
79A ALA* 1.3 63.6 + - - +
81A ALA* 3.2 6.2 + - - +
82A GLU* 3.1 46.7 + - + +
126A VAL* 2.9 47.4 + - + -
129A GLY* 3.1 29.9 + - - -
130A SER* 3.9 9.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A LEU 2.9 18.2 + - - +
76A ARG 3.8 1.8 - - - +
78A HIS* 1.3 76.6 - - - +
80A LEU* 1.3 57.9 + - - +
82A GLU* 3.1 12.0 + - - +
83A GLY 3.5 0.3 + - - -
84A LEU* 3.1 30.9 + - + +
89A TYR* 3.6 28.9 - - + -
126A VAL* 3.8 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A ARG* 2.9 31.9 + - + +
77A GLN* 4.5 3.4 - - - +
79A ALA* 1.3 78.7 - - - +
81A ALA* 1.3 59.7 + - - +
82A GLU 3.5 0.2 + - - -
83A GLY* 3.6 8.5 + - - -
84A LEU 3.4 22.3 - - - +
85A THR* 4.0 13.9 - - - +
86A GLU* 3.7 28.0 - - + +
89A TYR* 4.0 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A GLN 3.3 18.6 + - - +
78A HIS* 3.2 8.9 + - - +
79A ALA 3.2 0.4 - - - -
80A LEU* 1.3 78.5 - - - +
82A GLU* 1.3 64.4 + - + +
83A GLY 3.4 0.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A HIS* 3.1 45.6 + - + +
79A ALA* 3.1 9.1 + - - +
81A ALA* 1.3 83.1 - - + +
83A GLY* 1.3 56.4 + - - +
84A LEU* 3.6 2.9 - - + +
125A ARG* 2.8 60.2 + - + +
126A VAL* 4.5 9.0 - - + -
129A GLY* 5.7 1.4 - - - -
----------------------------------------------------------
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