Contacts of the helix formed by residues 77 - 88 (chain A) in PDB entry 2GQ3
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 77 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A TRP* 4.5 4.2 - - + -
71A ARG* 6.3 0.6 - - - +
75A PRO 3.3 6.5 + - - +
76A ILE* 1.3 69.7 - - - +
78A MET* 1.3 59.5 + - - +
79A ASP* 3.2 19.8 + - - +
80A ALA* 3.1 28.1 + - + +
81A TYR* 2.8 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A ILE* 3.2 25.0 + - + +
77A ASP* 1.3 69.8 + - - +
79A ASP* 1.3 61.6 + - - +
81A TYR* 3.7 16.2 - - + +
82A ARG* 2.9 36.1 + - + +
576A GLU* 3.7 55.2 - - + +
579A LEU* 3.9 34.5 - - + +
580A THR* 4.5 7.4 - - - +
581A ILE* 5.5 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ASP* 3.2 10.4 + - - +
78A MET* 1.3 76.5 - - - +
80A ALA* 1.3 62.3 + - - +
82A ARG* 3.6 14.9 + - - +
83A GLN* 3.0 24.5 + - - +
576A GLU* 4.5 9.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A TRP* 4.3 11.7 + - + +
71A ARG* 5.9 2.7 - - - +
77A ASP* 3.1 34.2 + - + +
79A ASP* 1.3 75.1 - - - +
81A TYR* 1.3 64.4 + - - +
83A GLN* 3.3 8.7 + - - +
84A PHE* 3.0 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ILE* 5.1 5.2 - - + +
67A TRP* 3.6 38.9 - + + -
68A HIS* 4.0 21.4 + + - -
76A ILE* 4.2 7.6 - - + -
77A ASP 2.8 20.5 + - - +
78A MET* 3.7 24.2 - - + +
80A ALA* 1.3 69.6 - - - +
82A ARG* 1.3 67.6 + - - +
84A PHE* 3.1 8.3 + + - +
85A LEU* 3.0 52.1 + - + +
436A ARG* 2.9 42.6 + - - -
470A THR* 5.0 2.3 - - - +
471A SER* 4.4 3.3 + - - -
579A LEU* 4.1 13.5 - - + -
581A ILE* 4.3 10.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A MET* 2.9 24.5 + - + +
79A ASP* 3.7 15.0 + - - +
81A TYR* 1.3 72.9 - - - +
83A GLN* 1.3 65.4 + - - +
85A LEU* 3.3 9.0 + - - +
86A THR* 3.0 26.6 + - - +
91A LEU* 4.1 12.7 - - + +
574A THR* 6.1 0.2 - - - -
575A ILE* 3.7 28.8 - - - +
576A GLU* 3.8 36.5 + - - +
579A LEU* 4.0 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A ASP 3.0 16.1 + - - +
80A ALA* 3.4 8.5 - - - +
81A TYR 3.2 0.2 - - - -
82A ARG* 1.3 82.2 - - - +
84A PHE* 1.3 58.2 + - - +
86A THR* 3.0 9.5 + - - -
87A GLU* 2.9 56.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A GLN* 3.6 30.3 - - + -
64A ILE* 4.1 11.4 - - + -
67A TRP* 3.4 49.8 - + + +
80A ALA 3.0 12.7 + - - +
81A TYR* 3.4 11.2 - + - +
83A GLN* 1.3 75.9 - - - +
85A LEU* 1.3 71.4 + - + +
87A GLU* 3.1 24.1 + - - +
88A ILE* 3.2 54.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ILE* 4.2 21.3 - - + -
81A TYR* 3.0 47.3 + - + +
82A ARG* 3.7 7.9 - - - +
83A GLN 3.2 0.2 - - - -
84A PHE* 1.3 82.1 - - + +
86A THR* 1.3 59.7 + - - +
88A ILE* 4.2 4.3 - - + -
89A GLY 3.6 0.7 + - - -
90A TYR* 2.9 59.9 + - + -
91A LEU* 3.0 17.8 + - + -
579A LEU* 3.6 37.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A ARG* 3.0 15.0 + - - +
83A GLN* 3.0 11.9 + - - +
85A LEU* 1.3 73.9 - - - +
87A GLU* 1.3 66.7 + - + +
89A GLY* 3.2 13.0 + - - -
91A LEU* 3.6 29.1 + - - +
92A LEU* 5.9 0.2 - - - +
93A PRO* 6.3 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A GLN* 2.9 49.2 + - + +
84A PHE* 3.1 17.7 + - - +
86A THR* 1.3 81.9 - - + +
88A ILE* 1.3 61.3 + - + +
89A GLY 3.2 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A LEU* 3.3 35.2 - - + +
63A GLN* 3.5 33.2 + - + +
64A ILE* 4.1 17.7 - - + -
84A PHE* 3.2 60.1 + - + +
85A LEU* 3.8 9.4 - - + +
87A GLU* 1.3 79.9 - - + +
89A GLY* 1.3 58.7 + - - +
90A TYR* 3.9 9.9 - - + +
----------------------------------------------------------
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