Contacts of the helix formed by residues 81 - 91 (chain H) in PDB entry 5GJQ
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 ALA 81 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80H LEU* 1.3 74.8 - - - +
82H ALA* 1.3 65.3 + - - +
83H ASP 3.1 1.8 - - - -
84H LYS* 4.2 2.0 - - - +
85H GLN* 3.0 36.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 82 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80H LEU* 4.6 4.9 - - - +
81H ALA* 1.3 77.0 - - - +
83H ASP* 1.3 59.8 + - + +
85H GLN* 5.0 0.2 - - - +
86H THR* 3.5 14.7 - - - -
137I SER* 5.2 5.6 - - - +
138I PHE* 6.6 0.2 - - + -
453x LYS* 6.4 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 83 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80H LEU 3.3 2.9 + - - +
82H ALA* 1.3 80.3 - - + +
84H LYS* 1.3 55.6 + - - +
85H GLN 2.9 2.7 - - - -
86H THR* 2.4 17.6 + - - -
87H LEU* 2.2 39.4 + - + +
102I LEU* 5.4 2.2 - - + -
135I ILE 5.4 0.9 - - - +
136I LEU* 5.2 0.4 - - - -
137I SER* 3.4 48.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 84 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80H LEU* 2.4 46.8 + - + +
81H ALA* 4.2 1.6 - - - +
83H ASP* 1.3 66.6 - - - +
85H GLN* 1.3 52.9 + - - +
87H LEU* 3.7 9.2 - - - +
88H GLN* 2.7 46.5 + - - +
98I LYS* 5.4 8.5 - - + -
102I LEU* 4.2 21.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 85 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81H ALA* 3.0 27.9 + - + +
82H ALA 5.0 0.2 - - - +
83H ASP 2.6 5.2 + - - -
84H LYS* 1.3 71.0 - - - +
86H THR* 1.3 52.3 + - - +
88H GLN* 2.7 12.3 + - - +
89H SER* 2.3 41.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 86 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82H ALA 3.5 17.2 + - - -
83H ASP* 2.4 15.9 + - - -
85H GLN* 1.3 72.2 - - - +
87H LEU* 1.3 52.5 + - - -
89H SER* 2.3 27.6 + - - -
90H GLU* 2.5 46.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 87 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83H ASP* 2.2 40.0 + - + +
84H LYS* 3.7 0.9 - - - +
86H THR* 1.3 66.0 - - - -
88H GLN* 1.3 50.5 - - - +
90H GLU* 3.1 2.4 - - - -
91H GLN* 2.1 45.9 + - + +
102I LEU* 3.6 27.6 - - + -
134I SER* 6.4 2.5 - - - -
135I ILE 5.6 2.2 - - - +
136I LEU* 3.7 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 88 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84H LYS* 2.7 35.1 + - - +
85H GLN* 2.7 4.4 + - - +
87H LEU* 1.3 70.1 - - - +
89H SER* 1.3 52.6 + - - +
91H GLN* 2.8 30.4 + - - +
92H PRO* 2.7 32.6 - - - +
102I LEU* 4.2 8.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 89 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85H GLN* 2.3 28.6 + - - -
86H THR* 2.3 42.3 + - - -
88H GLN* 1.3 64.7 - - - +
90H GLU* 1.3 58.6 + - - +
92H PRO* 2.5 27.3 - - - +
93H LEU* 3.0 10.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 90 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86H THR* 2.5 38.9 + - - +
87H LEU* 3.1 2.7 - - - +
89H SER* 1.3 75.7 + - - +
91H GLN* 1.3 57.4 + - - +
92H PRO* 3.1 3.8 - - - -
93H LEU* 2.6 51.5 + - + +
94H GLN 4.4 0.9 + - - +
134I SER* 4.1 21.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 91 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87H LEU* 2.1 40.4 + - + +
88H GLN* 2.8 36.7 + - - +
90H GLU* 1.3 70.0 - - - +
92H PRO* 1.4 61.8 - - + +
93H LEU 3.6 0.2 + - - -
94H GLN 5.2 3.1 + - - +
102I LEU* 2.8 43.9 + - - +
136I LEU* 4.8 5.3 - - + +
156I VAL* 4.7 15.4 - - - +
----------------------------------------------------------
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