Contacts of the helix formed by residues 72 - 90 (chain c) in PDB entry 6QXT
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 THR 72 (chain c).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69c ASP* 5.2 4.7 - - - -
70c ILE 3.6 5.4 + - - -
71c ASN* 1.3 73.8 - - - +
73c SER* 1.3 62.3 + - - +
74c GLN* 3.3 7.6 - - - -
75c VAL* 3.8 13.1 - - - +
76c LEU* 2.8 30.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 73 (chain c).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72c THR* 1.3 73.1 - - - +
74c GLN* 1.3 58.7 + - - +
76c LEU* 3.9 3.7 - - - +
77c LYS* 2.9 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 74 (chain c).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72c THR* 3.3 4.1 - - - -
73c SER* 1.3 75.2 - - - +
75c VAL* 1.3 61.7 + - - +
77c LYS* 3.3 5.9 + - - +
78c LEU* 2.9 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 75 (chain c).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70c ILE 4.0 12.8 - - - +
71c ASN* 5.1 0.4 - - - -
72c THR* 3.4 23.6 + - - +
73c SER 3.4 0.4 - - - -
74c GLN* 1.3 79.7 - - - +
76c LEU* 1.3 57.3 + - - +
78c LEU* 3.4 5.0 + - - +
79c LEU* 2.9 29.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 76 (chain c).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71c ASN* 5.9 3.3 - - + +
72c THR 2.8 22.3 + - - +
73c SER* 4.1 4.0 - - - +
75c VAL* 1.3 71.3 - - - +
77c LYS* 1.3 61.0 + - - +
79c LEU* 3.9 6.1 - - - +
80c HIS* 2.9 31.9 + - - +
135c VAL 5.1 10.8 - - - +
136c ARG* 6.0 4.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 77 (chain c).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73c SER 2.9 20.3 + - - +
74c GLN* 3.6 7.6 - - - +
75c VAL 3.2 0.2 - - - -
76c LEU* 1.3 77.0 - - - +
78c LEU* 1.3 57.6 + - - +
80c HIS* 3.9 4.1 - - - +
81c THR* 2.9 31.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 78 (chain c).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74c GLN 2.9 17.1 + - - +
75c VAL* 4.0 4.9 - - - +
77c LYS* 1.3 77.8 - - - +
79c LEU* 1.3 57.3 + - - +
81c THR* 3.8 4.9 - - - -
82c ASP* 2.9 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 79 (chain c).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75c VAL 2.9 19.0 + - - +
76c LEU* 3.9 6.7 - - - +
78c LEU* 1.3 74.3 - - - +
80c HIS* 1.3 59.8 + - - +
82c ASP* 3.1 7.5 + - - +
83c ILE* 2.9 28.9 + - - +
135c VAL 5.7 4.3 - - - +
136c ARG* 6.2 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 80 (chain c).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76c LEU 2.9 18.3 + - - +
77c LYS* 4.0 4.7 - - - +
79c LEU* 1.3 76.2 - - - +
81c THR* 1.3 56.8 + - - +
83c ILE* 3.4 6.4 + - - +
84c VAL* 2.9 29.3 + - - +
127c LEU* 5.9 6.1 - - + +
130c ILE* 5.0 17.3 - - + +
131c LYS* 6.0 1.8 - - + +
135c VAL* 6.4 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 81 (chain c).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77c LYS 2.9 19.5 + - - -
78c LEU* 3.9 6.3 - - - -
80c HIS* 1.3 76.7 - - - +
82c ASP* 1.3 57.3 + - - +
84c VAL* 3.7 6.9 - - - +
85c SER* 2.9 28.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 82 (chain c).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78c LEU 2.9 19.7 + - - +
79c LEU* 3.1 7.8 + - - +
81c THR* 1.3 74.8 - - - +
83c ILE* 1.3 59.9 + - - +
85c SER* 3.2 8.2 + - - -
86c GLN* 2.9 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 83 (chain c).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111b GLU* 5.5 12.1 - - + +
79c LEU 2.9 15.6 + - - +
80c HIS* 3.9 6.3 - - - +
82c ASP* 1.3 77.4 - - - +
84c VAL* 1.3 57.5 + - - +
86c GLN* 3.3 8.3 + - - +
87c LEU* 2.9 30.1 + - - +
130c ILE* 5.9 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 84 (chain c).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80c HIS 2.9 17.7 + - - +
81c THR* 3.7 7.9 - - - +
83c ILE* 1.3 76.7 - - - +
85c SER* 1.3 58.2 + - - +
87c LEU* 3.5 6.0 + - - +
88c ASN* 2.9 29.3 + - - +
126c LEU* 5.9 7.9 - - + -
127c LEU* 5.9 8.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 85 (chain c).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81c THR 2.9 17.2 + - - -
82c ASP* 3.2 8.5 + - - -
84c VAL* 1.3 74.8 - - - +
86c GLN* 1.3 60.0 + - - +
88c ASN* 3.1 7.1 + - - +
89c ASP* 2.9 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 86 (chain c).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111b GLU* 5.4 12.3 - - + +
82c ASP 2.9 15.6 + - - +
83c ILE* 3.3 8.7 + - - +
85c SER* 1.3 76.5 - - - +
87c LEU* 1.3 60.9 + - - +
89c ASP* 3.3 19.2 + - - +
90c LYS* 3.8 7.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 87 (chain c).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111b GLU* 5.8 7.3 - - + +
83c ILE 2.9 16.7 + - - +
84c VAL* 3.9 6.5 - - - +
86c GLN* 1.3 75.9 - - - +
88c ASN* 1.3 56.7 + - - +
90c LYS* 3.1 25.0 + - - +
93c VAL* 5.3 3.5 - - + +
94c ARG* 3.6 17.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 88 (chain c).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84c VAL 2.9 18.2 + - - +
85c SER* 3.1 9.4 + - - +
87c LEU* 1.3 74.3 - - - +
89c ASP* 1.3 63.8 + - - +
90c LYS 3.2 5.0 + - - -
91c PRO* 4.7 2.3 - - - +
94c ARG* 5.2 4.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 89 (chain c).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85c SER 2.9 12.6 + - - +
86c GLN* 3.6 13.9 - - - +
87c LEU 3.3 0.8 - - - -
88c ASN* 1.3 76.3 - - - +
90c LYS* 1.3 57.9 + - - +
91c PRO 4.0 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 90 (chain c).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86c GLN 3.8 6.3 + - - +
87c LEU* 3.1 18.7 + - - +
88c ASN 3.2 2.6 - - - +
89c ASP* 1.3 80.0 - - + +
91c PRO* 1.3 64.9 - - - +
92c GLU* 3.4 1.8 - - + +
93c VAL* 4.2 18.8 - - + +
94c ARG* 3.4 10.9 + - - +
----------------------------------------------------------
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