Contacts of the helix formed by residues 60 - 69 (chain A) in PDB entry 6G0P
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 60 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ARG* 3.6 39.5 - - + +
59A GLN* 1.3 82.2 - - - +
61A ASN* 1.3 59.7 + - - +
62A GLN* 3.5 5.8 + - - +
63A LEU* 3.0 32.1 + - + +
64A GLN* 2.9 28.7 + - - +
120A TRP 4.0 6.3 - - - +
121A ASN* 5.1 1.3 - - - -
122A ALA 4.8 2.1 + - - -
167A GLU* 3.4 20.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A THR* 1.3 71.9 - - - +
62A GLN* 1.3 56.7 + - - +
64A GLN* 3.4 21.6 + - - +
65A TYR* 3.0 28.2 + - - +
165A PRO* 3.8 18.8 - - - +
166A THR 2.8 29.0 + - - +
167A GLU* 2.8 22.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 62 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A THR* 4.0 2.3 + - - +
61A ASN* 1.3 74.4 - - - +
63A LEU* 1.3 61.2 + - - +
65A TYR* 3.3 9.3 + - - +
66A LEU* 2.9 32.6 + - - +
122A ALA* 3.6 23.4 + - + +
123A GLN* 5.7 0.2 - - - +
164A LEU* 3.9 25.8 - - + +
165A PRO* 3.0 35.2 + - + +
166A THR* 5.0 1.6 - - - +
167A GLU* 3.0 24.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 63 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ARG 3.8 21.5 - - - +
59A GLN* 5.1 1.1 - - - -
60A THR* 3.0 29.6 + - + +
62A GLN* 1.3 72.3 - - - +
64A GLN* 1.3 65.5 + - - +
66A LEU* 3.2 5.9 + - + +
67A LEU* 3.1 19.6 + - - +
114A LEU* 3.8 27.1 - - + +
119A TYR* 3.8 20.0 - - + +
120A TRP 3.8 20.9 - - - +
121A ASN* 3.7 23.8 - - - +
122A ALA* 3.8 13.7 - - - +
125A CYS* 4.1 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A GLN* 5.5 6.1 + - + +
60A THR 2.9 17.2 + - - +
61A ASN* 3.6 21.5 - - - +
63A LEU* 1.3 74.1 - - - +
65A TYR* 1.3 58.5 + - - +
67A LEU* 3.2 5.6 + - - -
68A ARG* 2.8 46.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 65 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A ASN 3.0 14.5 + - - +
62A GLN 3.4 6.7 - - - +
64A GLN* 1.3 74.3 - - - +
66A LEU* 1.3 61.5 + - - +
68A ARG* 5.1 0.9 - - - -
69A VAL* 2.8 64.5 + - + +
70A VAL* 3.0 24.8 + - + -
160A LYS* 2.7 38.8 + - - +
163A GLU* 3.5 23.2 + - - +
164A LEU* 3.8 19.5 - - + -
165A PRO* 3.4 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A GLN 2.9 14.8 + - - +
63A LEU* 3.2 11.4 + - + +
65A TYR* 1.3 77.3 - - - +
67A LEU* 1.3 57.3 + - - +
70A VAL* 3.5 26.8 - - + +
71A LEU* 2.8 30.5 + - - +
114A LEU* 4.0 5.9 - - + +
122A ALA* 3.6 45.8 - - + +
125A CYS* 3.9 27.1 - - + -
126A ILE* 4.1 12.1 - - + -
129A PHE* 4.5 6.9 - - + -
157A PHE* 4.7 0.4 - - + -
161A ILE* 4.0 17.9 - - + -
164A LEU* 4.6 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A LEU 3.1 12.1 + - - +
64A GLN* 3.7 7.4 - - - +
66A LEU* 1.3 77.1 - - - +
68A ARG* 1.3 88.5 + - + +
69A VAL 3.4 0.2 - - - -
71A LEU* 3.7 16.7 - - + +
72A LYS* 3.3 26.5 + - - +
111A LYS* 4.6 5.6 - - + +
114A LEU* 3.8 35.6 - - + +
115A GLU* 4.3 31.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A GLN* 2.8 38.9 + - + +
65A TYR* 5.1 0.2 - - - -
67A LEU* 1.3 98.9 - - + +
69A VAL* 1.3 66.3 + - + +
72A LYS* 3.5 19.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A TYR* 2.8 56.2 + - + +
68A ARG* 1.3 85.9 - - + +
70A VAL* 1.3 63.7 + - - +
71A LEU 3.7 0.4 - - - -
72A LYS* 4.0 1.3 - - - +
73A THR* 2.6 35.4 + - - +
160A LYS* 4.2 19.9 - - + +
----------------------------------------------------------
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