Contacts of the helix formed by residues 66 - 82 (chain B) in PDB entry 1Q6X
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 GLY 66 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B ARG 4.7 6.1 - - - -
61B PHE 4.6 3.1 - - - -
63B ALA* 2.8 20.0 + - - -
64B PRO 3.2 0.8 - - - -
65B GLY* 1.3 80.3 - - - +
67B LEU* 1.3 66.0 + - - -
68B GLY 3.3 2.9 - - - -
69B GLU* 3.5 3.4 + - - +
70B THR* 3.1 24.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 67 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B ARG 4.9 1.4 + - - -
61B PHE* 3.8 27.9 + - + +
66B GLY* 1.3 71.6 - - - -
68B GLY* 1.3 63.5 + - - +
70B THR* 3.1 11.4 + - + -
71B LEU* 2.9 42.3 + - + +
527B CYS* 3.8 24.0 - - - -
531B PRO* 3.6 36.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 68 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B LEU* 3.6 13.7 - - - +
61B PHE* 3.0 47.3 + - - -
67B LEU* 1.3 78.0 - - - +
69B GLU* 1.3 56.1 + - - +
71B LEU* 3.3 2.1 + - - +
72B GLN* 2.8 29.8 + - - +
519B LEU* 4.7 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 69 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B LEU* 4.0 17.5 - - + -
32B GLN* 4.7 5.4 + - - -
61B PHE 4.6 0.8 + - - -
62B GLY 4.4 7.0 - - - +
63B ALA 4.1 8.5 - - - +
64B PRO* 3.7 14.3 - - - +
65B GLY* 2.9 29.2 + - - +
66B GLY 3.5 7.1 + - - +
67B LEU 3.3 0.4 - - - -
68B GLY* 1.3 71.6 - - - +
70B THR* 1.3 66.2 + - - +
72B GLN* 3.4 5.0 + - - +
73B GLU* 3.1 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 70 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B GLY 4.7 3.8 + - - -
66B GLY 3.1 13.9 + - - -
67B LEU* 3.1 15.9 + - + -
69B GLU* 1.3 78.5 - - - +
71B LEU* 1.3 68.3 + - + +
73B GLU* 3.3 12.9 + - - +
74B LYS* 3.2 33.8 + - + +
526B LEU* 6.5 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 71 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B PHE* 4.1 17.3 - - + -
67B LEU* 2.9 40.9 + - + +
68B GLY 3.7 3.6 - - - +
70B THR* 1.3 81.9 - - + +
72B GLN* 1.3 57.0 + - - +
74B LYS* 3.0 8.3 + - + +
75B LEU* 2.8 27.7 + - - +
519B LEU* 3.5 35.7 - - + +
522B LEU* 3.9 14.8 - - + +
523B ALA* 3.8 35.4 - - + +
526B LEU* 4.7 11.2 - - + -
527B CYS* 5.0 2.9 - - - -
534B PHE* 4.9 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 72 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B VAL* 4.1 9.4 - - - +
29B PRO 2.9 27.5 + - - -
30B PRO* 3.9 1.6 - - - +
31B LEU* 3.3 28.8 - - + +
68B GLY 2.8 18.1 + - - +
69B GLU* 3.7 9.2 - - - +
71B LEU* 1.3 76.2 - - - +
73B GLU* 1.3 62.6 + - - +
75B LEU* 3.2 7.9 + - - +
76B LEU* 3.0 30.4 + - + +
515B HIS* 2.7 25.4 + - - -
519B LEU* 4.0 9.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 73 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B GLU 3.1 12.7 + - - +
70B THR* 3.5 14.4 - - - +
71B LEU 3.2 0.2 - - - -
72B GLN* 1.3 77.3 - - - +
74B LYS* 1.3 72.2 + - + +
76B LEU* 3.4 10.0 + - - +
77B GLU* 3.2 33.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 74 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B THR* 3.2 24.7 + - + +
71B LEU* 3.0 12.4 + - + +
73B GLU* 1.3 87.1 + - - +
75B LEU* 1.3 59.1 + - - +
77B GLU* 3.2 30.3 + - - +
78B ARG* 3.0 25.6 + - - +
522B LEU* 4.3 18.7 - - + +
526B LEU* 4.1 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 75 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B VAL* 3.8 21.3 - - + -
71B LEU 2.8 12.1 + - - +
72B GLN* 3.2 12.8 + - - +
74B LYS* 1.3 74.5 - - - +
76B LEU* 1.3 66.1 + - - +
78B ARG* 3.0 12.8 + - - +
79B GLN* 2.9 20.8 + - - +
85B TRP* 3.8 27.1 - - + -
515B HIS* 3.5 34.1 - - + +
518B ALA* 3.8 30.3 - - + -
519B LEU* 4.2 7.6 - - + -
522B LEU* 3.8 13.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 76 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B VAL* 3.7 36.3 - - + +
72B GLN* 3.0 23.5 + - + +
73B GLU* 3.8 11.0 - - + +
74B LYS 3.3 0.2 - - - -
75B LEU* 1.3 75.9 - - - +
77B GLU* 1.3 61.7 + - - +
79B GLN* 3.3 22.5 + - - +
80B GLU* 3.3 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 77 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B GLU* 3.2 25.0 + - + +
74B LYS* 3.3 34.3 + - - +
75B LEU 3.1 0.4 - - - -
76B LEU* 1.3 77.6 - - - +
78B ARG* 1.3 63.6 + - - +
80B GLU* 3.2 19.7 + - - +
81B LYS* 3.3 42.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 78 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B LYS 3.0 12.2 + - - +
75B LEU* 3.0 20.1 + - + +
77B GLU* 1.3 78.6 - - - +
79B GLN* 1.3 60.7 + - - +
81B LYS* 3.2 7.9 + - - +
82B THR* 2.9 47.6 + - + +
84B ASN 5.8 0.4 + - - -
85B TRP* 3.0 33.1 + - + -
88B GLU* 3.6 32.1 + - - +
89B TYR* 3.3 41.5 + - - -
522B LEU* 4.5 9.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 79 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B LYS* 2.8 37.6 + - + +
26B LEU 2.9 24.7 + - - +
27B PRO* 3.8 3.6 - - - +
28B VAL* 3.5 27.7 - - + +
75B LEU 2.9 12.2 + - - +
76B LEU* 3.5 20.7 - - - +
77B GLU 3.2 0.4 - - - -
78B ARG* 1.3 77.9 - - - +
80B GLU* 1.3 59.6 + - + +
82B THR* 3.2 7.4 - - - +
85B TRP* 4.0 25.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 80 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B LYS* 3.4 14.2 + - - +
76B LEU* 3.3 22.1 + - - +
77B GLU* 3.2 12.5 + - - +
78B ARG 3.2 0.8 - - - -
79B GLN* 1.3 83.6 - - + +
81B LYS* 1.3 61.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 81 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B LYS* 4.9 0.2 - - - -
77B GLU* 3.4 41.3 + - - +
78B ARG* 3.2 7.9 + - - +
80B GLU* 1.3 82.1 - - + +
82B THR* 1.3 62.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 82 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B LYS* 2.7 26.4 + - - -
78B ARG* 2.9 38.4 + - + +
79B GLN* 3.2 6.6 - - - +
81B LYS* 1.3 84.8 - - + +
83B ALA* 1.3 60.4 + - - +
84B ASN 3.9 10.5 - - - +
85B TRP* 3.3 23.0 + - - +
----------------------------------------------------------
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