Contacts of the helix formed by residues 58 - 70 (chain D) in PDB entry 1THF
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 LYS 58 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51D ASP* 4.1 17.0 - - + +
53D THR* 5.0 1.1 - - - +
54D ALA* 3.3 34.1 + - - -
55D SER 3.4 27.6 + - - +
56D VAL 3.0 4.9 + - - +
57D GLU* 1.3 73.2 - - - +
59D ARG* 1.3 86.5 + - - +
61D THR* 3.3 7.1 + - - -
62D MET* 2.7 46.6 + - + +
81D GLY 4.2 9.6 - - - +
82D GLY 2.9 27.8 + - - +
83D ILE* 6.1 2.2 - - + -
84D HIS* 3.8 11.3 + - - -
88D THR* 5.2 8.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 59 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55D SER 5.0 0.4 + - - -
57D GLU 3.4 0.8 - - - -
58D LYS* 1.3 99.7 - - - +
60D LYS* 1.3 61.4 + - - +
62D MET* 3.9 2.6 - - - +
63D LEU* 3.1 36.1 + - + +
85D ASP* 4.6 7.1 + - - -
87D GLU* 3.0 22.8 - - - +
88D THR* 3.2 38.7 + - + +
91D GLU* 2.7 39.6 + - - +
92D LEU* 5.4 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 60 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57D GLU* 3.2 54.0 + - - +
59D ARG* 1.3 79.6 - - - +
61D THR* 1.3 71.1 + - + +
63D LEU* 3.3 13.1 + - + +
64D GLU* 3.3 21.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 61 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D ASP* 4.2 16.5 + - + +
15D GLY* 4.0 26.7 + - - -
51D ASP* 4.6 4.7 + - - -
56D VAL 5.3 0.2 + - - -
57D GLU* 2.7 44.5 + - + +
58D LYS* 3.3 10.2 + - - -
60D LYS* 1.3 81.5 - - + +
62D MET* 1.3 58.5 + - - +
64D GLU* 3.4 11.7 + - - +
65D LEU* 3.1 25.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 62 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D VAL* 3.8 31.9 - - + -
15D GLY* 5.3 0.9 - - - -
49D PHE* 4.8 5.6 - - + +
51D ASP* 4.1 24.5 - - + +
58D LYS* 2.7 30.6 + - + +
59D ARG* 3.9 2.9 - - - +
61D THR* 1.3 74.2 + - - +
63D LEU* 1.3 64.0 + - - +
65D LEU* 3.2 19.8 + - + +
66D VAL* 2.9 22.9 + - - +
79D VAL* 3.9 27.4 - - + -
80D GLY 5.6 2.2 - - - +
92D LEU* 3.7 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 63 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59D ARG* 3.1 29.3 + - + +
60D LYS* 3.7 9.6 - - + +
61D THR 3.3 0.2 - - - -
62D MET* 1.3 76.4 - - - +
64D GLU* 1.3 62.0 + - - +
66D VAL* 3.3 3.7 + - - +
67D GLU* 3.0 32.1 + - - +
88D THR* 5.2 0.7 - - + +
91D GLU* 3.5 38.1 - - + +
92D LEU* 3.7 23.6 - - + -
95D ARG* 3.6 34.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 64 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60D LYS 3.3 10.1 + - - +
61D THR* 3.7 13.2 - - - +
62D MET 3.3 0.2 - - - -
63D LEU* 1.3 78.3 - - - +
65D LEU* 1.3 61.9 + - - +
67D GLU* 3.3 16.0 + - - +
68D LYS* 3.1 44.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 65 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D VAL* 3.9 32.1 - - + -
15D GLY* 3.7 24.0 - - - +
32D PRO* 3.8 22.9 - - + -
49D PHE* 4.1 18.4 - - + -
61D THR 3.1 13.8 + - - +
62D MET* 3.2 26.2 + - + +
64D GLU* 1.3 75.6 - - - +
66D VAL* 1.3 66.7 + - + +
68D LYS* 3.3 11.3 + - - +
69D VAL* 2.9 48.4 + - + +
77D PHE* 5.1 0.7 - - + -
79D VAL* 4.9 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 66 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62D MET* 2.9 20.8 + - + +
63D LEU* 3.6 5.6 - - - +
65D LEU* 1.3 79.3 - - + +
67D GLU* 1.3 63.2 + - - +
70D ALA* 2.9 25.1 + - - +
77D PHE* 4.1 9.8 - - + -
79D VAL* 3.7 30.3 - - + -
92D LEU* 3.6 27.1 - - + +
95D ARG* 3.7 15.0 - - + +
96D GLY 3.9 0.9 - - - -
97D ALA* 3.4 30.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 67 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63D LEU* 3.0 20.6 + - - +
64D GLU* 3.6 17.2 - - - +
65D LEU 3.3 0.2 - - - -
66D VAL* 1.3 77.3 - - - +
68D LYS* 1.3 63.2 + - + +
70D ALA* 4.2 1.9 - - - +
71D GLU* 3.6 24.2 + - - +
95D ARG* 3.2 47.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 68 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D GLY 5.0 4.8 + - - -
16D ARG* 5.9 2.4 - - - +
31D ASP* 4.9 6.3 + - - -
32D PRO* 4.6 16.7 - - - +
33D VAL* 3.7 19.0 - - + +
64D GLU* 3.1 43.0 + - + +
65D LEU* 3.9 6.5 - - - +
67D GLU* 1.3 76.4 - - + +
69D VAL* 1.3 65.5 + - + +
71D GLU* 3.3 27.1 - - - +
72D GLN* 3.6 12.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 69 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32D PRO* 3.8 36.3 - - + +
33D VAL* 4.2 7.9 - - + -
49D PHE* 3.9 17.5 - - + -
65D LEU* 2.9 32.8 + - + +
66D VAL 4.1 1.6 - - - +
68D LYS* 1.3 71.9 - - - +
70D ALA* 1.3 64.0 + - - +
72D GLN* 3.0 13.6 + - - -
73D ILE* 3.0 47.2 + - + +
77D PHE* 3.7 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 70 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66D VAL 2.9 18.4 + - - +
67D GLU 4.2 2.7 - - - +
69D VAL* 1.3 78.0 - - - +
71D GLU* 1.3 60.1 + - - +
72D GLN 3.5 0.2 + - - -
73D ILE* 3.9 12.0 - - - +
77D PHE* 3.9 11.6 - - + -
95D ARG 3.8 5.6 - - - +
96D GLY* 3.7 34.5 - - - +
----------------------------------------------------------
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