Contacts of the helix formed by residues 65 - 75 (chain D) in PDB entry 3NBN
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 65 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D GLY 3.8 15.8 - - - +
31D ASP 3.9 3.4 - - - -
32D GLN* 3.8 14.7 + - - +
63D GLY 2.7 4.8 + - - -
64D SER* 1.3 74.8 - - - +
66D TRP* 1.3 66.5 + - - +
67D LYS 3.1 2.3 - - - +
68D LYS* 3.5 21.9 + - - +
69D LYS* 3.3 20.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 66 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32D GLN* 3.8 28.7 - - + -
33D THR 3.3 32.3 + - - +
34D VAL* 4.4 7.2 - - + -
61D LEU* 3.2 42.5 - - + +
62D MET 2.9 29.6 + - - -
63D GLY 3.4 13.6 + - - +
65D GLY* 1.3 76.8 - - - +
67D LYS* 1.3 57.8 + - - +
69D LYS* 3.1 6.8 + - + +
70D LYS* 3.0 28.2 + - - +
85D PRO* 4.3 23.8 - - + -
131D MET* 4.0 25.1 - - + -
133D TYR* 4.0 15.3 - + - -
139D ILE* 4.9 1.6 - - + -
326D PHE* 4.7 6.5 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 67 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64D SER* 5.8 0.7 - - - -
65D GLY 4.1 1.5 - - - +
66D TRP* 1.3 75.1 - - - +
68D LYS* 1.3 75.0 + - - +
69D LYS 3.0 0.9 - - - -
70D LYS* 2.8 29.8 + - + +
71D GLU* 2.8 36.9 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
30D GLY* 5.0 8.7 - - - +
64D SER* 3.4 35.9 + - - +
65D GLY* 3.5 11.0 - - - +
66D TRP 3.5 0.2 - - - -
67D LYS* 1.3 107.6 - - - +
69D LYS* 1.3 57.8 + - - +
71D GLU* 3.8 18.8 - - - +
72D GLN* 3.0 32.6 + - - +
75D ARG* 4.7 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 69 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32D GLN* 3.8 13.7 - - - +
65D GLY 3.3 12.3 + - - +
66D TRP* 3.1 11.1 + - + +
67D LYS 3.0 1.2 - - - -
68D LYS* 1.3 75.7 - - - +
70D LYS* 1.3 62.9 + - - +
72D GLN* 3.6 25.8 - - + +
73D MET* 2.9 46.0 + - + +
133D TYR* 3.5 42.9 - - + +
137D ASP* 5.8 1.0 + - - -
328D GLU* 3.0 40.1 + - + +
332D PRO* 4.8 8.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 70 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66D TRP 3.0 12.0 + - - +
67D LYS* 2.8 15.0 + - + +
69D LYS* 1.3 73.9 - - - +
71D GLU* 1.3 65.4 - - + +
73D MET* 3.5 1.2 + - - +
74D GLU* 3.2 33.3 + - - +
80D GLU* 3.2 45.0 + - - +
83D SER* 2.9 43.2 + - - +
84D GLN* 4.9 7.6 + - - +
85D PRO* 4.9 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 71 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67D LYS* 2.8 53.5 + - + +
68D LYS* 3.8 21.5 + - - +
70D LYS* 1.3 71.8 - - + +
72D GLN* 1.3 66.6 + - - +
73D MET 3.1 1.2 + - - -
74D GLU* 4.0 2.8 - - - +
75D ARG* 3.1 41.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 72 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68D LYS 3.0 21.3 + - - +
69D LYS* 3.6 25.6 - - + +
71D GLU* 1.3 70.9 - - - +
73D MET* 1.3 60.9 + - - +
75D ARG* 3.0 32.7 + - - +
76D ASP* 2.6 40.6 + - - +
331D GLY* 5.4 1.6 - - - -
332D PRO* 3.9 27.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 73 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69D LYS* 2.9 42.5 + - - +
70D LYS 3.7 3.8 - - - +
71D GLU 3.2 1.0 - - - -
72D GLN* 1.3 79.6 - - - +
74D GLU* 1.3 63.6 + - - +
76D ASP* 3.0 25.2 + - - +
78D CYS* 3.1 27.3 - - + -
83D SER* 4.1 24.7 - - - -
133D TYR* 4.2 28.3 - - + -
135D ASN* 3.1 37.0 - - - +
137D ASP* 4.0 8.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 74 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70D LYS* 3.2 19.6 + - - +
71D GLU* 4.1 2.9 - - - +
73D MET* 1.3 73.7 - - - +
75D ARG* 1.3 53.3 + - + +
76D ASP 2.6 17.7 + - - -
77D GLY* 2.7 13.5 + - - -
78D CYS* 3.2 28.1 + - - +
79D SER 3.1 19.8 - - - +
80D GLU* 3.0 34.4 + - - +
83D SER* 3.6 15.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 75 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68D LYS 4.7 1.0 + - - -
71D GLU* 3.1 29.1 + - - +
72D GLN* 3.0 41.7 + - - +
74D GLU* 1.3 71.4 - - + +
76D ASP* 1.3 65.1 + - - +
77D GLY 3.7 0.2 - - - -
----------------------------------------------------------
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