Contacts of the helix formed by residues 81 - 90 (chain D) in PDB entry 3M0A
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 SER 81 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76D TRP* 4.6 1.3 - - - -
79D GLY 3.8 3.9 + - - -
80D ASP* 1.3 73.3 - - - +
82D PRO* 1.4 56.6 - - - +
83D THR* 3.7 9.2 + - - -
84D GLU* 3.3 27.5 + - - +
85D LYS* 2.8 38.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 82 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D VAL* 3.9 7.0 - - + -
49D SER* 3.5 32.5 - - - +
50D LEU* 3.9 15.3 - - + -
53D ALA* 3.8 18.2 - - + -
55D PHE* 3.9 5.0 - - + -
76D TRP* 3.6 32.7 - - + -
80D ASP 3.6 8.7 - - - +
81D SER* 1.4 80.0 - - - +
83D THR* 1.3 61.4 + - - +
85D LYS* 4.1 1.1 - - + +
86D HIS* 2.8 34.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 83 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49D SER* 4.8 4.7 + - - -
52D ARG* 5.7 3.6 - - - +
53D ALA* 3.7 20.0 + - + +
81D SER* 3.2 8.3 + - - -
82D PRO* 1.3 81.4 - - - +
84D GLU* 1.3 64.9 + - - +
86D HIS* 3.4 4.2 - - - +
87D LYS* 3.2 17.0 + - - +
96D VAL* 5.1 1.9 - - - +
98D SER 5.7 5.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 84 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81D SER* 3.2 22.7 + - - +
83D THR* 1.3 76.5 - - - +
85D LYS* 1.3 55.6 + - - +
87D LYS* 2.8 30.5 + - - +
88D LYS* 3.0 24.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 85 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73D LEU* 4.2 25.3 - - + +
74D ASP 5.0 9.5 + - - -
75D ASN 5.7 1.4 + - - -
76D TRP* 4.2 14.3 - - + -
80D ASP* 3.7 24.8 + - + +
81D SER 2.8 22.4 + - - +
82D PRO* 4.1 4.9 - - + +
84D GLU* 1.3 70.8 - - - +
86D HIS* 1.3 61.7 + - - +
88D LYS* 4.1 15.9 - - + +
89D LEU* 3.3 43.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 86 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53D ALA* 2.8 28.3 + - - +
55D PHE* 3.6 11.3 - + + -
66D CYS* 3.4 17.4 - - + +
69D CYS* 3.7 3.1 - - - -
71D LEU* 3.4 26.2 - - + +
73D LEU* 4.7 0.8 - - - +
82D PRO 2.8 24.4 + - - +
83D THR* 3.4 6.7 - - - +
84D GLU 3.0 0.6 + - - -
85D LYS* 1.3 70.0 - - - +
87D LYS* 1.4 64.9 + - - +
89D LEU* 2.9 14.6 + - - +
90D TYR 3.3 14.3 + - - +
93D CYS* 4.0 0.8 - - - -
95D PHE* 4.2 9.4 - + - -
96D VAL* 4.3 18.6 - - + +
401D ZN 2.2 35.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 87 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83D THR 3.2 8.0 + - - +
84D GLU* 2.8 15.3 + - - +
86D HIS* 1.4 73.2 - - - +
88D LYS* 1.3 61.7 + - - +
89D LEU 3.2 1.6 + - - -
90D TYR 3.7 0.7 + - - -
91D PRO* 3.5 29.3 - - + +
96D VAL* 3.8 21.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 88 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84D GLU* 3.0 35.0 + - + +
85D LYS* 4.0 14.8 - - - +
87D LYS* 1.3 71.5 - - - +
89D LEU* 1.3 68.7 + - + +
90D TYR 3.6 0.2 - - - -
91D PRO* 5.1 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 89 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71D LEU* 4.1 19.4 - - + +
73D LEU* 3.7 25.4 - - + -
85D LYS* 3.3 39.7 + - + +
86D HIS 2.9 4.5 + - - +
88D LYS* 1.3 89.7 - - + +
90D TYR* 1.3 66.3 + - - +
91D PRO* 4.3 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 90 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69D CYS* 3.9 42.5 + - + +
71D LEU* 4.3 26.0 - - + -
86D HIS* 3.3 8.0 + - - +
87D LYS 4.1 1.8 - - - -
89D LEU* 1.3 82.1 - - - +
91D PRO* 1.3 69.3 - - - +
92D SER* 3.1 26.7 - - - -
93D CYS* 3.6 19.4 - - - +
96D VAL* 3.6 4.7 - - - +
----------------------------------------------------------
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