Contacts of the helix formed by residues 57 - 66 (chain A) in PDB entry 4XXL
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 57 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A GLY 3.3 9.9 - - - +
49A VAL 3.6 11.7 - - - -
50A ASP 3.6 22.8 + - - -
51A LYS 3.9 9.2 - - - -
52A GLU* 4.1 8.6 + - - +
55A GLY 3.7 1.2 + - - -
56A PRO* 1.3 77.2 - - - +
58A TYR* 1.3 65.5 + - - +
59A LYS* 3.6 5.5 + - - +
60A LYS* 3.1 30.3 + - - +
61A VAL* 3.0 20.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ALA* 5.4 2.0 - - + -
43A CYS* 3.5 14.6 - - + +
44A PHE* 4.1 21.8 - + - -
47A HIS* 3.4 36.9 - + + +
48A GLY 2.9 20.4 + - - +
49A VAL* 4.3 1.8 - - - +
56A PRO 4.3 0.2 - - - -
57A SER* 1.3 75.7 - - - +
59A LYS* 1.3 57.5 + - - +
61A VAL* 3.6 9.1 - - + +
62A ALA* 2.8 30.5 + - - +
110A LEU* 5.7 0.2 - - + -
113A TRP* 4.3 14.6 - + - -
114A ILE* 3.9 40.2 - - + +
117A LEU* 3.6 22.0 - - + -
201A HEC 3.2 44.1 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A VAL* 3.0 20.8 + - + +
50A ASP* 3.5 24.0 + - + +
57A SER* 3.2 4.2 - - - +
58A TYR* 1.3 75.7 - - - +
60A LYS* 1.3 56.4 + - - +
62A ALA* 3.3 3.5 + - - +
63A GLU* 2.9 57.0 + - - +
117A LEU* 3.8 26.3 - - + +
118A TRP* 4.3 13.0 + - - -
119A SER 5.9 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A GLU* 4.5 16.8 - - - +
56A PRO* 4.4 17.0 - - + -
57A SER* 3.1 25.0 + - - +
59A LYS* 1.3 72.6 - - - +
61A VAL* 1.3 66.3 + - - +
63A GLU* 3.3 20.1 + - + +
64A LYS* 2.9 24.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A PRO* 3.8 17.3 - - + -
57A SER 3.0 13.8 + - - +
58A TYR* 3.6 15.0 - - + +
60A LYS* 1.3 78.3 - - - +
62A ALA* 1.3 64.2 + - - +
64A LYS* 3.1 7.5 + - + +
65A TYR* 3.0 39.9 + - + +
75A LEU* 4.0 11.2 - - + -
114A ILE* 4.0 5.6 - - + -
115A LEU* 5.3 0.4 - - + -
201A HEC 3.8 49.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 62 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A TYR 2.8 12.8 + - - +
59A LYS 3.5 1.6 - - - +
61A VAL* 1.3 76.6 - - - +
63A GLU* 1.3 58.3 + - - +
65A TYR* 3.3 1.7 + - - +
66A ARG* 3.0 30.0 + - - +
114A ILE 3.3 24.2 - - - +
115A LEU* 3.6 21.5 - - - +
117A LEU 3.9 0.2 - - - -
118A TRP* 3.4 31.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 63 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A LYS* 2.9 45.1 + - - +
60A LYS* 3.6 25.3 + - + +
61A VAL 3.1 0.4 - - - -
62A ALA* 1.3 77.3 - - - +
64A LYS* 1.3 62.2 + - - +
65A TYR 3.2 0.2 + - - -
66A ARG* 3.3 28.2 + - - +
118A TRP* 4.0 18.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A LYS* 2.9 16.0 + - + +
61A VAL* 3.1 11.4 + - + +
63A GLU* 1.3 77.2 - - - +
65A TYR* 1.3 89.2 + - + +
66A ARG 3.6 1.6 + - - +
68A LYS* 3.5 19.3 - - - +
201A HEC 2.7 31.0 + - - +
----------------------------------------------------------
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 VAL* 3.0 31.0 + - + +
62A ALA 3.6 0.9 - - - +
64A LYS* 1.3 106.7 + - + +
66A ARG* 1.3 68.3 + - - +
67A GLY 3.2 0.9 + - - -
68A LYS* 3.0 42.6 + - + +
71A ALA* 4.0 21.5 - - + +
74A LYS* 4.1 31.1 + - + +
75A LEU* 3.7 15.8 - - + +
115A LEU* 3.6 26.4 - - + +
201A HEC 2.6 32.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ALA 3.0 16.4 + - - +
63A GLU* 3.3 22.5 + - - +
64A LYS 3.4 1.4 - - - +
65A TYR* 1.3 77.2 - - - +
67A GLY* 1.3 60.5 + - - +
68A LYS* 3.3 6.6 + - - +
115A LEU 6.0 0.4 - - - -
118A TRP* 3.3 68.9 - - + +
----------------------------------------------------------
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