Contacts of the helix formed by residues 50 - 60 (chain A) in PDB entry 2D4H
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 50 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A THR* 1.3 77.8 - - - +
51A LYS* 1.3 62.7 + - - +
52A SER 3.3 2.7 - - - -
53A TYR* 3.4 13.6 + - - +
129A ASN* 4.3 0.2 - - - -
183A ARG* 2.6 26.1 + - - -
593A 5GP 2.8 44.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ILE* 3.8 20.4 - - + +
44A VAL 3.8 27.6 - - - +
45A GLY* 3.8 5.1 + - - +
46A LEU 2.8 31.5 + - - -
47A TYR* 3.5 10.3 - - - +
49A THR* 3.5 10.3 - - - +
50A GLY* 1.3 76.6 - - - +
52A SER* 1.3 63.6 + - - +
54A LEU* 2.9 18.2 + - - +
55A MET* 3.1 11.8 + - - +
97A ASP* 3.8 20.2 - - - +
98A THR 3.4 25.2 + - - -
99A GLU* 5.4 1.9 - - - +
100A GLY 5.4 0.2 - - - +
129A ASN* 3.6 15.9 - - + +
183A ARG* 4.5 1.8 - - - +
593A 5GP 2.9 18.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A LYS* 1.3 73.5 - - - +
53A TYR* 1.3 56.0 + - - +
55A MET* 3.2 8.7 + - - +
56A ASN* 2.9 42.8 + - - -
64A GLY 4.8 1.9 + - - -
66A SER* 4.4 14.0 + - - -
97A ASP* 4.3 4.7 + - - -
99A GLU* 6.1 1.1 - - - -
252A LYS* 5.5 3.1 - - - -
593A 5GP 2.8 30.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A GLY 3.4 12.8 + - - +
51A LYS 3.2 0.6 - - - -
52A SER* 1.3 74.6 - - - +
54A LEU* 1.3 63.1 + - + +
56A ASN* 4.0 0.2 - - - +
57A LYS* 2.9 51.0 + - + +
64A GLY 2.9 31.2 - - - +
65A PHE* 3.3 35.7 - + + +
183A ARG* 4.7 1.3 - - - +
255A ASP* 3.0 28.0 + - - -
258A LEU* 3.7 9.9 - - + +
262A PHE* 3.4 32.5 - + - -
263A VAL* 4.2 9.9 - - - +
266A VAL* 3.5 31.6 - - + -
593A 5GP 4.7 7.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ILE* 3.8 27.1 - - + -
51A LYS* 2.9 8.8 + - - +
53A TYR* 1.3 76.7 - - + +
55A MET* 1.3 57.3 + - - +
57A LYS* 3.8 4.4 - - - +
58A LEU* 2.8 37.6 + - - +
127A VAL* 4.5 0.9 - - + -
129A ASN* 3.7 16.4 - - - +
181A THR* 3.8 16.2 - - + +
183A ARG* 3.2 29.8 - - - +
238A PHE* 3.7 21.3 - - + -
266A VAL* 3.8 18.4 - - + -
269A PHE* 3.9 23.1 - - + -
270A CYS* 4.8 0.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 55 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A PRO* 3.9 29.6 - - + -
43A ILE* 4.3 12.6 - - + -
51A LYS 3.1 9.0 + - - +
52A SER* 3.2 11.9 + - - +
54A LEU* 1.3 76.9 - - - +
56A ASN* 1.3 56.7 + - - +
58A LEU* 3.1 7.3 + - - +
59A ALA* 2.7 37.3 + - - +
79A TRP* 5.0 6.3 - - + +
80A MET 5.2 0.2 - - - -
81A TRP* 4.0 15.0 - - + -
95A LEU* 3.8 35.5 - - - +
96A LEU 4.4 2.2 - - - +
97A ASP* 3.5 43.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 56 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A PRO* 5.6 1.2 - - - +
52A SER* 2.9 28.0 + - - +
53A TYR 4.0 0.2 - - - +
55A MET* 1.3 77.2 - - - +
57A LYS* 1.3 61.2 + - - +
59A ALA 3.2 1.2 + - - -
60A GLY 3.1 4.5 + - - -
61A LYS* 2.9 40.9 + - + +
64A GLY* 3.3 32.5 - - - +
81A TRP* 3.2 28.9 - - - -
252A LYS* 3.2 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 57 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A TYR* 2.9 46.4 + - + +
54A LEU 3.9 1.8 - - - +
56A ASN* 1.3 76.2 - - - +
58A LEU* 1.3 60.9 + - - +
60A GLY* 3.4 12.4 + - - -
61A LYS 3.0 28.7 + - - -
62A LYS* 3.1 15.7 + - - +
64A GLY* 4.2 8.9 - - - +
255A ASP* 2.8 33.0 + - - +
263A VAL 6.1 0.2 - - - +
266A VAL* 4.0 20.2 - - + +
267A ALA* 5.5 2.5 - - + +
270A CYS* 3.7 23.4 - - - -
274A PHE* 4.3 5.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A VAL* 4.8 1.6 - - + -
43A ILE* 3.8 21.5 - - + -
54A LEU 2.8 21.8 + - - +
55A MET 3.5 3.6 - - - +
57A LYS* 1.3 71.9 - - - +
59A ALA* 1.3 61.9 + - - +
60A GLY* 3.1 5.8 + - - -
83A VAL* 4.4 1.6 - - - +
86A PRO* 5.2 1.4 - - - +
93A LEU* 3.9 11.1 - - + +
95A LEU* 3.8 26.5 - - + -
269A PHE* 3.7 20.6 - - + -
270A CYS* 3.5 32.3 - - - -
273A ILE* 3.9 21.5 - - + -
274A PHE* 3.6 37.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A MET 2.7 19.5 + - - +
56A ASN 3.2 5.6 + - - +
58A LEU* 1.3 72.6 - - - +
60A GLY* 1.3 56.9 + - - +
61A LYS 3.3 3.6 + - - +
81A TRP* 3.6 42.1 - - + -
83A VAL* 3.6 29.5 - - + +
95A LEU* 3.6 9.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A ASN 3.1 2.4 + - - -
57A LYS* 3.4 9.6 + - - -
58A LEU 3.1 5.8 + - - -
59A ALA* 1.3 78.6 - - - +
61A LYS* 1.3 65.3 + - - +
62A LYS* 3.4 7.0 + - - +
274A PHE* 5.9 2.0 - - - -
----------------------------------------------------------
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