Contacts of the helix formed by residues 52 - 62 (chain F) in PDB entry 4XCS
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 CYS 52 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173E CYS* 2.1 70.9 - - + +
174E PRO* 3.4 13.6 + - - -
175E ALA* 4.3 1.4 - - - +
50F PHE 4.1 0.8 + - - -
51F VAL* 1.3 76.0 - - - +
53F PRO* 1.3 72.9 - - - +
54F THR* 2.9 17.7 - - - -
55F GLU* 3.0 22.5 + - + +
56F ILE 4.0 0.9 + - - -
150F GLY* 5.9 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 53 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174E PRO 4.0 4.9 - - - +
176E GLY* 3.8 20.6 - - - -
48F PHE 5.3 0.7 - - - +
51F VAL* 3.1 12.1 - - + +
52F CYS* 1.3 86.0 - - - +
54F THR* 1.3 59.9 + - + +
56F ILE* 3.2 10.1 + - + +
57F ILE* 2.9 40.0 + - + +
87F TRP* 4.4 8.3 - - + -
95F GLY 4.2 13.7 - - - +
96F GLY 4.5 6.3 - - - +
97F LEU* 3.9 23.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 54 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173E CYS* 3.1 8.0 - - - -
201E CPS 6.1 5.6 - - - +
52F CYS* 2.9 24.3 - - - -
53F PRO* 1.3 77.2 - - + +
55F GLU* 1.3 63.3 + - - +
57F ILE* 3.9 13.4 - - + +
58F ALA* 3.0 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 55 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173E CYS* 4.3 1.2 - - - -
42F PHE* 5.3 5.1 - - + -
44F TYR* 2.6 28.0 + - - +
51F VAL* 5.2 0.3 - - - +
52F CYS* 3.0 18.7 + - + +
54F THR* 1.3 81.7 + - - +
56F ILE* 1.3 62.9 + - - +
58F ALA* 3.4 8.2 + - - +
59F PHE* 3.3 30.4 + - + -
128F ARG* 2.8 38.4 + - - -
150F GLY* 3.4 12.0 - - - -
151F ARG* 2.8 44.9 + - + +
201F GOL 4.4 1.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 56 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42F PHE* 6.5 0.9 - - - -
44F TYR* 3.4 24.2 - - + +
48F PHE* 3.5 37.7 - - + -
51F VAL* 3.6 20.2 - - + -
52F CYS 4.6 0.2 - - - +
53F PRO* 3.2 7.1 + - + +
55F GLU* 1.3 76.0 - - - +
57F ILE* 1.3 62.5 - - - +
59F PHE* 3.2 7.7 + - - +
60F SER* 2.9 25.8 + - - -
75F GLY* 6.1 1.6 - - - -
97F LEU* 4.2 19.3 - - + -
100F MET* 3.8 23.3 - - - -
102F ILE* 4.6 12.1 - - + +
104F LEU* 4.7 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 57 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53F PRO* 2.9 32.5 + - + +
54F THR* 3.9 14.1 - - + +
55F GLU 3.3 0.2 - - - -
56F ILE* 1.3 77.9 - - - +
58F ALA* 1.3 52.2 + - - +
60F SER* 3.2 6.4 + - - -
61F ASP* 2.7 56.1 + - - +
92F LYS* 4.0 30.1 - - + +
96F GLY 4.1 13.0 - - - +
97F LEU* 3.8 28.0 - - + +
100F MET* 4.1 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 58 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54F THR 3.0 18.3 + - - +
55F GLU* 3.7 5.6 - - - +
56F ILE 3.3 0.2 - - - -
57F ILE* 1.3 78.3 - - - +
59F PHE* 1.3 58.0 + - + +
61F ASP* 3.7 7.1 - - - +
62F ARG* 3.1 34.6 + - - +
151F ARG 5.8 1.8 - - - +
153F VAL* 3.8 18.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 59 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40F VAL* 5.1 0.4 - - + -
42F PHE* 3.5 43.7 - + + -
55F GLU* 3.3 25.2 + - + -
56F ILE* 3.2 10.3 + - - +
58F ALA* 1.3 77.2 - - - +
60F SER* 1.3 65.2 + - - +
62F ARG* 3.3 2.6 + - - -
63F ALA* 3.0 24.4 + - - +
66F PHE* 3.8 37.3 - + - -
73F VAL* 4.5 11.7 - - + +
102F ILE* 4.6 5.8 - - + +
151F ARG* 3.6 31.0 - - + -
153F VAL* 3.6 26.0 - - + -
156F THR* 3.6 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 60 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56F ILE 2.9 13.6 + - - -
57F ILE 3.5 7.0 - - - -
59F PHE* 1.3 75.7 - - - +
61F ASP* 1.3 65.6 + - - +
63F ALA* 3.2 10.0 + - - +
99F PRO 4.3 1.6 + - - -
100F MET* 3.3 30.5 - - - +
101F ASN* 2.8 52.0 + - - +
102F ILE* 4.2 17.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 61 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57F ILE* 2.7 44.5 + - - +
58F ALA* 3.7 8.2 - - - +
60F SER* 1.3 77.2 + - - +
62F ARG* 1.3 65.5 + - + +
63F ALA 3.6 0.7 + - - -
64F GLU* 5.0 1.9 + - - +
92F LYS* 4.4 12.4 + - - -
101F ASN* 4.3 8.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 62 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58F ALA* 3.1 18.5 + - - +
59F PHE 3.6 2.7 - - - +
60F SER 3.3 0.4 - - - -
61F ASP* 1.3 85.1 - - + +
63F ALA* 1.3 64.1 + - - +
64F GLU* 3.0 4.3 - - - -
65F GLU* 2.8 62.0 + - - +
66F PHE* 3.7 7.0 - - + -
153F VAL* 3.4 37.6 - - + +
154F ASP* 3.2 29.5 + - - -
157F LEU* 3.7 8.3 - - - +
----------------------------------------------------------
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