Contacts of the helix formed by residues 80 - 89 (chain A) 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 SER 80 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A VAL 3.7 1.6 + - - -
79A ASP* 1.3 78.6 - - - +
81A HIS* 1.3 67.3 + - - +
82A PHE* 3.5 7.6 + - - +
83A SER* 3.2 23.6 + - - -
84A HIS* 3.1 19.6 + - - -
106A SER* 3.7 3.1 - - - -
108A PRO* 4.2 20.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A THR* 4.0 26.5 - - + +
20A VAL* 3.6 10.7 - - + +
26A PHE* 3.4 46.4 - + + -
80A SER* 1.3 76.5 - - - +
82A PHE* 1.3 87.8 + + - +
84A HIS* 3.3 7.5 + - - +
85A LEU 3.0 21.1 + - - -
106A SER* 3.4 23.0 + - - +
108A PRO* 5.3 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A PHE* 3.7 30.5 - + - -
80A SER* 3.2 7.2 + - - +
81A HIS* 1.3 106.6 - + - +
83A SER* 1.3 58.3 + - - +
85A LEU* 3.6 15.9 - - + +
86A ALA* 2.9 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A ASP* 2.6 27.9 + - - -
80A SER* 3.2 26.2 + - - -
82A PHE* 1.3 73.8 - - - +
84A HIS* 1.3 67.1 + - - +
86A ALA* 3.1 8.0 + - - +
87A TRP* 2.9 33.6 + - - -
202A CPS 5.1 5.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A VAL* 3.8 13.2 - - + +
48A PHE* 3.4 31.1 - + - -
76A ALA 4.9 0.2 - - - -
77A SER* 2.8 24.5 + - - -
79A ASP* 3.5 15.2 - - + +
80A SER 3.1 8.3 + - - -
81A HIS* 3.6 8.9 - - - +
82A PHE 3.2 0.4 - - - -
83A SER* 1.3 77.5 - - - +
85A LEU* 1.3 62.0 + - - +
87A TRP* 3.1 4.9 + - - +
88A VAL* 3.0 27.7 + - - +
104A LEU* 3.9 26.9 + - + -
105A VAL 3.2 32.1 - - - -
106A SER* 3.7 20.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A VAL* 3.9 6.4 - - + +
24A GLY* 4.1 20.9 - - - +
26A PHE* 4.0 27.4 - - + -
81A HIS 3.0 14.4 + - - +
82A PHE* 3.6 18.4 - - + +
83A SER 3.2 0.2 - - - -
84A HIS* 1.3 75.8 - - - +
86A ALA* 1.3 63.8 + - - +
88A VAL* 3.3 15.3 + - + +
89A ASN* 3.0 36.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A PHE 2.9 16.6 + - - +
83A SER* 3.1 7.6 + - - +
85A LEU* 1.3 77.1 - - - +
87A TRP* 1.3 57.2 + - - +
89A ASN* 3.4 7.2 + - - +
90A THR* 2.7 33.8 + - - -
202A CPS 3.9 28.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ASP* 5.4 0.4 + - - -
48A PHE* 3.5 38.3 - + + +
49A THR* 3.5 30.2 - - + +
53A PRO* 4.4 11.7 - - + -
79A ASP* 4.1 4.1 + - - -
83A SER* 2.9 36.8 + - - +
84A HIS* 3.1 8.9 + - - +
86A ALA* 1.3 78.3 - - - +
88A VAL* 1.3 62.4 + - - +
90A THR* 3.2 11.3 + - - +
95A GLY 3.5 22.2 - - - -
96A GLY* 3.9 17.5 - - - -
97A LEU* 3.1 46.0 + - + -
202A CPS 3.7 58.9 - - + +
176B GLY* 4.5 7.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A VAL* 4.1 17.9 - - + -
22A PRO 5.9 2.5 - - - +
24A GLY* 5.4 3.8 - - - -
84A HIS 3.0 15.8 + - - +
85A LEU* 3.5 21.5 - - + +
87A TRP* 1.3 78.4 - - - +
89A ASN* 1.3 60.0 + - + +
90A THR 3.2 3.7 + - - -
97A LEU* 4.2 5.6 - - + -
98A GLY* 3.1 37.3 - - - +
99A PRO* 3.7 6.9 - - + +
100A MET* 3.8 18.6 - - + +
104A LEU* 3.6 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A LEU* 3.0 28.3 + - + +
86A ALA* 3.6 7.2 - - - +
87A TRP 3.2 0.2 - - - -
88A VAL* 1.3 77.0 - - + +
90A THR* 1.3 56.6 + - - +
91A PRO* 3.8 7.7 - - - +
----------------------------------------------------------
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