Contacts of the helix formed by residues 80 - 89 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B VAL 3.8 0.8 + - - -
79B ASP* 1.3 79.8 - - - +
81B HIS* 1.3 62.3 + - - +
82B PHE* 3.3 22.2 + - - +
83B SER* 3.1 24.3 + - - -
84B HIS* 3.1 23.0 + - - -
106B SER* 3.6 4.5 - - - -
108B PRO* 4.3 20.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 81 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B THR* 3.6 30.4 - - + +
20B VAL* 3.4 15.0 - - + +
26B PHE* 3.4 45.6 - + + -
80B SER* 1.3 73.0 - - - +
82B PHE* 1.3 97.2 + + - +
84B HIS* 3.4 1.9 + - - -
85B LEU* 2.9 27.4 + - - +
106B SER* 3.1 22.4 + - - +
108B PRO* 6.0 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 82 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B PHE* 4.5 12.6 - + - -
80B SER* 3.3 17.2 - - - +
81B HIS* 1.3 108.0 - + - +
83B SER* 1.4 58.2 + - - +
85B LEU* 3.4 7.1 + - + +
86B ALA* 3.1 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 83 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ASP* 3.4 12.6 + - - +
79B ASP* 2.9 25.9 + - - -
80B SER* 3.1 18.1 + - - -
82B PHE* 1.4 77.4 - - - +
84B HIS* 1.3 66.6 + - - +
86B ALA* 3.3 7.6 + - - +
87B TRP* 3.0 21.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 84 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B VAL* 3.7 12.8 - - + -
44B TYR* 3.3 17.2 + + - -
47B ASP* 2.6 28.0 + - - -
76B ALA 4.9 0.2 - - - -
77B SER* 3.0 28.5 - - - -
79B ASP* 3.6 6.9 - - + +
80B SER 3.1 9.4 + - - -
81B HIS* 3.4 7.4 + - - +
83B SER* 1.3 77.5 - - - +
85B LEU* 1.3 63.4 + - - +
87B TRP* 3.2 2.5 + - - +
88B VAL* 3.0 26.5 + - - +
97B LEU* 5.0 0.9 - - - +
104B LEU* 3.3 38.8 - - + +
105B VAL 2.7 24.4 + - - -
106B SER* 3.5 18.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 85 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B VAL* 4.0 13.0 - - + +
24B GLY* 3.8 24.7 - - - +
26B PHE* 3.7 28.5 - - + -
81B HIS 2.9 18.0 + - - +
82B PHE* 3.8 5.6 - - + +
84B HIS* 1.3 76.7 - - - +
86B ALA* 1.3 57.5 + - - +
88B VAL* 3.2 12.6 + - + +
89B ASN* 2.8 50.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 86 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B PHE 3.1 17.8 + - - +
83B SER* 3.6 8.3 - - - +
84B HIS 3.2 0.2 - - - -
85B LEU* 1.3 77.8 - - - +
87B TRP* 1.3 50.2 + - - +
89B ASN* 3.4 7.0 + - - +
90B THR* 2.6 35.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 87 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ASP* 3.7 22.2 - - + +
48B PHE* 3.4 66.9 - + + -
51B VAL* 3.5 31.9 - - + -
53B PRO* 3.7 27.8 - - + -
56B ILE* 3.9 6.7 - - + -
83B SER 3.0 16.0 + - - +
84B HIS 3.8 3.6 - - - +
86B ALA* 1.3 74.7 - - - +
88B VAL* 1.3 64.4 + - - +
90B THR* 3.2 14.2 + - - +
95B GLY 3.4 16.6 + - - -
96B GLY* 3.4 20.7 - - - -
97B LEU* 2.9 54.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 88 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B VAL* 4.8 11.2 - - + -
24B GLY* 5.8 5.2 - - - -
84B HIS 3.0 18.2 + - - +
85B LEU* 3.4 18.2 - - + +
87B TRP* 1.3 79.1 - - - +
89B ASN* 1.3 65.9 + - - +
90B THR 3.3 3.1 + - - -
97B LEU* 4.1 10.1 - - + -
98B GLY* 3.4 33.3 - - - +
99B PRO* 4.4 9.9 - - + +
100B MET* 3.8 27.4 - - + +
104B LEU* 4.2 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 89 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B LEU* 2.8 42.9 + - - +
86B ALA* 3.4 7.4 + - - +
87B TRP 3.2 0.4 - - - -
88B VAL* 1.3 82.3 - - - +
90B THR* 1.3 57.7 + - - +
91B PRO* 3.5 9.1 - - - +
----------------------------------------------------------
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