Contacts of the helix formed by residues 110 - 116 (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 ARG 110 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45F PRO 4.9 2.6 + - - +
46F LEU* 5.8 3.8 - - - +
47F ASP* 6.1 0.2 - - - +
78F VAL* 3.5 56.8 + - + +
107F ASP* 2.9 22.5 + - - -
108F PRO* 3.0 21.6 + - - +
109F LYS* 1.3 78.0 - - - +
111F THR* 1.3 59.3 + - - +
113F ALA* 3.9 2.7 - - + -
114F GLN* 2.9 34.5 + - - +
119F LEU* 3.8 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 111 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107F ASP* 3.1 7.0 + - - -
109F LYS* 3.9 24.3 - - + +
110F ARG* 1.3 75.1 - - - +
112F ILE* 1.3 70.3 + - - +
114F GLN* 3.6 10.1 + - - +
115F ASP* 3.1 31.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 112 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15F PHE* 3.8 33.4 - - + -
17F ALA* 4.1 9.0 - - + -
41F PHE* 4.1 11.0 - - + -
43F PHE* 3.6 21.1 - - + -
105F VAL* 3.9 29.2 - - + -
106F SER 4.5 0.4 - - - +
107F ASP* 2.8 25.6 + - + +
111F THR* 1.3 79.8 - - - +
113F ALA* 1.3 66.4 + - - +
115F ASP* 3.2 5.0 + - - -
116F TYR* 2.9 42.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 113 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43F PHE* 3.5 28.7 - - + -
45F PRO* 5.3 0.7 - - + -
78F VAL* 4.8 1.1 - - + -
107F ASP* 2.9 12.0 + - - +
110F ARG* 3.7 13.7 - - + +
111F THR 3.3 0.2 - - - -
112F ILE* 1.3 78.1 - - - +
114F GLN* 1.3 60.0 + - - +
116F TYR 3.3 0.2 + - - -
117F GLY 3.1 4.0 + - - -
118F VAL* 2.9 34.1 + - - +
119F LEU* 4.0 25.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 114 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3F SER* 5.7 0.2 - - - -
4F GLY* 3.2 20.8 + - - -
5F ASN* 5.0 0.8 - - - +
109F LYS 4.2 7.1 + - - -
110F ARG* 2.9 32.2 + - - +
111F THR* 3.9 11.3 - - - +
112F ILE 3.2 0.2 - - - -
113F ALA* 1.3 71.8 - - - +
115F ASP* 1.3 66.4 + - - +
117F GLY* 3.2 4.7 + - - -
118F VAL 5.2 0.2 - - - +
119F LEU* 3.6 33.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 115 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5F ASN* 2.7 48.6 + - - +
6F ALA* 3.0 11.1 + - - +
13F PRO* 3.9 18.5 - - + +
14F ASN 4.4 8.7 - - - +
15F PHE* 6.1 0.2 - - - +
111F THR* 3.1 19.0 + - - +
112F ILE* 3.6 5.6 - - - +
114F GLN* 1.3 81.8 - - - +
116F TYR* 1.3 66.7 + - + +
117F GLY 3.2 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 116 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3F SER 5.1 0.2 - - - -
6F ALA* 4.1 13.2 - - + +
12F ALA* 3.5 6.5 - - + +
13F PRO* 2.6 54.2 + - + -
14F ASN 5.5 0.7 - - - -
15F PHE* 4.4 6.5 - + + -
31F LEU* 3.4 17.3 - - - +
41F PHE* 4.1 21.3 - + + -
43F PHE* 5.6 0.9 - - + -
112F ILE* 2.9 37.9 + - + +
114F GLN 3.2 0.2 - - - -
115F ASP* 1.3 81.0 - - + +
117F GLY* 1.3 62.1 + - - +
118F VAL* 3.3 10.3 - - + +
131F PHE* 3.5 62.3 - + + -
133F ILE* 4.8 2.3 - - + +
139F LEU* 4.8 2.9 - - + -
142F ILE* 5.6 1.9 - - - +
----------------------------------------------------------
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