Contacts of the helix formed by residues 110 - 116 (chain D) 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 D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D LEU* 5.4 3.6 - - - +
78D VAL* 3.5 41.1 + - + +
107D ASP* 2.9 24.9 + - - +
108D PRO* 2.8 32.7 + - - +
109D LYS* 1.3 78.5 - - - +
111D THR* 1.3 57.8 + - - +
113D ALA* 3.7 2.4 + - - +
114D GLN* 3.1 37.9 + - - +
119D LEU* 3.7 20.6 - - + +
123D GLU 5.6 1.2 + - - -
124D GLY* 2.9 27.3 + - - +
125D ILE* 5.4 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 111 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107D ASP* 3.2 5.4 + - - -
109D LYS* 3.7 31.6 - - + +
110D ARG* 1.3 76.3 - - - +
112D ILE* 1.3 66.5 + - - +
114D GLN* 3.8 18.5 - - - +
115D ASP* 3.0 34.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 112 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D PHE* 3.8 46.0 - - + -
16D LYS 5.2 1.1 - - - +
17D ALA* 3.7 30.5 - - + -
41D PHE* 4.4 1.8 - - + -
43D PHE* 3.8 18.8 - - + -
105D VAL* 4.1 11.0 - - + -
106D SER 4.2 3.8 - - - +
107D ASP* 2.9 20.2 + - + +
111D THR* 1.3 79.5 - - - +
113D ALA* 1.3 59.2 + - - +
115D ASP* 3.2 5.3 + - - +
116D TYR* 2.8 39.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 113 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43D PHE* 3.7 14.7 - - + -
78D VAL* 4.4 7.0 - - + -
107D ASP* 2.8 20.4 + - - +
110D ARG 3.8 4.9 - - - +
112D ILE* 1.3 73.5 - - - +
114D GLN* 1.3 60.9 + - - +
116D TYR 3.4 0.2 + - - -
117D GLY 3.2 3.3 + - - -
118D VAL* 3.0 48.1 + - + +
119D LEU* 3.5 21.9 + - + -
126D SER* 4.4 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 114 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0C HIS 4.4 0.5 - - - +
4D GLY* 3.2 17.2 + - - +
109D LYS 3.9 4.2 - - - +
110D ARG* 3.1 41.0 + - - +
111D THR* 3.8 19.5 + - - +
113D ALA* 1.3 73.3 - - - +
115D ASP* 1.3 67.7 + - - +
117D GLY* 3.0 12.5 + - - -
119D LEU* 3.1 28.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 115 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D GLY* 4.4 0.4 - - - -
5D ASN* 2.9 44.2 + - - +
6D ALA* 3.0 11.6 + - - +
13D PRO* 4.0 21.0 - - + +
14D ASN 4.9 6.4 - - - +
15D PHE* 6.2 0.3 - - - +
111D THR* 3.0 22.8 + - - +
112D ILE* 3.5 6.6 - - - +
114D GLN* 1.3 82.2 + - - +
116D TYR* 1.3 61.3 + - + +
117D GLY 3.1 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 116 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C MET* 5.8 0.5 - - - +
6D ALA* 4.0 12.8 - - + +
12D ALA* 3.5 15.8 - - + +
13D PRO* 2.6 53.2 + - + -
15D PHE* 4.1 15.1 - + - -
31D LEU* 3.8 8.7 - - - +
41D PHE* 3.7 29.6 - + - -
43D PHE* 4.3 3.4 - - + -
112D ILE* 2.8 31.1 + - + +
113D ALA 3.4 3.6 + - - +
115D ASP* 1.3 75.9 - - + +
117D GLY* 1.3 61.8 + - - +
118D VAL* 3.4 7.7 - - + +
131D PHE* 3.3 62.0 - + + -
133D ILE* 5.1 0.7 - - + -
139D LEU* 5.2 1.6 - - + -
142D ILE* 5.4 1.4 - - - +
144D VAL* 5.4 1.0 - - - +
----------------------------------------------------------
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