Contacts of the helix formed by residues 112 - 120 (chain A) in PDB entry 4R1Z
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 THR 112 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A PRO* 4.4 3.3 + - - +
111A ARG* 1.3 76.0 + - - +
113A VAL* 1.3 76.2 + - + +
114A THR* 3.0 9.3 + - + +
115A THR* 3.1 15.2 + - - +
116A ASP* 2.9 27.0 + - - -
224A LYS* 5.4 5.2 - - + -
225A ASP* 5.5 2.2 - - - +
226A SER* 3.3 46.0 + - - +
402A ARG* 5.8 2.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A THR* 1.3 76.9 - - + +
114A THR* 1.3 78.4 + - + +
116A ASP* 3.5 8.3 + - - +
117A LEU* 3.3 25.9 + - + +
242A LEU* 4.5 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A THR* 3.0 4.7 + - + -
113A VAL* 1.3 84.5 - - + +
115A THR* 1.3 69.2 + - - +
116A ASP 3.0 1.1 - - - -
117A LEU* 2.8 21.2 + - - +
118A LEU* 3.0 11.7 + - - +
221A THR 4.5 15.3 - - - +
222A VAL* 3.8 17.9 - - - +
224A LYS* 5.3 7.9 - - + -
226A SER* 3.5 22.0 + - - +
242A LEU* 5.2 10.1 - - + -
245A LEU* 4.5 20.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A PRO 3.9 7.2 + - - +
112A THR* 3.1 35.4 + - - +
114A THR* 1.3 81.7 + - - +
116A ASP* 1.3 59.3 + - - +
118A LEU* 3.8 8.7 - - - -
119A THR* 2.6 41.1 + - - +
127A PHE* 3.5 43.1 - - + +
222A VAL* 5.1 6.3 - - + -
226A SER* 3.9 16.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A ARG* 3.2 40.5 + - - +
112A THR 2.9 24.2 + - - +
113A VAL* 3.6 7.7 + - - +
114A THR 2.8 0.2 + - - -
115A THR* 1.3 83.0 + - - +
117A LEU* 1.3 64.9 + - + +
119A THR* 4.6 0.2 + - - -
120A ARG* 2.9 25.3 + - - -
121A ASP* 3.0 36.8 + - - +
122A GLY* 4.4 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A VAL* 3.3 18.6 + - + +
114A THR* 2.8 10.6 + - - +
116A ASP* 1.3 76.4 - - + +
118A LEU* 1.3 66.8 + - - +
119A THR 3.3 0.7 + - - -
120A ARG* 3.8 8.3 + - - +
121A ASP* 6.1 0.2 - - - +
242A LEU* 5.5 3.8 - - + -
245A LEU* 3.7 27.1 - - + -
246A ARG* 3.7 40.2 - - + +
249A ILE* 3.9 23.6 - - + +
252A ARG* 4.5 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A THR 3.0 10.6 + - - +
115A THR* 3.6 12.3 - - - +
117A LEU* 1.3 79.5 - - - +
119A THR* 1.3 69.5 + - + +
127A PHE* 4.7 12.1 - - + -
218A ILE* 3.5 35.2 - - + -
222A VAL* 4.8 9.0 - - + -
245A LEU* 5.3 1.8 - - + +
249A ILE* 3.7 17.2 - - + +
252A ARG* 2.9 32.1 + - - +
305A MET* 3.0 7.0 - - + +
309A ASP* 5.2 1.8 - - - +
601A AER 4.0 41.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A THR 2.6 23.7 + - - +
116A ASP* 4.1 0.3 + - - -
118A LEU* 1.3 89.2 - - + +
120A ARG* 1.3 72.2 + - - +
121A ASP 3.8 0.3 + - - -
122A GLY* 2.9 19.1 + - - -
123A LYS* 3.0 14.9 + - - -
124A ASP* 3.3 40.2 - - + +
127A PHE* 3.8 20.9 - - + +
305A MET* 3.5 16.0 - - + +
309A ASP* 4.8 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A ASP 2.9 8.9 + - - -
117A LEU 3.8 5.6 + - - +
118A LEU 3.6 1.2 - - - -
119A THR* 1.3 81.3 - - - +
121A ASP* 1.3 70.5 + - - +
123A LYS* 3.0 32.4 + - + +
249A ILE* 5.4 1.2 - - - +
252A ARG* 4.4 1.8 - - - +
253A ASP* 2.6 42.6 + - - +
256A LEU* 5.4 2.4 - - - +
257A GLN* 5.2 1.4 + - - -
301A ASP* 3.2 37.3 + - - +
304A LEU* 3.7 32.3 - - - +
305A MET* 3.7 24.9 - - + +
----------------------------------------------------------
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