Contacts of the helix formed by residues 109 - 120 (chain A) in PDB entry 2QCT
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 109 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A LYS* 3.9 32.5 - - + +
85A ILE* 4.9 9.3 - - + +
103A GLN* 5.2 2.3 + - - +
105A PRO* 3.2 9.5 - - - +
106A LEU* 2.7 38.8 + - + +
108A THR* 1.3 92.7 - - - +
110A LEU* 1.3 55.6 + - - +
111A LEU 3.4 2.0 - - - -
112A ASP* 3.6 17.3 - - - +
113A PHE* 2.6 34.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A PRO* 4.0 11.7 - - + -
106A LEU 3.4 16.3 + - - +
107A SER* 3.8 15.0 + - - +
108A THR 3.8 1.0 - - - -
109A THR* 1.3 77.1 - - - +
111A LEU* 1.3 53.7 + - - +
113A PHE* 2.8 9.8 + - - +
114A TRP* 2.7 40.5 + - + -
140A GLU* 3.7 27.8 - - + +
141A ARG 3.3 22.9 - - - +
142A TYR* 4.1 4.9 - - + -
153A PHE* 3.7 33.4 - - + -
132B TYR* 6.1 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A THR* 3.7 17.0 - - - +
78A SER* 6.2 1.1 - - - -
81A ASP* 4.2 13.2 - - - +
108A THR 5.5 0.9 - - - -
109A THR 3.4 0.2 - - - -
110A LEU* 1.3 77.8 - - - +
112A ASP* 1.3 67.1 + - - +
114A TRP* 3.4 2.4 + - - +
115A ARG* 2.9 40.6 + - + +
153A PHE* 4.0 20.1 - - - +
154A GLY* 3.8 22.7 - - - -
155A PRO* 4.1 2.5 - - + -
156A PHE* 4.0 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A LYS* 4.7 13.0 - - - +
73A LEU* 4.0 12.3 - - + +
81A ASP* 4.7 4.2 - - - +
82A SER* 4.9 4.2 + - - +
84A TYR 4.3 13.6 - - - +
85A ILE* 4.0 10.7 - - + +
108A THR 3.4 20.8 - - - +
109A THR* 3.3 18.2 + - + +
110A LEU 3.1 0.4 - - - -
111A LEU* 1.3 80.4 - - - +
113A PHE* 1.3 65.9 + - - +
115A ARG* 2.9 31.8 + - - +
116A MET* 3.1 21.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A ILE* 3.9 11.6 - - + +
102A THR* 5.0 7.9 - - + -
105A PRO* 4.1 18.4 - - + -
109A THR 2.6 18.3 + - - +
110A LEU* 2.8 14.8 + - - +
112A ASP* 1.3 76.3 - - - +
114A TRP* 1.3 72.0 + + - -
116A MET* 3.2 15.7 + - + +
117A ILE* 3.2 40.0 + - + +
125A ILE* 4.3 8.1 - - + -
142A TYR* 3.3 57.4 - + + -
224A CYS* 3.9 24.0 - - - -
226A HIS* 4.7 9.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A LEU 2.7 24.8 + - - +
111A LEU* 4.0 4.7 - - - +
113A PHE* 1.3 79.7 - + - +
115A ARG* 1.3 68.0 + - - +
117A ILE* 3.6 30.9 - - + +
118A TRP* 3.0 22.8 + + - +
125A ILE* 4.4 9.2 - - + -
142A TYR* 2.9 40.7 + + + +
143A TRP* 4.5 0.7 - - - -
153A PHE* 3.0 42.2 - + + -
156A PHE* 4.0 22.1 - - + -
158A VAL* 3.3 23.8 - - + -
174A LEU* 4.2 14.8 - - + -
176A VAL* 3.6 36.8 - - + -
185A ILE* 4.9 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A LEU* 3.4 32.4 + - + +
75A LEU* 2.5 40.3 + - + +
76A ILE* 4.2 4.8 - - - +
77A THR* 4.2 5.2 - - + +
81A ASP* 3.0 35.9 + - - +
82A SER 3.1 30.3 + - - +
111A LEU* 2.9 39.3 + - + +
112A ASP* 2.9 28.5 + - - +
114A TRP* 1.3 74.4 - - - +
116A MET* 1.3 55.1 + - - +
118A TRP* 2.9 3.6 + - - +
119A GLU* 2.5 38.7 + - - +
156A PHE* 3.8 19.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A VAL* 4.3 15.5 - - + -
73A LEU* 3.5 24.6 - - + +
85A ILE* 3.8 23.1 - - + -
87A ALA* 3.9 22.2 - - - -
100A ILE* 4.4 14.4 - - + -
102A THR* 3.7 18.2 - - + +
112A ASP 3.1 6.2 + - - +
113A PHE* 3.4 26.7 - - + +
115A ARG* 1.3 80.2 - - - +
117A ILE* 1.3 69.9 + - + +
118A TRP 3.0 1.0 + - - -
119A GLU* 4.4 0.9 - - - +
120A TYR* 3.0 32.6 + - + +
224A CYS* 4.1 15.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A PHE* 3.2 31.9 + - + +
114A TRP* 3.6 30.3 - - + +
116A MET* 1.3 82.9 - - + +
118A TRP* 1.3 64.2 + - + +
121A SER* 3.2 2.3 + - - -
122A VAL* 3.0 57.1 + - + +
125A ILE* 3.9 12.1 - - + -
176A VAL* 5.9 0.2 - - + -
185A ILE* 4.1 13.9 - - + -
224A CYS* 3.7 38.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A LEU* 3.9 17.3 - - + -
114A TRP* 3.0 9.5 + + - +
115A ARG 2.9 8.7 + - - +
117A ILE* 1.3 79.3 - - + +
119A GLU* 1.3 66.3 + - - +
120A TYR 2.9 3.8 + - - -
121A SER* 3.0 3.5 + - - -
156A PHE* 3.6 18.8 - + + -
176A VAL* 2.9 54.7 - - + -
178A PHE* 3.5 37.3 - + + -
181A GLU* 3.7 28.3 - - + -
183A ARG* 2.7 68.5 + - + +
185A ILE* 5.6 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A LEU* 3.3 11.8 - - - +
74A SER* 2.7 45.0 + - - -
75A LEU* 3.3 30.4 + - + +
115A ARG 2.5 20.1 + - - +
116A MET* 4.6 0.4 - - - -
118A TRP* 1.3 74.3 - - - +
120A TYR* 1.3 87.8 + - + +
121A SER* 3.5 2.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A VAL* 3.8 22.6 - - + +
72A GLU* 2.8 31.7 + - - +
73A LEU* 4.8 3.4 - - + -
89A PHE* 3.3 34.3 - + - -
97A LYS* 4.4 13.6 + - + -
100A ILE* 5.5 1.3 - - + -
116A MET* 3.0 24.3 + - + +
119A GLU* 1.3 108.3 + - + +
121A SER* 1.3 73.7 + - - +
122A VAL* 3.4 13.0 + - + -
221A VAL* 3.8 8.0 - - - +
222A PRO* 3.9 15.7 - - + +
----------------------------------------------------------
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