Contacts of the helix formed by residues 105 - 118 (chain A) in PDB entry 2HZA
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 MSE 105 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A THR 3.7 19.1 - - - +
46A GLN* 4.2 3.2 - - - +
47A GLN 3.7 14.8 - - - +
50A THR* 3.0 21.2 + - - +
51A GLN 4.2 7.9 - - - +
52A GLY 3.2 32.3 - - - +
53A PHE 3.4 23.6 - - - +
54A ALA* 4.7 0.4 - - + -
103A GLY 3.4 10.8 + - - +
104A ASP* 1.3 71.1 - - - +
106A GLY* 1.3 56.6 + - - +
108A VAL* 3.5 19.7 + - + +
109A GLN* 2.9 29.6 + - - +
128A CYS* 3.7 25.3 - - - -
129A LEU 3.8 4.9 - - - -
130A PRO* 3.9 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A GLN 3.7 14.6 - - - -
47A GLN 3.8 4.8 + - - -
48A HIS* 3.4 26.0 - - - -
104A ASP* 2.9 10.3 + - - -
105A MSE 1.3 75.0 - - - +
107A ASP* 1.3 61.0 + - - +
109A GLN* 3.2 3.7 + - - +
110A HIS* 2.8 33.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A HIS* 3.8 12.5 + - - -
81A LEU* 4.2 18.6 - - + +
104A ASP* 2.9 31.3 + - + +
106A GLY* 1.3 71.5 - - - +
108A VAL* 1.3 66.0 - - - +
110A HIS* 3.1 10.3 + - - +
111A PHE* 2.8 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A ALA* 3.7 21.1 - - + -
81A LEU* 4.1 17.3 - - + -
101A LEU* 3.6 32.8 - - + -
102A LYS 4.0 22.2 - - - +
104A ASP 2.9 15.9 + - - +
105A MSE 3.6 24.9 - - + +
107A ASP* 1.3 74.2 - - - +
109A GLN* 1.3 59.2 + - - +
111A PHE* 3.1 4.7 + - - +
112A ALA* 2.8 27.4 + - - +
126A LEU* 4.4 8.1 - - + -
128A CYS* 4.5 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A GLU* 5.1 4.0 - - - +
46A GLN* 3.1 49.9 + - + +
47A GLN* 5.6 0.2 + - - -
105A MSE 2.9 18.5 + - - +
106A GLY* 3.4 4.9 - - - +
108A VAL* 1.3 77.1 - - - +
110A HIS* 1.3 85.9 + - - +
112A ALA* 3.2 4.5 + - - +
113A ASP* 2.7 49.4 + - - -
126A LEU* 3.7 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A HIS* 2.6 38.5 + + - -
106A GLY 2.8 22.9 + - - -
107A ASP* 3.1 10.3 + - - +
109A GLN* 1.3 97.9 + - - +
111A PHE* 1.3 63.1 + - - +
113A ASP* 3.5 5.2 + - - +
114A ASP* 2.8 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A LEU* 4.2 11.2 - - + -
74A THR* 3.7 20.0 - - + -
75A GLN* 4.3 26.2 - - + -
78A HIS* 3.5 45.1 - + + -
81A LEU* 4.0 17.3 - - + -
99A ALA* 5.9 1.3 - - + -
101A LEU* 4.1 28.7 - - + -
107A ASP 2.8 12.7 + - - +
108A VAL 3.4 6.5 - - - +
110A HIS* 1.3 74.9 - - - +
112A ALA* 1.3 70.6 + - - +
114A ASP* 3.0 22.0 + - + +
115A VAL* 3.1 35.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A LEU* 3.9 26.5 - - + -
101A LEU* 5.4 0.4 - - + -
108A VAL* 2.8 13.6 + - + +
109A GLN 3.2 9.2 + - - +
111A PHE* 1.3 78.5 - - + +
113A ASP* 1.3 53.0 + - - +
115A VAL* 2.9 5.2 + - - +
116A ILE* 2.7 42.4 + - + +
126A LEU* 3.6 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A GLN* 2.7 33.8 + - - +
110A HIS* 3.8 9.5 - - - +
112A ALA* 1.3 76.2 - - - +
114A ASP* 1.3 67.6 + - - +
116A ILE* 4.3 14.2 - - - +
117A ALA* 2.8 29.3 + - - +
126A LEU* 5.9 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A THR* 5.6 5.8 - - + -
78A HIS* 5.3 6.3 + - + -
110A HIS* 2.8 21.9 + - - +
111A PHE* 3.0 15.0 + - + +
113A ASP* 1.3 77.6 - - - +
115A VAL* 1.3 62.4 + - + +
117A ALA* 4.0 4.2 - - - +
118A GLN* 3.3 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A LEU* 4.3 5.8 - - + -
58A TYR* 4.1 37.2 - - + +
71A ILE* 5.2 13.9 - - + +
74A THR* 4.7 6.5 - - + -
75A GLN* 5.9 1.1 - - + -
111A PHE* 3.4 45.8 - - + +
112A ALA 2.9 8.3 + - - +
114A ASP* 1.3 76.2 - - + +
116A ILE* 1.3 65.8 + - - +
117A ALA 3.1 2.2 + - - -
118A GLN* 3.5 33.0 + - - +
121A VAL* 4.0 9.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A LEU* 3.7 29.6 - - + -
57A SER 5.4 0.2 - - - +
58A TYR* 5.5 2.2 - - + -
112A ALA* 2.7 30.2 + - + +
113A ASP* 4.2 12.1 - - - +
115A VAL* 1.3 73.6 - - + +
117A ALA* 1.3 61.9 + - - +
118A GLN 3.7 4.7 - - - +
121A VAL* 3.8 21.0 - - + +
124A GLY* 3.9 26.2 - - - +
125A HIS* 3.8 19.3 - - - +
126A LEU* 4.5 4.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A ASP 2.8 20.3 + - - +
114A ASP* 4.0 6.3 - - - +
116A ILE* 1.3 75.3 - - - +
118A GLN* 1.3 73.6 + - - +
119A ARG* 4.2 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A LEU* 3.5 13.7 - - + +
70A ARG* 3.4 35.3 + - - +
71A ILE* 4.0 13.1 - - - +
74A THR* 4.3 18.6 + - - +
114A ASP 3.3 21.1 + - - +
115A VAL* 3.5 27.6 + - - +
116A ILE 3.7 1.7 - - - +
117A ALA* 1.3 87.7 - - - +
119A ARG* 1.3 65.8 + - - +
121A VAL* 3.7 24.3 + - + +
----------------------------------------------------------
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