Contacts of the helix formed by residues 105 - 122 (chain A) in PDB entry 1I73
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 SER 105 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A LEU* 1.3 78.8 - - - +
106A GLU* 1.3 64.7 + - - +
107A ALA* 3.5 8.9 + - - +
108A GLU* 2.8 43.3 + - - +
109A VAL* 3.0 20.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A TYR* 3.8 50.3 + - + +
104A LEU 3.8 0.4 + - - -
105A SER* 1.3 73.4 - - - +
107A ALA* 1.3 58.8 + - - +
109A VAL* 3.2 3.6 + - - +
110A GLU* 2.9 39.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A SER* 3.2 7.9 + - - +
106A GLU* 1.3 78.9 - - - +
108A GLU* 1.3 59.0 + - + +
110A GLU* 3.4 12.5 + - - +
111A ARG* 2.9 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A LEU* 3.5 23.6 - - + +
105A SER* 2.8 46.8 + - - +
107A ALA* 1.3 79.0 - - + +
109A VAL* 1.3 62.4 + - - +
111A ARG* 3.7 6.4 - - - +
112A ALA* 3.0 23.9 + - - +
184A ASN* 3.3 31.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A ILE* 4.4 5.8 - - + -
100A TYR* 3.8 26.5 - - + -
101A THR* 3.9 22.7 - - + +
104A LEU* 3.9 17.5 - - + +
105A SER 3.0 15.5 + - - +
106A GLU 3.2 7.2 + - - +
108A GLU* 1.3 76.4 - - - +
110A GLU* 1.3 62.5 + - - +
112A ALA* 3.3 2.4 + - - +
113A ILE* 3.1 31.9 + - + +
142A PHE* 4.1 18.4 - - + -
191A LEU* 4.1 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A TYR* 5.0 1.7 + - - -
97A ILE* 3.9 24.1 - - + +
100A TYR* 2.6 27.1 + - + +
106A GLU* 2.9 26.3 + - - +
107A ALA* 3.7 11.9 - - - +
109A VAL* 1.3 75.4 - - - +
111A ARG* 1.3 57.4 + - - +
113A ILE* 3.8 1.6 - - - +
114A LYS* 2.9 31.1 + - - +
130A ARG* 3.7 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A ALA 2.9 18.8 + - - +
108A GLU* 3.7 7.0 - - - +
109A VAL 3.3 0.2 - - - -
110A GLU* 1.3 76.3 - - - +
112A ALA* 1.3 67.4 + - - +
114A LYS* 3.5 33.9 - - - +
115A ASP* 2.9 60.9 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
104A LEU* 5.7 0.7 - - + -
108A GLU 3.0 19.1 + - - +
109A VAL 3.6 4.5 - - - +
111A ARG* 1.3 76.6 - - - +
113A ILE* 1.3 59.5 + - - +
115A ASP* 4.9 0.7 - - - -
116A ALA* 3.0 29.6 + - - +
184A ASN* 6.2 3.8 - - + -
191A LEU* 3.9 19.5 - - + -
192A PHE* 3.6 39.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A TYR* 3.7 27.4 - - + -
97A ILE* 3.9 17.9 - - + -
109A VAL* 3.1 24.5 + - + +
110A GLU 3.8 2.7 - - - +
112A ALA* 1.3 74.6 - - - +
114A LYS* 1.3 65.6 + - - +
116A ALA* 3.2 4.8 + - - +
117A PHE* 3.0 36.4 + - + -
140A ILE* 3.9 22.0 - - + -
142A PHE* 5.8 0.9 - - + -
176A PHE* 4.7 4.9 - - + -
191A LEU* 4.8 12.6 - - + -
195A ALA* 3.8 24.9 - - + -
199A PHE* 4.1 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A TYR* 3.9 20.1 + - - +
110A GLU 2.9 22.2 + - - +
111A ARG* 3.5 35.4 - - - +
113A ILE* 1.3 73.7 - - - +
115A ASP* 1.3 62.3 + - - +
117A PHE* 3.4 4.3 + - - +
118A GLU* 3.0 28.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A ARG* 2.9 58.9 + - - +
112A ALA* 4.9 0.4 - - - -
114A LYS* 1.3 81.0 - - - +
116A ALA* 1.3 62.3 + - - +
118A GLU* 3.3 8.9 + - - +
119A LEU* 3.2 26.5 + - - +
192A PHE* 3.6 19.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A ALA 3.0 19.4 + - - +
113A ILE 3.2 5.1 + - - +
115A ASP* 1.3 75.8 - - - +
117A PHE* 1.3 62.4 + - - +
119A LEU* 3.4 11.0 + - - +
120A TRP* 3.3 20.6 + - - -
192A PHE* 3.6 15.8 - - + +
195A ALA* 3.9 2.9 - - + -
196A ALA* 3.5 32.3 - - - +
199A PHE* 3.8 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A TYR* 3.3 54.5 - + + -
113A ILE* 3.0 26.2 + - + -
114A LYS* 3.7 6.7 - - - +
116A ALA* 1.3 75.3 - - - +
118A GLU* 1.3 66.1 + - - +
120A TRP* 3.1 6.5 + + - +
121A SER 3.0 16.5 + - - -
128A PHE* 3.5 57.4 - + + -
138A ILE* 4.0 17.3 - - + -
140A ILE* 3.8 3.1 - - + -
199A PHE* 3.5 48.7 - + + -
203A LEU* 5.8 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A LYS* 3.0 19.0 + - + +
115A ASP* 3.3 11.6 + - - +
117A PHE* 1.3 75.9 - - - +
119A LEU* 1.3 63.0 + - - +
121A SER* 3.9 13.7 + - - -
122A VAL* 3.0 44.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A ASP 3.2 15.8 + - - +
116A ALA 3.5 5.4 - - - +
117A PHE 3.1 0.6 - - - -
118A GLU* 1.3 77.9 - - + +
120A TRP* 1.3 63.2 + - + +
122A VAL* 3.4 18.6 - - - +
123A ALA* 3.9 2.4 + - - +
192A PHE* 3.7 12.6 - - + -
196A ALA* 3.6 29.2 - - + -
227A TYR* 3.5 58.3 - - + +
228A SER* 4.5 5.6 - - - -
229A LEU* 3.5 35.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A ALA 3.3 23.4 + - - -
117A PHE* 3.1 7.9 + + - +
119A LEU* 1.3 78.5 - - + +
121A SER* 1.3 60.8 + - - +
123A ALA* 3.1 10.6 + - - +
124A SER* 2.6 28.0 + - - +
128A PHE* 4.3 4.9 - - + -
196A ALA* 2.9 33.1 + - - +
199A PHE* 4.0 13.9 - - + +
200A GLY* 3.5 17.7 - - - +
203A LEU* 3.8 23.8 - - + -
205A LEU* 3.5 33.9 - - + -
214A LEU* 3.9 13.2 - - + -
215A MET* 4.1 8.1 - - - -
229A LEU* 3.6 29.6 - - + -
233A ASP* 3.9 18.8 - - + -
237A ILE* 3.7 25.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A PHE 3.0 13.4 + - - -
118A GLU* 3.2 23.8 + - - -
120A TRP* 1.3 78.1 - - - +
122A VAL* 1.3 58.2 + - - +
124A SER* 2.9 25.8 - - - +
126A LEU 2.6 26.9 + - - +
127A ILE* 4.1 7.3 - - - +
128A PHE* 4.0 14.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A GLU* 3.0 38.5 + - + +
119A LEU* 3.4 19.5 - - + +
121A SER* 1.3 75.6 - - - +
123A ALA* 1.3 57.0 + - + +
124A SER 3.6 1.1 - - - -
228A SER* 5.8 3.8 - - - +
229A LEU 6.4 0.4 - - - +
----------------------------------------------------------
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