Contacts of the helix formed by residues 106 - 116 (chain A) in PDB entry 3ECS
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 LEU 106 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A ARG* 4.0 19.7 - - + +
103A ARG* 3.4 15.5 - - + +
104A ILE 3.1 0.6 - - - -
105A SER* 1.3 88.3 - - - +
107A SER* 1.3 66.3 + - - +
108A ARG 3.4 1.3 - - - -
109A ASN* 3.4 25.6 + - + +
110A LYS* 3.2 37.7 + - + +
121F ASP* 5.6 4.3 - - - +
510F SO4 4.0 19.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A ARG* 3.9 3.4 + - - -
104A ILE* 3.0 27.1 + - - +
106A LEU* 1.3 78.9 - - - +
108A ARG* 1.3 58.1 + - - +
110A LYS* 3.1 3.9 + - - +
111A ILE* 2.8 34.5 + - - +
231A GLU* 3.6 24.3 - - - +
232A SER* 4.8 1.7 + - - -
233A PHE* 5.1 0.9 - - - -
287A ASP* 3.3 37.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ASP* 2.5 35.7 + - - -
20A MSE 4.4 2.2 - - - +
21A ALA* 3.1 29.9 - - - +
104A ILE 5.0 0.4 + - - -
105A SER 5.2 1.7 - - - +
106A LEU 3.4 1.0 - - - +
107A SER* 1.3 78.6 - - - +
109A ASN* 1.3 57.7 + - - +
111A ILE* 3.4 8.6 + - - +
112A ALA* 3.0 29.6 + - - +
132A ARG* 3.4 31.8 - - - +
133A VAL* 4.2 14.2 - - + +
136A ARG* 3.6 31.3 + - + +
231A GLU* 3.4 23.6 + - + +
501A SO4 4.8 0.6 + - - -
601A CL 3.5 27.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A SER 5.2 2.1 + - - -
106A LEU* 3.4 29.0 + - + +
107A SER 3.3 0.4 - - - -
108A ARG* 1.3 75.1 - - - +
110A LYS* 1.3 59.3 + - + +
112A ALA* 3.2 1.9 + - - +
113A ASP* 2.8 40.9 + - - +
136A ARG* 2.7 39.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A ARG* 5.2 11.3 + - - +
106A LEU* 3.2 33.7 + - - +
107A SER 3.1 7.9 + - - +
109A ASN* 1.3 80.8 - - + +
111A ILE* 1.3 62.2 + - - +
113A ASP* 3.3 9.5 + - - +
114A LEU* 3.0 34.9 + - + +
287A ASP* 3.9 36.1 - - + +
117F THR* 4.7 11.2 - - + -
120F LYS* 5.4 1.1 - - - +
146F LYS* 5.2 7.1 - - - +
510F SO4 2.9 41.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A SER 2.8 24.6 + - - +
108A ARG* 3.9 4.9 - - - +
110A LYS* 1.3 71.4 - - - +
112A ALA* 1.3 57.5 + - - +
114A LEU* 4.1 4.0 - - - +
115A CYS* 3.0 29.5 + - - +
133A VAL* 3.5 27.8 - - + -
137A VAL* 4.4 1.6 - - + -
229A VAL* 3.6 20.9 - - + -
230A ALA* 3.3 33.2 - - - +
231A GLU* 3.6 18.6 - - + +
285A PHE* 3.6 10.5 - - + +
286A THR 3.7 7.2 - - - -
287A ASP 3.7 18.8 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
108A ARG 3.0 18.1 + - - +
109A ASN 3.5 4.7 - - - +
111A ILE* 1.3 74.3 - - - +
113A ASP* 1.3 67.5 + - - +
116A HIS* 2.9 30.7 + - - +
133A VAL* 5.7 0.2 - - - +
136A ARG* 3.7 39.7 - - + +
137A VAL* 4.0 12.1 - - - +
140A ALA* 3.7 8.5 - - + +
----------------------------------------------------------
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 ASN* 2.8 30.6 + - - +
110A LYS* 3.6 2.8 - - - +
112A ALA* 1.3 76.5 - - - +
114A LEU* 1.3 63.9 + - - +
116A HIS* 3.1 29.9 + - - -
117A THR* 4.3 4.9 + - - -
140A ALA* 6.0 0.7 - - - +
113F ASP 4.6 4.3 - - - +
114F LEU* 5.9 0.3 - - - -
116F HIS* 3.9 20.2 + - - +
117F THR* 3.2 41.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A LYS* 3.0 20.9 + - + +
111A ILE* 4.1 3.8 - - - +
113A ASP* 1.3 80.1 - - - +
115A CYS* 1.3 56.6 + - - +
117A THR* 2.9 26.6 - - - +
118A PHE* 3.9 7.4 - - - -
285A PHE* 4.0 6.8 - - + -
286A THR 3.7 22.9 - - - +
287A ASP* 5.4 1.6 - - - -
289A GLY* 3.8 22.7 - - - +
290A VAL* 4.3 15.9 - - + +
114F LEU* 5.4 1.8 - - + +
117F THR* 4.4 13.7 - - + -
118F PHE* 3.4 40.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A ILE 3.0 19.6 + - - +
114A LEU* 1.3 74.9 - - - +
116A HIS* 1.3 58.3 + - - +
117A THR 2.7 12.6 + - - -
118A PHE* 2.9 16.6 + - - +
119A ILE* 4.3 3.2 - - - +
137A VAL* 3.8 20.0 - - + -
194A ILE* 4.8 13.5 - - - -
227A TYR* 5.1 4.5 - - - -
229A VAL* 3.7 21.8 - - + -
285A PHE* 3.5 35.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A ALA 2.9 28.3 + - - +
113A ASP* 3.1 24.2 + - - -
115A CYS* 1.3 75.5 - - - +
117A THR* 1.3 67.7 + - - +
118A PHE 3.3 0.6 + - - -
119A ILE* 3.6 19.6 + - - +
137A VAL* 3.5 23.4 - - - +
140A ALA* 3.5 27.3 + - + +
141A ALA* 3.7 7.6 - - - +
144A ALA* 3.8 17.4 - - + +
146A LYS* 3.4 18.8 - - - +
113F ASP* 2.6 34.9 + - + -
----------------------------------------------------------
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