Contacts of the helix formed by residues 107 - 122 (chain A) in PDB entry 3IEW
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 107 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ILE* 4.2 10.5 - - + -
27A ILE* 3.7 29.4 - - + -
100A ILE* 3.5 42.4 - - + +
102A ALA* 4.3 7.6 - - + -
105A PRO* 3.6 24.9 - - + +
106A LYS* 1.3 72.7 - - - +
108A ALA* 1.3 65.9 + - - +
109A PRO* 3.3 3.6 - - - -
110A HIS* 2.9 19.4 + - - +
111A ILE* 3.1 18.8 + - + +
114A MET* 4.5 5.4 - - + -
133A ALA* 4.1 14.6 - - + -
901A CDP 2.8 24.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A LYS* 5.5 1.1 - - + -
107A LEU* 1.3 76.1 - - - +
109A PRO* 1.3 66.4 - - + +
110A HIS 3.0 5.4 + - - -
111A ILE* 3.3 20.7 + - - +
112A ASP* 4.7 2.6 + - - -
901A CDP 3.0 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A LYS* 3.9 18.4 - - + +
107A LEU 3.4 2.2 - - - -
108A ALA* 1.3 94.5 - - + +
110A HIS* 1.3 80.5 + - + +
112A ASP 5.4 0.7 - - - -
113A ALA* 5.7 1.0 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
25A VAL* 4.0 20.4 - - + +
26A THR 5.2 0.7 - - - -
27A ILE* 3.9 25.9 - - + +
28A PRO* 3.9 24.0 - - + +
106A LYS 3.8 22.0 + - - -
107A LEU* 2.9 8.5 + - - +
109A PRO* 1.3 94.1 + - + +
111A ILE* 1.3 65.2 + - - +
112A ASP 3.4 2.2 - - - -
113A ALA* 3.2 11.9 + - - +
114A MET* 3.1 38.9 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
100A ILE* 4.4 3.8 - - + -
107A LEU* 3.1 22.0 + - + +
108A ALA* 3.3 13.7 + - - +
110A HIS* 1.3 74.2 - - - +
112A ASP* 1.3 74.2 + - - +
114A MET* 3.1 15.8 + - - +
115A ARG* 3.0 22.5 + - + +
131A VAL* 3.5 49.5 - - + +
132A LYS 4.4 0.2 - - - -
133A ALA* 4.1 24.0 - - + +
901A CDP 5.0 2.9 - - - +
58C ASP* 5.6 0.7 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
108A ALA 4.7 2.5 + - - -
109A PRO 5.4 0.6 + - - -
110A HIS 3.4 0.4 - - - -
111A ILE* 1.3 83.1 - - - +
113A ALA* 1.3 58.3 + - - +
115A ARG* 3.4 26.4 + - - +
116A ALA* 3.0 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A VAL* 3.8 17.7 - - + -
109A PRO 5.7 0.9 + - - +
110A HIS* 3.2 14.0 + - - +
111A ILE 3.2 0.8 - - - -
112A ASP* 1.3 77.5 - - - +
114A MET* 1.3 64.0 + - - +
116A ALA* 3.4 7.3 + - - +
117A ASN* 3.1 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ILE* 3.5 42.6 - - + +
23A GLY* 3.7 15.4 - - - +
25A VAL* 3.7 4.7 - - + +
27A ILE* 3.9 17.5 - - + -
42A LEU* 4.0 13.5 - - + -
100A ILE* 3.6 27.6 - - + -
107A LEU* 4.5 10.3 - - + -
110A HIS* 3.1 25.7 + - + +
111A ILE* 3.1 11.8 + - - +
113A ALA* 1.3 74.4 - - - +
115A ARG* 1.3 64.2 + - - +
117A ASN* 3.2 4.0 + - - +
118A ILE* 3.1 29.2 + - - +
131A VAL* 4.3 8.5 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
111A ILE* 3.0 13.4 + - + +
112A ASP* 3.5 29.5 + - - +
114A MET* 1.3 77.3 - - - +
116A ALA* 1.3 56.2 + - - +
118A ILE* 3.4 2.4 + - - +
119A ALA* 2.9 30.7 + - - +
126A LEU* 2.7 62.9 + - - +
127A ASP* 4.3 2.2 - - - +
129A VAL* 3.0 43.5 + - + +
130A ASN* 4.5 5.1 + - - +
131A VAL* 4.3 11.2 - - + +
55C ALA* 4.2 17.2 + - - +
----------------------------------------------------------
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 ASP 3.0 16.1 + - - +
113A ALA* 3.7 8.3 - - - +
115A ARG* 1.3 78.4 - - - +
117A ASN* 1.3 59.6 + - - +
119A ALA* 3.5 1.9 + - - +
120A ALA* 3.0 29.1 + - - +
126A LEU* 3.9 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A GLY 2.9 25.0 + - - +
24A GLY* 3.6 19.8 + - - -
25A VAL* 3.7 6.9 - - - +
43A LEU* 5.9 0.7 - - + -
76A ARG* 3.2 44.4 + - - +
113A ALA* 3.1 16.0 + - - +
114A MET 3.2 6.3 + - - +
116A ALA* 1.3 76.5 - - - +
118A ILE* 1.3 58.2 + - + +
120A ALA* 3.3 1.7 + - - -
121A ASP* 3.0 28.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A GLY* 4.9 0.4 - - - -
42A LEU* 3.9 13.2 - - + -
43A LEU* 3.5 22.7 - - + -
46A ILE* 3.4 31.9 - - + -
79A LEU* 4.5 10.5 - - + -
96A VAL* 4.9 1.8 - - + -
114A MET* 3.1 17.3 + - + +
115A ARG 3.7 3.4 - - - +
117A ASN* 1.3 72.1 - - + +
119A ALA* 1.3 67.4 + - - +
121A ASP* 3.2 2.5 + - - +
122A LEU* 2.9 47.5 + - + +
129A VAL* 3.8 16.6 - - + -
131A VAL* 3.9 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A ARG 2.9 17.8 + - - +
116A ALA 3.8 4.0 - - - +
118A ILE* 1.3 76.8 - - - +
120A ALA* 1.3 61.8 + - - +
122A LEU 3.7 0.2 - - - -
123A ASP* 3.0 4.2 + - - -
124A LEU* 2.8 48.5 + - - +
125A PRO 4.1 9.2 - - - +
126A LEU* 3.9 21.5 - - + +
129A VAL* 4.0 15.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A ARG* 4.1 11.4 - - - +
80A ARG* 5.6 0.5 - - - -
116A ALA 3.0 17.2 + - - +
117A ASN* 3.5 5.4 - - - +
118A ILE 3.2 0.2 - - - -
119A ALA* 1.3 77.8 - - - +
121A ASP* 1.3 62.0 + - - +
123A ASP* 3.2 13.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A LEU* 4.9 0.5 - - - +
76A ARG* 2.9 43.3 + - - +
79A LEU* 3.8 25.4 - - + +
80A ARG* 2.9 59.5 + - + +
83A ALA* 4.2 5.0 - - - +
117A ASN* 3.0 17.6 + - - +
118A ILE 3.8 4.0 - - - +
120A ALA* 1.3 76.2 - - - +
122A LEU* 1.3 63.2 + - - +
123A ASP 3.3 1.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A ILE* 4.5 2.7 - - + -
50A LEU* 3.7 28.7 - - + -
79A LEU* 3.8 17.3 - - + -
83A ALA* 3.8 24.0 - - + +
93A ILE* 3.9 15.3 - - + +
96A VAL* 3.7 29.8 - - + -
118A ILE* 2.9 35.8 + - + +
119A ALA 4.3 0.4 - - - +
121A ASP* 1.3 76.5 - - - +
123A ASP* 1.3 70.9 + - - +
124A LEU* 3.3 27.2 + - + +
----------------------------------------------------------
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