Contacts of the helix formed by residues 117 - 133 (chain A) in PDB entry 1ECD
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 ALA 117 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A THR* 3.9 18.4 - - + +
12A SER* 4.0 20.2 - - - +
113A ASP 5.0 1.9 + - - +
114A PHE* 3.1 12.4 + - + +
116A GLY* 1.3 76.7 - - - +
118A GLU* 1.3 58.8 + - - +
119A ALA 3.5 2.0 - - - -
120A ALA* 3.4 6.1 + - + +
121A TRP* 2.9 47.7 + - + -
----------------------------------------------------------
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
----------------------------------------------------------
105A VAL* 5.8 0.2 - - - +
109A LYS* 3.9 23.1 + - - -
114A PHE* 3.1 38.3 + - + +
115A ALA* 3.5 18.7 + - - +
116A GLY 3.5 0.6 - - - -
117A ALA* 1.3 79.0 - - - +
119A ALA* 1.3 57.8 + - - +
121A TRP* 3.6 2.4 + - - +
122A GLY* 2.9 24.8 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
5A GLN* 4.3 5.0 - - - +
115A ALA 5.0 0.6 + - - -
116A GLY 5.6 0.2 - - - -
117A ALA 3.5 0.2 - - - -
118A GLU* 1.3 77.6 - - - +
120A ALA* 1.3 60.9 + - - +
122A GLY* 3.3 2.1 + - - -
123A ALA* 3.0 27.7 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
1A LEU* 4.7 0.9 - - - +
5A GLN* 3.6 40.8 - - + +
8A THR* 3.7 22.2 - - + -
9A VAL* 3.5 5.8 - - + +
117A ALA 3.4 9.9 + - - +
119A ALA* 1.3 75.7 - - - +
121A TRP* 1.3 61.6 + - - +
123A ALA* 3.4 3.8 + - - +
124A THR* 2.9 31.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A VAL* 3.6 41.2 - - + +
12A SER* 2.9 24.8 + - - -
13A PHE* 4.0 22.7 - + + -
66A PHE* 4.5 3.6 - + - -
70A ILE* 4.0 19.5 - - + -
104A PHE* 3.6 39.0 - + - -
108A MET* 3.9 9.0 - - + +
114A PHE* 3.3 33.4 - + + -
117A ALA* 2.9 30.7 + - + +
118A GLU 3.7 3.8 - - - +
120A ALA* 1.3 72.7 - - - +
122A GLY* 1.3 60.4 + - - +
124A THR* 3.6 5.3 - - + -
125A LEU* 2.9 51.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A ARG* 4.0 13.1 + - - -
118A GLU 2.9 16.2 + - - -
119A ALA* 3.3 4.9 + - - -
121A TRP* 1.3 74.1 - - - +
123A ALA* 1.3 57.3 + - - +
125A LEU* 5.3 0.7 - - - -
126A ASP* 2.9 41.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A LEU* 3.9 12.1 - - + +
5A GLN* 3.5 32.3 - - - +
119A ALA 3.0 9.3 + - - +
120A ALA 3.5 8.3 - - - +
122A GLY* 1.3 75.6 - - - +
124A THR* 1.3 62.3 + - - +
126A ASP* 3.8 5.5 - - - +
127A THR* 2.8 31.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A LEU* 3.5 19.0 - - - +
5A GLN 5.1 0.3 + - - -
6A ILE* 5.6 0.3 - - - -
9A VAL* 3.5 13.4 - - + +
70A ILE* 4.2 16.8 - - + -
73A LEU* 4.0 32.0 - - + +
120A ALA 2.9 16.0 + - - -
121A TRP* 3.6 16.8 - - + -
122A GLY 3.3 0.2 - - - -
123A ALA* 1.3 79.1 - - - +
125A LEU* 1.3 61.8 + - + +
127A THR* 3.3 5.8 + - - +
128A PHE* 2.9 29.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A PHE* 4.5 21.5 - - + -
70A ILE* 6.2 0.2 - - + -
101A ARG* 3.6 35.7 - - + +
104A PHE* 4.6 9.2 - - + -
105A VAL* 3.9 23.8 - - + -
121A TRP* 2.9 44.7 + - + +
122A GLY* 5.3 0.2 - - - -
124A THR* 1.3 76.9 - - + +
126A ASP* 1.3 61.8 + - - +
128A PHE* 4.3 9.2 - - + -
129A PHE* 2.9 55.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A ARG* 2.9 29.6 + - - +
122A GLY* 2.9 22.9 + - - +
123A ALA* 3.8 5.0 - - - +
125A LEU* 1.3 77.5 - - - +
127A THR* 1.3 56.8 + - - +
129A PHE* 5.1 0.4 - - - -
130A GLY* 2.9 27.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A LEU* 4.3 25.3 + - + +
74A PRO* 5.9 2.9 - - + +
76A ILE* 4.5 13.9 - - + -
123A ALA 2.8 20.2 + - - -
124A THR* 3.4 7.0 - - - +
126A ASP* 1.3 76.1 - - - +
128A PHE* 1.3 65.0 + - - +
130A GLY* 3.7 0.9 - - - -
131A MET* 3.1 29.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A PHE* 4.0 30.3 - + - -
69A ILE* 3.3 40.8 - - + -
73A LEU* 6.3 1.1 - - + -
76A ILE* 4.1 24.5 - - + -
80A VAL* 4.2 11.9 - - + -
83A PHE* 5.9 4.0 - + + -
124A THR* 2.9 22.9 + - + +
125A LEU* 3.5 7.2 + - + +
127A THR* 1.3 73.9 - - - +
129A PHE* 1.3 82.6 + + - +
131A MET* 3.2 5.9 + - - +
132A ILE* 3.1 51.9 + - + +
137A HEM 4.9 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A PHE* 6.0 0.9 - + - -
97A LEU* 3.4 40.6 - - + -
98A ASN* 5.0 4.0 - - - +
100A PHE* 4.5 11.4 - + - -
101A ARG* 3.7 40.2 - - + +
125A LEU* 2.9 42.1 + - + +
126A ASP* 4.7 0.7 - - - +
128A PHE* 1.3 92.5 - + - +
130A GLY* 1.3 60.4 + - - +
132A ILE* 4.0 17.7 - - + -
133A PHE* 2.9 62.9 + + + +
137A HEM 5.4 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A ASP 2.9 23.1 + - - -
127A THR 3.7 1.6 - - - -
128A PHE 3.2 0.2 - - - -
129A PHE* 1.3 78.9 - - - +
131A MET* 1.3 58.4 + - - -
133A PHE* 4.2 3.8 - - - +
134A SER* 3.4 21.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A ILE* 3.2 35.4 - - + -
77A GLU* 3.7 39.5 - - - +
80A VAL* 4.0 11.9 - - + -
127A THR* 3.1 20.0 + - + +
128A PHE 3.2 7.1 + - - +
130A GLY* 1.3 72.9 - - - +
132A ILE* 1.3 67.8 + - - +
134A SER* 2.8 23.8 + - - +
135A LYS* 3.4 31.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A VAL* 4.0 20.2 - - + -
83A PHE* 4.0 23.3 - - + -
84A VAL* 4.9 1.3 - - + -
97A LEU* 3.8 22.2 - - + -
128A PHE* 3.1 47.2 + - + +
129A PHE* 3.4 23.5 + - + +
131A MET* 1.3 78.3 - - - +
133A PHE* 1.3 62.3 + - + +
135A LYS* 3.0 6.2 + - - +
136A MET* 2.9 50.1 + - + +
137A HEM 5.6 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A HIS* 3.6 48.3 - + + -
97A LEU* 3.8 28.3 - - + -
98A ASN* 3.7 35.9 - - - -
129A PHE* 2.9 34.3 + + + +
130A GLY* 4.2 5.4 - - - +
132A ILE* 1.3 85.2 - - + +
134A SER* 1.3 59.5 + - - +
135A LYS 3.2 0.2 - - - -
136A MET* 3.3 16.0 - - - +
----------------------------------------------------------
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