Contacts of the helix formed by residues 122 - 135 (chain A) in PDB entry 1CCW
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 PRO 122 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A GLY 3.3 8.5 - - - +
121A THR* 1.3 99.8 - - + +
123A PRO* 1.3 71.4 - - + +
124A GLU* 3.5 19.5 - - + +
125A VAL* 3.0 30.9 + - + +
126A GLY 3.7 1.2 + - - -
800A CNC 5.0 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ILE* 4.3 13.2 - - + -
23A LEU* 4.0 20.9 - - + -
26A ALA* 3.7 25.4 - - + -
27A PHE* 3.9 3.4 - - + -
121A THR 3.5 2.2 - - - +
122A PRO* 1.3 82.0 - - + +
124A GLU* 1.3 69.9 + - - +
126A GLY* 3.1 5.2 + - - +
127A ILE* 2.9 32.3 + - + +
800A CNC 3.6 35.4 - - + +
471B PHE* 5.3 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ALA* 4.5 8.8 - - - +
122A PRO* 3.1 19.4 - - + +
123A PRO* 1.3 94.4 - - - +
125A VAL* 1.3 61.9 + - + +
127A ILE* 3.7 15.3 - - + +
128A ALA* 3.1 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A TYR* 4.1 12.8 - - + -
121A THR* 4.0 7.9 - - + -
122A PRO* 3.0 34.9 + - + +
124A GLU* 1.3 78.0 - - + +
126A GLY* 1.3 57.5 + - - +
128A ALA* 3.4 4.7 + - - +
129A ASP* 2.9 44.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A PHE* 3.7 8.9 - - - -
89A TYR* 4.0 4.5 - - - -
117A TYR* 3.9 16.2 - - - -
122A PRO 3.7 3.4 + - - -
123A PRO 3.1 6.7 + - - -
125A VAL* 1.3 80.9 - - - +
127A ILE* 1.3 55.9 + - - +
129A ASP* 3.4 1.4 + - - +
130A LEU* 2.9 31.5 + - - +
800A CNC 4.1 18.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ALA* 3.8 34.3 - - + +
27A PHE* 3.7 28.3 - - + +
30A ALA* 3.9 22.7 - - + -
32A PHE* 4.6 3.6 - - + -
123A PRO 2.9 26.6 + - - +
124A GLU* 3.7 14.6 - - + +
125A VAL 3.3 0.2 - - - -
126A GLY* 1.3 76.2 - - - +
128A ALA* 1.3 58.0 + - - +
130A LEU* 3.3 2.4 + - - +
131A LYS* 2.9 50.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A GLU 3.1 17.1 + - - +
125A VAL* 3.7 5.8 - - - +
127A ILE* 1.3 77.3 - - - +
129A ASP* 1.3 67.1 + - - +
131A LYS* 3.3 9.5 + - - +
132A LYS* 3.0 23.9 + - - +
137A GLU* 4.3 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A TYR* 3.4 2.0 - - - +
115A ARG* 3.6 31.5 + - - +
117A TYR* 2.6 40.8 + - - +
125A VAL* 2.9 26.0 + - - +
126A GLY 3.8 1.1 - - - +
128A ALA* 1.3 79.8 - - - +
130A LEU* 1.3 58.6 + - - +
132A LYS* 3.3 8.7 + - - +
133A ASP* 2.8 34.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ILE* 3.6 31.0 - - + -
27A PHE* 4.0 14.4 - - + -
32A PHE* 3.6 20.9 - - + -
57A ALA* 3.8 14.4 - - + -
59A LEU* 4.5 4.5 - - + -
87A LEU* 3.7 26.0 - - + -
89A TYR* 3.2 24.2 - - + +
126A GLY 2.9 17.9 + - - +
127A ILE 3.9 3.1 - - - +
129A ASP* 1.3 74.8 - - - +
131A LYS* 1.3 66.3 + - - +
133A ASP 3.7 0.4 - - - +
134A LEU* 2.8 38.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 3.7 43.1 - - + -
30A ALA* 4.6 7.6 - - - +
32A PHE* 4.4 3.4 - - + -
127A ILE* 2.9 40.5 + - - +
128A ALA* 3.8 5.3 - - - +
130A LEU* 1.3 77.7 - - - +
132A LYS* 1.3 57.0 + - - +
134A LEU 3.2 1.0 + - - -
135A ASN 2.9 24.8 + - - -
136A ILE* 3.0 32.3 + - + +
137A GLU* 3.1 27.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A ARG* 3.9 20.4 - - - +
128A ALA 3.0 13.0 + - - +
129A ASP* 3.5 12.6 - - - +
131A LYS* 1.3 76.9 - - - +
133A ASP* 1.3 67.6 + - - +
135A ASN* 3.1 18.1 + - - +
137A GLU* 3.7 16.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A LEU* 4.0 25.9 - - + +
89A TYR* 2.6 29.0 + - - +
114A ASP* 5.5 1.0 - - - +
115A ARG* 2.7 36.3 + - - +
129A ASP 2.8 19.0 + - - +
130A LEU 4.0 1.1 - - - +
131A LYS 3.3 0.2 - - - -
132A LYS* 1.3 80.7 - - - +
134A LEU* 1.3 62.9 + - - +
135A ASN* 3.7 1.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A LYS* 3.9 36.8 - - + -
6A ILE* 5.8 0.4 - - + -
32A PHE* 4.3 2.2 - - + -
56A ASP* 4.1 26.0 - - + +
57A ALA* 5.4 0.2 - - + -
87A LEU* 3.8 22.7 - - + -
130A LEU* 2.8 39.2 + - + +
133A ASP* 1.3 79.2 - - - +
135A ASN* 1.3 73.1 + - - +
136A ILE* 3.3 23.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A LYS 2.9 4.7 + - - -
132A LYS* 3.1 14.1 + - - +
133A ASP 3.3 2.4 - - - +
134A LEU* 1.3 81.4 - - - +
136A ILE* 1.3 62.1 + - - +
137A GLU 3.7 3.6 - - - +
----------------------------------------------------------
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