Contacts of the helix formed by residues 127 - 138 (chain A) in PDB entry 1W1W
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 127 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A THR* 4.8 1.7 - - - +
126A VAL* 1.3 77.5 - - - +
128A TYR* 1.3 68.6 + - - +
129A LYS* 3.7 11.4 + - - +
130A ASP* 2.6 39.7 + - - -
131A TYR 3.1 3.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A GLY* 2.3 33.3 + - - -
52A VAL* 3.9 9.7 - - - -
109A ARG* 4.0 2.4 + - - -
117A THR* 4.4 9.4 - - - -
119A TYR* 2.8 53.0 + + + -
126A VAL 3.5 1.0 + - - -
127A SER* 1.3 71.3 - - - +
129A LYS* 1.3 57.1 + - - +
131A TYR* 3.2 2.2 + + - +
132A SER* 2.8 36.4 + - - -
135A LEU* 6.1 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A SER* 2.7 11.7 + - - +
128A TYR* 1.3 80.1 - - - +
130A ASP* 1.3 63.5 + - - +
132A SER* 3.2 25.4 + - - -
133A ILE* 3.0 33.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ILE* 4.0 7.3 - - - +
126A VAL* 3.1 31.6 - - + +
127A SER* 2.6 30.0 + - - +
129A LYS* 1.3 74.6 - - - +
131A TYR* 1.3 56.4 + - - -
133A ILE* 2.7 40.4 + - + +
134A PHE* 3.4 3.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A VAL* 2.5 33.4 + - - -
51A GLY* 3.8 0.4 - - - -
107A LEU* 3.6 23.9 - - + +
108A MET 3.1 33.0 + - - -
109A ARG* 4.1 0.5 - - - +
119A TYR* 3.0 48.5 - + + -
120A LYS 3.5 19.1 - - - -
121A ILE* 4.0 9.9 - - + -
126A VAL* 3.5 10.0 - - + +
127A SER 3.1 4.0 + - - +
128A TYR* 3.4 8.5 - + - +
130A ASP* 1.3 75.0 - - - +
132A SER* 1.3 66.5 + - - +
134A PHE* 3.1 12.4 + - + +
135A LEU* 3.1 42.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A TYR* 2.8 27.6 + - - -
129A LYS* 3.5 28.3 + - - -
131A TYR* 1.3 80.3 - - - +
133A ILE* 1.3 61.7 + - - +
134A PHE 3.0 0.2 - - - -
135A LEU* 3.4 10.5 + - - +
136A GLU* 3.0 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A LYS* 3.0 27.0 + - + +
130A ASP* 2.7 49.4 - - + +
132A SER* 1.3 76.5 - - - +
134A PHE* 1.3 58.7 + - - +
136A GLU* 4.0 6.3 - - - -
137A ASN* 2.8 39.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A TYR* 4.3 8.5 - + - -
100A LYS* 3.9 26.7 - - + -
103A LYS* 5.2 3.8 - - - -
105A VAL* 3.5 33.9 - - + -
107A LEU* 3.3 41.3 - - + -
121A ILE* 3.2 35.4 - - + -
130A ASP 3.4 3.2 + - - +
131A TYR 3.1 5.0 + - - +
132A SER 3.0 0.8 - - - -
133A ILE* 1.3 76.9 - - - +
135A LEU* 1.3 71.2 + - + +
136A GLU 3.0 2.3 + - - -
137A ASN* 3.3 11.5 + - - +
138A GLU* 3.4 30.0 + - + +
140A ILE* 5.3 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A LEU* 3.4 44.9 - - + +
51A GLY* 3.5 4.0 - - - +
107A LEU* 3.7 30.1 - - + -
128A TYR* 6.1 0.7 - - + -
131A TYR* 3.1 43.2 + - + +
132A SER* 3.4 8.0 + - - +
134A PHE* 1.3 81.6 - - + +
136A GLU* 1.3 58.3 + - - +
138A GLU 3.7 2.0 + - - -
140A ILE* 2.8 53.7 + - + +
142A ILE* 4.4 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A SER* 3.0 20.1 + - - +
133A ILE* 4.1 8.3 - - + +
134A PHE 3.0 0.6 - - - -
135A LEU* 1.3 74.6 - - - +
137A ASN* 1.3 67.7 + - - +
138A GLU 3.0 5.2 - - - -
139A ASN* 3.1 15.8 + - - -
140A ILE 5.4 0.4 - - - -
141A LEU* 4.1 31.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A LYS* 4.2 10.2 + - - +
133A ILE* 2.8 26.9 + - - +
134A PHE* 3.3 6.5 + - - +
136A GLU* 1.3 81.7 - - - +
138A GLU* 1.3 70.5 + - - +
139A ASN 3.4 2.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A GLY 5.1 1.7 + - - -
98A TYR* 2.8 48.1 + - + +
100A LYS* 2.5 49.4 + - - +
134A PHE* 3.4 26.3 + - + +
135A LEU 4.3 0.2 - - - +
136A GLU 3.0 1.0 - - - -
137A ASN* 1.3 90.6 - - - +
139A ASN* 1.3 69.0 - - - +
140A ILE* 2.7 22.0 + - + +
1152A PRO* 4.0 5.4 - - - +
----------------------------------------------------------
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