Contacts of the helix formed by residues 127 - 135 (chain A) in PDB entry 1W7L
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 CYS 127 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A TYR* 3.8 22.7 - - + +
104A LEU* 4.1 6.7 - - - -
125A PHE* 3.0 31.3 + - + -
126A ASP* 1.3 81.0 - - - +
128A TYR* 1.3 73.6 + - - +
129A GLU 3.2 0.2 - - - -
130A PRO* 3.4 10.4 - - + +
131A MET* 3.0 55.4 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
104A LEU* 3.7 33.9 - - + -
108A PHE* 4.0 15.6 - + + -
120A ILE* 3.9 21.1 - - + -
121A ILE 5.9 0.2 - - - -
124A PHE* 3.8 15.9 - - + -
125A PHE* 3.2 38.4 + + + +
127A CYS* 1.3 85.1 - - - +
129A GLU* 1.3 61.7 + - - +
131A MET* 4.0 1.0 - - - +
132A THR* 3.0 30.0 + - - -
179A VAL* 3.5 31.2 - - + -
181A ASN* 3.2 25.9 - - + +
213A ASP* 2.6 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A ILE* 4.0 9.8 - - + +
124A PHE* 3.6 30.1 - - + -
126A ASP 3.6 1.7 + - - +
128A TYR* 1.3 80.0 - - - +
130A PRO* 1.3 69.7 - - + +
132A THR* 3.3 6.1 + - - -
133A MET* 3.0 41.7 + - - +
139A PRO* 4.1 5.7 - - + +
141A PHE* 3.7 29.0 - - + -
385A TYR 4.7 1.7 - - - +
386A SER* 4.7 9.2 - - - -
387A VAL* 5.1 5.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ILE* 3.6 39.1 - - + +
126A ASP* 3.2 19.5 - - - +
127A CYS* 3.4 18.4 - - + +
129A GLU* 1.3 92.9 - - + +
131A MET* 1.3 55.6 + - + +
133A MET* 3.6 4.3 - - + +
134A MET* 2.8 31.0 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
101A TYR* 3.7 35.0 - - + +
104A LEU* 3.9 6.7 - - - -
105A PHE* 3.8 33.9 - - + -
108A PHE* 3.6 39.7 - - + +
109A GLN* 4.9 1.9 + - - -
127A CYS* 3.0 45.5 + - + +
128A TYR 4.0 0.2 - - - +
130A PRO* 1.3 74.4 - - + +
132A THR* 1.3 65.1 + - - +
134A MET* 3.6 5.5 + - - +
135A ALA* 3.2 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A PHE* 3.3 22.9 - - - -
112A VAL* 4.6 1.6 - - + -
118A VAL* 3.7 30.2 - - + +
120A ILE* 3.9 2.6 - - - +
128A TYR 3.0 17.9 + - - -
129A GLU* 3.4 8.7 - - - -
131A MET* 1.3 76.3 - - - +
133A MET* 1.3 60.3 + - - +
135A ALA* 3.3 9.9 + - - +
137A GLY* 2.9 46.8 + - - +
139A PRO* 3.7 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ARG* 4.4 5.9 - - - +
11A ASP 3.8 21.5 - - - +
12A GLY* 4.1 12.8 - - - +
13A ILE* 3.8 18.4 - - + -
129A GLU* 3.0 39.2 + - - +
130A PRO* 3.3 7.8 + - - +
132A THR* 1.3 73.6 - - - +
134A MET* 1.3 60.3 + - - +
136A GLY* 2.9 20.8 + - - -
137A GLY 4.0 7.8 - - - +
139A PRO* 4.1 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ARG* 3.4 63.7 + - + +
10A LEU* 4.3 9.6 - - + -
13A ILE* 3.8 20.1 - - + +
105A PHE* 3.9 32.5 - - + -
109A GLN* 4.1 15.4 + - - +
130A PRO 2.8 20.2 + - - +
131A MET* 4.0 7.0 - - - +
133A MET* 1.3 73.4 - - - +
135A ALA* 1.3 58.9 + - - +
136A GLY* 3.2 1.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A PHE* 3.8 16.6 - - + +
109A GLN* 4.0 15.9 - - - +
112A VAL* 3.2 36.2 - - + +
113A ASP* 3.6 9.5 - - - +
114A GLU 3.9 1.0 + - - -
131A MET 3.2 16.5 + - - +
132A THR 3.7 4.3 - - - +
133A MET 3.1 1.0 - - - -
134A MET* 1.3 76.5 - - - +
136A GLY* 1.3 57.0 + - - +
137A GLY 3.3 3.0 + - - -
----------------------------------------------------------
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