Contacts of the helix formed by residues 157 - 169 (chain A) in PDB entry 6W6Y
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 ASP 157 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ASN* 3.7 0.7 - - - -
155A VAL* 3.5 2.3 - - - +
156A PHE* 1.3 81.2 - - + +
158A LYS* 1.3 60.4 + - - +
159A ASN* 3.1 15.8 + - - +
160A LEU* 2.9 41.0 + - + +
161A TYR* 2.9 29.1 + - - +
201A AMP 5.2 5.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 158 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ASN* 3.5 26.0 - - - +
156A PHE 3.4 4.8 + - - +
157A ASP* 1.3 73.9 - - - +
159A ASN* 1.3 62.5 + - - +
161A TYR* 3.2 1.8 + - + +
162A ASP* 2.8 59.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 159 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A ASP* 3.1 12.6 + - - +
158A LYS* 1.3 79.4 + - - +
160A LEU* 1.3 63.6 + - - +
162A ASP* 3.3 9.3 + - - +
163A LYS* 3.0 29.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 160 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A PRO* 3.5 39.0 - - + -
155A VAL* 4.1 13.0 - - + -
157A ASP* 2.9 24.1 + - + +
158A LYS 3.3 0.2 - - - -
159A ASN* 1.3 73.3 - - - +
161A TYR* 1.3 65.9 + - - +
163A LYS* 3.2 25.1 + - + +
164A LEU* 2.9 31.0 + - + +
201A AMP 3.7 35.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 161 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LEU* 3.3 28.8 - - + +
18A ILE* 4.1 16.1 + - + -
19A LYS* 3.6 17.1 - - - -
20A ASN* 3.4 50.4 + - + +
155A VAL* 4.0 12.7 - - + +
157A ASP 2.9 17.0 + - - +
158A LYS* 3.2 3.3 + - + +
160A LEU* 1.3 77.1 - - - +
162A ASP* 1.3 82.9 + - - +
164A LEU* 3.2 7.0 + - - +
165A VAL* 3.0 50.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 162 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A LYS* 2.8 57.6 + - - +
159A ASN* 3.8 9.0 - - - +
161A TYR* 1.3 93.2 - - - +
163A LYS* 1.3 56.9 + - - +
165A VAL* 3.5 4.2 + - - +
166A SER* 2.9 32.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 163 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A PRO* 6.0 2.2 - - + +
137A ILE* 4.2 22.9 - - + -
159A ASN* 3.0 19.8 + - - +
160A LEU* 3.6 26.3 - - + +
162A ASP* 1.3 77.7 - - - +
164A LEU* 1.3 56.7 + - - +
166A SER* 3.7 4.8 - - - -
167A SER* 2.9 32.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 164 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ILE* 4.3 12.3 - - + -
126A LEU* 3.4 25.4 - - + -
136A PRO* 3.5 36.8 - - + +
137A ILE* 3.7 13.7 - - + +
140A LEU* 4.1 22.5 - - + +
155A VAL* 4.0 17.5 - - + -
160A LEU* 2.9 32.7 + - + +
161A TYR* 3.5 6.3 - - - +
163A LYS* 1.3 74.8 - - - +
165A VAL* 1.3 60.1 + - - +
167A SER* 3.4 3.8 + - - -
168A PHE* 3.0 29.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 165 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LEU* 3.8 31.6 - - + -
12A LEU* 5.1 6.5 - - + -
18A ILE* 4.1 12.1 - - + -
140A LEU* 5.9 0.2 - - - -
161A TYR* 3.0 42.3 + - + +
162A ASP* 4.0 4.5 - - - +
164A LEU* 1.3 76.4 - - + +
166A SER* 1.3 63.6 + - - +
168A PHE* 3.2 5.9 + - - +
169A LEU* 3.0 44.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 166 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A ASP 2.9 19.0 + - - -
163A LYS* 3.7 6.7 - - - -
165A VAL* 1.3 77.3 - - - +
167A SER* 1.3 61.0 + - - +
169A LEU* 3.3 14.7 + - - +
170A GLU* 3.4 20.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 167 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A ILE* 3.3 42.6 - - - +
141A ARG* 3.8 11.3 + - - -
163A LYS 2.9 19.3 + - - -
164A LEU 3.7 3.1 - - - -
166A SER* 1.3 73.6 - - - +
168A PHE* 1.3 66.8 + - - +
170A GLU* 3.3 34.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 168 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LEU* 3.5 46.9 - - + -
13A THR* 3.8 22.7 - - + -
140A LEU* 4.2 21.5 - - + -
141A ARG* 5.5 10.3 - - + -
144A VAL* 3.9 25.4 - - + -
164A LEU 3.0 18.3 + - - +
165A VAL* 3.7 6.7 - - - +
167A SER* 1.3 77.8 + - - +
169A LEU* 1.3 64.1 + - + +
170A GLU 3.2 7.3 + - - -
7B SER* 3.8 9.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 169 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LEU* 5.2 1.3 - - + -
165A VAL* 3.0 39.1 + - + +
166A SER* 3.8 7.0 - - - +
167A SER 3.2 0.4 - - - -
168A PHE* 1.3 83.5 - - + +
170A GLU* 1.3 63.8 + - - +
7B SER* 3.7 40.4 - - - +
8B GLY* 3.9 15.5 - - - +
19B LYS* 4.4 17.5 - - - +
29B LYS* 3.5 15.8 + - - -
----------------------------------------------------------
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