Contacts of the helix formed by residues 139 - 149 (chain A) in PDB entry 1SLY
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 139 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A CYS* 2.0 48.0 - - - -
128A LEU* 4.3 12.8 - - - -
135A GLN* 4.2 11.7 - - + -
136A PRO 3.2 13.0 + - - +
138A ALA* 1.3 78.6 - - - +
140A ASP* 1.3 63.6 + - - +
142A LEU* 3.0 19.4 + - - +
143A PHE* 3.2 43.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A GLN* 5.2 3.1 - - - +
136A PRO 4.3 4.7 - - - +
137A ASN* 2.8 46.0 + - - +
139A CYS* 1.3 72.1 - - - +
141A LYS* 1.3 57.0 + - - +
143A PHE* 3.8 13.0 + - - +
144A SER* 3.0 28.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A ALA* 5.8 0.9 - - - -
88A TRP* 4.5 9.1 - - + -
107A ASN* 2.6 35.5 + - - +
110A TYR* 3.5 47.5 - - + +
137A ASN 4.4 0.8 + - - +
138A ALA* 3.0 36.9 + - - +
140A ASP* 1.3 75.6 - - - +
142A LEU* 1.4 64.4 + - - +
144A SER* 3.6 4.6 + - - -
145A VAL* 3.1 29.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A CYS* 3.8 21.8 - - - +
109A TYR* 3.6 27.6 - - + +
110A TYR* 4.0 12.3 - - - +
113A TRP* 5.6 0.4 - - + -
121A ALA* 4.1 13.0 - - + +
122A TRP* 4.0 16.2 - - + -
125A ALA* 4.0 33.4 - - + +
128A LEU* 4.1 14.6 - - + -
138A ALA 5.2 0.2 - - - +
139A CYS* 3.0 13.7 + - - +
141A LYS* 1.4 79.4 - - - +
143A PHE* 1.3 70.9 + - + +
145A VAL* 3.0 20.0 + - + +
146A TRP* 3.0 13.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A ALA* 3.4 28.7 - - + -
128A LEU* 3.7 34.5 - - + -
129A TRP* 3.7 34.5 - + + -
135A GLN* 4.5 9.2 - - + -
139A CYS* 3.2 36.7 + - + +
140A ASP* 4.1 12.1 - - - +
142A LEU* 1.3 81.7 - - + +
144A SER* 1.3 57.1 + - - +
146A TRP* 3.7 22.1 - + + +
147A ARG* 3.2 29.6 + - - +
152A GLN* 4.9 0.9 + - - -
160A ARG* 4.1 12.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A ASP 3.0 19.2 + - - -
141A LYS* 3.6 5.7 + - - -
142A LEU 3.1 1.2 + - - -
143A PHE* 1.3 74.0 - - - +
145A VAL* 1.3 68.7 + - - +
147A ARG* 4.1 5.8 - - - +
148A ALA* 3.1 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 145 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A TYR* 3.6 25.4 - - + +
113A TRP* 4.0 43.5 + - + +
122A TRP* 3.6 12.5 - - + -
141A LYS* 3.1 20.8 + - - +
142A LEU* 3.1 11.4 - - + +
144A SER* 1.3 79.1 - - - +
146A TRP* 1.3 56.6 + - - +
148A ALA* 3.3 7.0 + - - +
149A SER* 2.9 29.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A TRP* 3.4 45.6 + + + +
125A ALA* 3.5 25.1 - - + -
126A LYS* 3.6 33.4 - - + -
129A TRP* 3.5 35.9 - + + -
142A LEU 3.0 15.2 + - - +
143A PHE* 3.7 14.4 - + - +
145A VAL* 1.3 69.6 - - - +
147A ARG* 1.3 65.1 + - - +
149A SER* 2.6 24.4 + - - -
150A GLY 3.8 1.0 + - - -
151A LYS 3.3 22.7 + - - -
152A GLN* 3.2 49.9 - - + +
153A ASP 4.9 0.7 - - - -
156A ALA* 4.8 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A TRP* 6.3 0.7 - - - -
143A PHE 3.2 16.6 + - - +
144A SER* 4.1 5.8 - - - +
146A TRP* 1.3 78.5 - - - +
148A ALA* 1.3 62.1 + - - +
150A GLY* 3.2 13.9 + - - -
152A GLN* 3.5 30.4 + - - +
157A TYR* 3.0 34.7 + - - -
179A GLN* 3.1 31.4 + - - +
180A MET 3.8 4.2 + - - -
181A PRO* 3.4 24.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A SER 3.1 20.9 + - - +
145A VAL* 3.6 7.2 - - + +
146A TRP 3.2 0.2 - - - -
147A ARG* 1.3 78.4 - - - +
149A SER* 1.3 60.1 + - - +
150A GLY 3.1 1.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A TRP* 3.5 23.4 + - - -
145A VAL 2.9 12.5 + - - -
146A TRP 2.6 18.1 + - - -
148A ALA* 1.3 77.1 - - - +
150A GLY* 1.3 55.2 + - - +
151A LYS* 2.9 38.9 + - - +
----------------------------------------------------------
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