Contacts of the strand formed by residues 154 - 161 (chain A) in PDB entry 3ESF
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 LEU 154 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A VAL* 4.0 16.2 - - + -
130A GLN 3.5 3.4 - - - +
131A ASP* 4.3 9.9 - - + +
132A THR* 4.5 1.3 - - - -
138A LYS* 3.7 24.7 - - - +
140A PHE* 3.7 45.8 - - + -
148A PRO* 3.7 26.0 - - + +
149A LEU* 4.5 6.2 - - - +
151A GLU* 3.6 23.3 + - + +
152A ALA 3.6 2.5 + - - +
153A ASP* 1.3 94.2 - - - +
155A LYS* 1.3 61.2 + - - +
156A PRO* 3.9 6.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 155 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A VAL* 3.3 2.9 - - - -
130A GLN* 2.8 60.5 + - - +
132A THR* 3.7 22.2 - - + -
154A LEU* 1.3 72.0 - - - +
156A PRO* 1.3 78.0 - - + +
157A ILE* 3.6 8.9 + - + +
194A GLN* 3.0 20.5 + - + +
195A PHE 2.9 25.8 + - - -
197A ARG* 2.9 35.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 156 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A PHE* 4.1 24.9 - - + -
78A PHE* 3.3 23.6 - - + -
127A TRP* 3.6 29.6 - - + -
128A LEU 3.9 4.7 - - - +
129A VAL* 4.0 5.3 - - + -
148A PRO* 4.0 9.0 - - + -
149A LEU* 3.9 21.5 - - + -
154A LEU 3.9 2.9 - - - +
155A LYS* 1.3 92.6 - - + +
157A ILE* 1.3 64.2 + - - +
194A GLN* 3.7 8.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 157 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A PHE* 3.4 14.4 - - - -
95A LEU* 4.7 7.6 - - + -
128A LEU* 2.9 33.7 + - + +
129A VAL 4.2 2.9 - - - -
130A GLN* 4.0 13.9 - - + +
137A LEU* 4.4 10.5 - - + -
155A LYS* 3.9 20.2 - - - +
156A PRO* 1.3 81.2 - - - +
158A LEU* 1.3 65.2 + - - +
190A HIS* 3.7 13.7 + - - -
191A ALA* 3.6 32.3 - - + +
194A GLN* 3.7 9.6 - - - +
195A PHE* 3.5 33.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 158 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A PHE* 3.7 4.9 - - - -
82A SER* 3.6 25.1 - - - +
109A PHE* 4.9 4.5 - - + -
113A PHE* 5.2 4.9 - - + -
127A TRP* 3.3 7.4 - - - -
128A LEU* 3.0 43.9 + - + +
157A ILE* 1.3 80.2 - - + +
159A THR* 1.3 63.6 + - - +
182A PHE* 5.1 6.1 - - + -
183A TRP* 5.9 0.2 - - + -
186A VAL* 3.5 23.1 - - + -
187A ASN 3.6 23.3 - - - +
188A TRP* 3.5 33.7 - - + -
190A HIS* 4.5 1.1 - - - +
191A ALA* 3.7 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 159 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A ASN 3.8 9.6 - - - +
78A PHE* 3.9 8.5 - - + -
79A TYR* 3.5 38.1 - - + +
82A SER* 3.1 24.6 + - - -
113A PHE* 4.7 0.9 - - - -
125A TRP* 3.5 16.6 - - + +
126A ALA 3.0 16.7 + - - -
127A TRP* 3.4 32.3 - - + -
158A LEU* 1.3 74.4 - - - +
160A CYS* 1.3 59.9 + - - +
182A PHE* 3.4 11.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 160 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A TYR* 4.0 1.3 - - - -
113A PHE* 3.9 18.1 - - + -
117A ALA* 4.9 2.2 - - - -
125A TRP* 3.6 1.4 - - - -
126A ALA* 2.9 33.2 + - + -
159A THR* 1.3 76.0 - - - +
161A ASP* 1.3 66.5 + - - +
162A VAL* 3.5 11.4 + - - +
178A TYR* 3.6 30.5 - - - -
179A VAL* 4.8 7.2 - - - -
182A PHE* 3.7 38.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 161 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A HIS* 2.9 9.7 + - - -
76A HIS* 3.3 2.4 + - - -
79A TYR* 3.4 28.8 - - + -
124A GLY 3.7 1.0 - - - +
125A TRP* 3.5 29.3 - - + -
160A CYS* 1.3 69.3 - - - +
162A VAL* 1.3 62.0 + - - +
163A TRP* 3.2 27.1 + - - -
165A HIS* 3.6 0.5 + - - -
166A ALA* 3.7 11.2 - - + +
178A TYR* 2.6 33.1 + - - -
198A FE 2.0 33.4 - - - -
----------------------------------------------------------
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