Contacts of the strand formed by residues 160 - 168 (chain A) in PDB entry 3I5D
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 LYS 160 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A THR* 3.6 10.4 - - - +
129A CYS 3.2 29.4 + - - +
130A THR 6.1 0.7 - - - +
152A CYS* 4.6 7.2 - - - -
153A VAL 3.4 14.1 - - - +
154A SER* 3.7 11.0 - - - +
155A TYR* 3.8 2.0 - - - +
159A VAL* 1.3 78.2 - - - +
161A THR* 1.3 62.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 161 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A ALA* 3.9 2.7 - - + -
121A GLU* 3.2 39.8 - - - +
122A ASN 4.8 1.8 - - - -
123A PRO* 5.1 5.2 - - - -
127A SER* 2.6 41.7 + - - -
128A THR* 4.2 3.4 - - - -
129A CYS* 3.7 11.4 - - - -
153A VAL* 2.5 36.6 + - - +
155A TYR* 3.8 17.0 - - + -
160A LYS* 1.3 75.4 - - - +
162A CYS* 1.3 62.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 162 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A GLU* 3.1 30.5 + - - +
127A SER 3.3 9.2 + - - +
128A THR 5.4 0.2 - - - -
129A CYS* 3.9 6.7 - - - -
134A ASP* 4.3 1.3 - - - -
135A CYS* 2.0 52.0 - - - -
148A ARG* 2.9 51.8 - - - +
161A THR* 1.3 77.8 + - - +
163A GLU* 1.3 61.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 163 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A LYS* 3.3 20.3 - - + +
119A CYS* 3.4 21.1 + - - +
148A ARG* 3.4 5.9 - - - +
149A THR* 3.0 47.8 + - + +
151A ARG* 3.1 33.9 + - - +
153A VAL* 3.5 29.7 - - + +
161A THR 3.4 3.2 + - - -
162A CYS* 1.3 71.9 - - - +
164A VAL* 1.3 63.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 164 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A LYS* 3.3 3.8 - - - -
119A CYS* 2.7 48.8 + - - +
121A GLU* 3.2 41.5 - - + +
144A GLY 5.4 1.6 - - - +
146A GLY* 3.8 20.2 - - - +
147A VAL 2.9 11.9 - - - +
148A ARG* 3.3 29.6 - - + -
149A THR 4.3 0.4 - - - +
162A CYS 3.8 0.2 - - - +
163A GLU* 1.3 75.3 - - - +
165A LEU* 1.3 60.0 + - - +
166A SER* 4.5 5.8 - - - -
170A LEU* 4.6 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 165 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A GLN* 5.6 1.6 - - - +
117A SER 3.1 13.2 - - - +
118A LYS* 3.7 10.0 - - + +
137A ARG* 5.6 1.1 - - - +
147A VAL* 2.6 57.1 + - + +
149A THR* 4.8 13.8 - - + +
164A VAL* 1.3 70.7 - - - +
166A SER* 1.3 63.0 + - - +
76B LEU* 4.0 14.6 - - + -
84B GLU* 3.5 39.0 - - + +
85B ARG 5.2 0.9 - - - +
86B ILE* 3.2 26.6 - - + +
401B NAG 5.1 5.6 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
115A THR 3.5 0.7 - - - +
116A GLN* 3.7 8.8 + - - +
117A SER 2.8 31.3 + - - +
145A ASP 3.1 16.3 + - - -
146A GLY* 3.5 15.9 - - - -
164A VAL* 4.5 9.2 - - - -
165A LEU* 1.3 80.1 - - - +
167A TRP* 1.3 80.9 + - - +
168A CYS* 3.4 5.1 + - - -
170A LEU* 4.6 5.4 - - - +
86B ILE* 3.6 16.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 167 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A GLN* 3.4 31.5 + - - +
115A THR* 3.6 39.9 - - - -
116A GLN* 3.5 27.2 - - + +
166A SER* 1.3 85.1 + - - +
168A CYS* 1.3 59.2 + - - +
169A PRO 3.5 11.7 - - - +
170A LEU* 4.1 6.4 + - - +
302A TYR* 4.3 1.3 - + - -
310A GLU* 3.7 26.9 - - + -
312A ARG* 3.3 58.5 - - + +
85B ARG* 3.8 2.2 - - - -
86B ILE* 3.8 13.7 + - + +
88B ASP* 3.8 13.5 + - + +
92B TYR* 3.4 35.9 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 168 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A ASN 3.5 2.1 - - - +
114A GLN* 3.3 2.6 - - - -
115A THR* 3.0 38.7 + - - +
117A SER* 3.9 24.5 - - - -
118A LYS 3.8 5.6 - - - +
119A CYS* 2.0 52.3 - - + -
164A VAL 4.4 1.1 - - - -
166A SER* 4.2 4.0 - - - -
167A TRP* 1.3 75.9 - - - +
169A PRO* 1.3 64.8 - - + +
170A LEU* 4.0 3.4 - - - -
----------------------------------------------------------
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