Contacts of the strand formed by residues 149 - 157 (chain A) in PDB entry 2IUK
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 ILE 149 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A ILE* 3.6 13.2 - - + -
120A PRO* 3.4 46.4 - - + +
139A LYS* 3.3 4.0 - - - -
140A LEU* 2.8 41.3 + - + +
143A ILE* 3.7 16.4 - - + -
146A HIS* 3.9 11.9 - - + +
147A GLY 3.7 12.6 - - - +
148A THR* 1.3 71.6 - - - +
150A GLU* 1.3 59.3 + - - +
151A PHE* 3.7 13.4 - - + -
171A VAL* 3.3 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 150 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A VAL 3.9 3.1 - - - +
139A LYS* 4.7 21.5 - - + +
148A THR* 3.7 10.5 + - - +
149A ILE* 1.3 76.2 - - - +
151A PHE* 1.3 64.1 + - - +
171A VAL* 3.3 18.4 - - - +
172A ASN* 2.9 38.0 + - - +
797A ASN* 2.9 35.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A LEU* 5.8 0.2 - - + -
120A PRO* 4.0 6.3 - - + -
121A GLY 3.8 1.3 - - - -
122A ALA* 3.6 34.8 - - - -
123A PHE* 3.8 29.4 - + + -
137A SER* 3.8 8.0 - - - -
138A VAL* 3.0 42.2 + - + +
140A LEU* 4.0 22.0 - - + -
149A ILE* 3.7 32.5 - - + -
150A GLU* 1.3 77.6 - - - +
152A VAL* 1.3 61.9 + - - +
153A CYS* 3.8 8.5 - - - -
170A PHE* 3.2 29.2 - - - +
171A VAL* 3.3 17.3 - - - +
172A ASN 4.6 0.7 - - - +
797A ASN* 5.3 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 152 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A VAL 4.4 3.6 - - - +
137A SER* 5.2 0.7 - - - -
151A PHE* 1.3 72.4 - - - +
153A CYS* 1.3 62.9 + - - +
154A ASN* 3.8 20.6 - - + +
169A PHE* 5.1 1.6 - - - -
170A PHE 4.4 8.8 + - - +
172A ASN* 4.2 12.5 - - + +
546A VAL* 6.0 1.6 - - - +
795A THR* 3.3 28.3 - - + +
797A ASN* 3.3 44.2 - - - +
798A TRP* 4.4 5.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 153 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A PHE* 3.6 35.9 - - - -
135A LEU* 3.7 22.2 - - + +
136A VAL 3.2 16.1 + - - +
137A SER* 4.2 10.3 - - - -
151A PHE* 3.8 10.7 - - - -
152A VAL* 1.3 76.5 - - - +
154A ASN* 1.3 71.8 + - - +
155A SER* 3.4 8.2 + - - -
169A PHE* 3.7 26.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 154 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A PHE* 3.4 28.2 - - + -
135A LEU 2.9 13.3 + - - -
136A VAL* 3.4 25.2 + - - +
152A VAL* 3.8 21.6 - - - +
153A CYS* 1.3 75.1 - - - +
155A SER* 1.3 58.6 + - - +
266A ASP* 4.3 8.5 - - - +
794A GLU* 3.8 31.3 - - - +
795A THR* 4.1 8.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 155 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A PHE* 3.5 7.4 - - - -
135A LEU* 2.9 29.1 + - - +
153A CYS 3.8 2.7 - - - -
154A ASN* 1.3 79.0 - - - +
156A TRP* 1.3 62.5 + - - +
157A VAL* 3.4 7.7 - - - +
167A ARG* 2.8 26.2 + - - -
169A PHE* 3.6 24.7 - - - -
266A ASP* 2.8 26.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 156 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A LYS* 3.9 28.3 - - + -
23A LEU* 3.9 43.5 - - + -
132A GLU* 3.6 22.2 - - + -
133A PHE 3.2 25.6 - - - -
134A PHE* 3.5 23.1 - + + -
155A SER* 1.3 69.1 + - - +
157A VAL* 1.3 61.2 + - - +
158A TYR* 3.9 16.6 - - + -
163A TYR* 2.9 18.4 + - - -
167A ARG* 3.0 9.5 + - - -
208A ARG* 5.4 0.5 - - - -
265A ARG* 3.2 49.4 - - + +
266A ASP* 3.3 20.3 + - - +
268A ASN 4.3 5.8 + - - -
269A PHE* 5.9 0.2 - - - +
270A GLY* 5.1 9.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 157 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A ILE* 4.0 22.2 - - + +
127A ASN* 3.2 22.9 - - + +
132A GLU* 3.4 13.3 - - - -
133A PHE* 2.9 33.7 + - + -
135A LEU* 3.8 25.8 - - + -
155A SER 3.4 16.2 - - - +
156A TRP* 1.3 73.4 - - - +
158A TYR* 1.3 64.2 + - - +
163A TYR* 4.1 1.8 - - + -
167A ARG* 4.2 15.0 - - + +
169A PHE* 4.1 13.2 - - + -
----------------------------------------------------------
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