Contacts of the strand formed by residues 148 - 154 (chain A) in PDB entry 3IAY
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 SER 148 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A ARG* 3.6 15.1 - - - +
141A GLY 3.3 6.5 - - - -
147A HIS* 1.3 71.8 - - - +
149A VAL* 1.3 62.9 + - - +
288A SER 4.4 0.5 + - - -
289A CYS* 3.4 9.7 - - - -
290A GLN* 3.0 30.2 + - - +
291A LEU* 3.0 25.3 + - - +
394A ASP* 3.0 28.7 + - - -
428A ARG* 3.6 14.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A ILE* 4.1 13.0 - - + -
115A PHE* 3.9 27.8 - - + -
140A PHE* 3.2 6.8 - - - -
141A GLY 2.9 31.7 + - - +
143A THR* 3.7 30.1 - - + -
147A HIS 3.8 2.2 - - - +
148A SER* 1.3 81.5 - - - +
150A LEU* 1.3 72.2 + - - +
151A CYS* 4.0 12.8 - - + +
289A CYS* 3.9 9.1 - - - -
291A LEU* 3.3 18.6 - - + +
293A VAL* 4.5 6.7 - - + -
428A ARG* 5.7 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 150 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A ARG* 3.6 52.3 - - + +
139A PHE 3.5 7.6 - - - +
140A PHE* 3.8 13.7 - - + -
149A VAL* 1.3 73.5 - - - +
151A CYS* 1.3 64.3 + - - +
152A ASN* 4.1 7.2 - - - +
286A VAL* 4.0 5.2 - - + -
287A SER* 3.5 36.6 - - - +
289A CYS* 3.7 7.2 - - - +
291A LEU 2.8 13.0 + - - +
292A GLU* 3.8 17.5 - - + -
293A VAL* 2.9 27.9 + - - +
429A LEU* 4.1 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A PHE* 3.7 25.6 - - + -
137A VAL 3.5 0.5 - - - +
139A PHE* 2.9 37.3 + - + +
149A VAL* 4.0 1.7 - - + -
150A LEU* 1.3 75.0 - - - +
152A ASN* 1.3 64.8 + - - +
153A VAL* 3.5 10.6 + - - +
270A ILE* 5.8 1.1 - - - -
272A LEU* 3.6 35.4 - - + -
293A VAL* 3.6 13.7 - - + -
295A ILE* 3.6 22.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 152 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A LEU* 3.6 25.0 - - + +
136A VAL* 4.1 10.2 - - + +
137A VAL 3.8 4.0 - - - -
138A ARG* 2.6 41.9 + - - +
150A LEU* 4.1 4.1 - - - +
151A CYS* 1.3 70.5 - - - +
153A VAL* 1.3 61.2 + - - +
154A THR* 3.6 2.4 + - + +
280A ILE* 3.7 13.7 - - - +
292A GLU* 4.8 4.6 + - - +
293A VAL 2.9 18.2 + - - -
294A SER* 3.2 24.0 + - - +
295A ILE* 2.9 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 153 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A THR 4.5 0.2 - - - +
136A VAL* 3.4 6.1 - - - +
137A VAL 2.8 33.6 + - - +
139A PHE* 3.6 30.3 - - + -
151A CYS* 4.1 14.1 - - - +
152A ASN* 1.3 74.4 - - - +
154A THR* 1.3 60.0 + - - +
156A PHE 5.1 0.5 + - - -
254A TYR* 5.0 1.0 + - - -
258A LEU* 4.0 19.3 - - + +
270A ILE* 6.0 0.9 - - + -
295A ILE* 3.4 4.5 - - + +
297A TYR* 3.4 38.4 - - + +
300A LEU* 3.7 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 154 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A LEU* 4.0 18.2 - - + -
130A ASP* 2.5 33.2 + - + +
133A THR 5.9 0.4 - - - -
135A THR 4.8 0.7 - - - -
136A VAL* 3.8 24.0 - - + -
152A ASN 3.9 11.0 - - - +
153A VAL* 1.3 74.3 - - - +
155A GLY* 1.3 63.9 + - - +
156A PHE 3.2 4.9 + - - -
294A SER* 4.3 10.5 - - - -
295A ILE 2.8 16.1 + - - +
296A ASN* 3.5 5.4 + - - -
297A TYR* 3.0 25.5 + - - +
----------------------------------------------------------
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