Contacts of the strand formed by residues 166 - 170 (chain A) in PDB entry 1IAX
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 GLN 166 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A GLY* 2.7 28.2 + - - -
143A ASP 2.9 16.7 + - - +
144A ALA* 3.1 13.2 - - + +
145A PHE 2.9 25.5 + - - -
160A ARG* 4.2 4.9 - - - +
164A GLY 4.1 0.6 + - - +
165A VAL* 1.3 79.0 - - - +
167A LEU* 1.3 65.6 + - - +
168A ILE* 4.8 4.2 - - + +
197A ILE* 3.5 38.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 167 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A PHE* 3.5 12.8 - - + -
147A VAL* 3.7 21.5 - - + -
151A TYR* 4.1 11.9 - - + +
155A PHE* 4.0 20.2 - - + +
156A ASN* 3.9 20.6 - - - +
159A LEU* 3.6 42.0 - - + -
160A ARG* 3.7 21.9 + - + +
165A VAL* 5.1 2.2 - - + -
166A GLN* 1.3 83.5 - - - +
168A ILE* 1.3 65.1 + - - +
169A PRO* 3.7 8.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 168 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A ALA* 3.7 28.0 - - + -
145A PHE 2.8 13.0 + - - +
146A LEU* 3.4 20.0 - - + +
147A VAL* 2.9 26.8 + - - +
166A GLN* 4.8 4.9 - - - +
167A LEU* 1.3 79.1 - - - +
169A PRO* 1.3 75.5 - - + +
188A ALA* 4.4 11.4 - - + +
192A ALA* 3.4 29.4 - - + -
197A ILE* 3.8 15.9 - - + -
199A VAL* 4.3 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 169 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A VAL* 3.4 9.2 - - + +
149A SER* 4.9 12.1 - - - +
151A TYR* 5.0 11.4 - - + +
167A LEU* 3.7 8.7 - - + +
168A ILE* 1.3 97.7 - - + +
170A ILE* 1.3 62.3 + - - +
171A HIS 4.3 0.7 + - - -
188A ALA* 4.0 5.9 - - - +
404A GLU* 5.9 3.6 - - + +
406A GLN* 5.0 13.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 170 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A LEU* 3.9 24.0 - - + -
147A VAL 3.0 20.9 + - - +
148A PRO* 3.9 13.5 - - + -
149A SER* 3.3 26.1 + - - +
168A ILE 4.3 4.5 - - - +
169A PRO* 1.3 75.6 - - - +
171A HIS* 1.3 73.8 + - - +
172A CYS* 3.9 2.1 - - - -
180A ILE* 4.8 7.4 - - + -
184A ALA* 3.7 25.4 - - + +
185A VAL* 4.3 27.1 - - + +
188A ALA* 3.8 19.1 - - + -
202A LEU* 4.4 9.2 - - + -
406A GLN* 4.5 1.1 - - - -
----------------------------------------------------------
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