Contacts of the strand formed by residues 493 - 498 (chain A) in PDB entry 2IAG
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 PRO 493 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A MET 3.7 6.7 - - - +
163A GLY* 4.5 2.5 - - - -
466A LEU* 3.8 2.3 - - - +
467A ILE* 3.1 38.9 + - + +
468A ASN 4.8 0.5 + - - -
471A VAL* 5.2 9.0 - - + +
491A ASP 3.8 8.1 - - - +
492A VAL* 1.3 90.4 - - + +
494A VAL* 1.3 63.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 494 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A GLU* 3.6 3.3 - - - +
162A MET* 2.8 46.1 + - + +
163A GLY 4.1 0.7 - - - +
164A LEU* 3.7 45.5 - - + +
167A PHE* 5.0 3.8 - - + -
300A LEU* 4.6 4.3 - - + -
464A LEU* 4.1 17.3 - - + -
465A GLU 3.1 16.8 - - - +
466A LEU* 4.0 19.5 - - + -
467A ILE* 3.9 9.4 - - - +
492A VAL 3.8 0.9 - - - +
493A PRO* 1.3 80.7 - - - +
495A ARG* 1.3 61.4 + - - +
496A TYR* 6.0 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 495 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A TRP* 3.4 57.7 - - + +
160A HIS 3.2 12.3 - - - +
161A GLU* 4.1 12.3 - - + -
464A LEU* 3.6 3.6 - - - +
465A GLU* 2.8 65.3 + - + +
466A LEU 5.4 1.3 + - - +
467A ILE* 4.0 20.1 - - + +
494A VAL* 1.3 74.6 - - - +
496A TYR* 1.3 62.8 + - - +
134B GLN* 5.1 3.8 - - - +
332B GLN* 3.2 41.2 + - - +
336B ASP* 5.3 0.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 496 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A LEU* 4.8 2.9 - - + -
151A ASP* 4.8 3.6 + - - +
152A ALA* 4.1 28.3 + - + +
155A ALA* 5.7 0.9 - - - +
159A TRP* 3.4 5.6 - - - -
160A HIS* 2.7 73.9 + - + +
162A MET* 4.0 20.6 - - + -
167A PHE* 3.7 31.2 - + + -
171A PHE* 4.2 13.9 - + - -
462A LEU* 3.7 26.7 - - + -
463A ASP 3.1 13.5 - - - +
464A LEU* 3.8 14.6 - - + -
494A VAL* 6.0 0.2 - - + -
495A ARG* 1.3 75.9 - - - +
497A ARG* 1.3 68.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 497 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A SER 4.1 6.7 - - - +
158A GLY* 3.6 22.0 - - - +
159A TRP* 3.4 47.3 - - + +
160A HIS* 5.0 1.1 - - - -
462A LEU* 3.1 12.1 - - - +
463A ASP* 2.7 62.8 + - + -
465A GLU* 5.6 0.2 + - - -
496A TYR* 1.3 80.9 - - - +
498A ILE* 1.3 66.5 + - - +
500A PRO* 3.5 28.8 - - - +
133B LEU* 5.5 8.9 - - - +
336B ASP* 3.5 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 498 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A LEU* 4.2 15.7 - - + -
152A ALA* 3.5 34.9 - - + +
153A THR* 4.2 18.8 - - - +
156A GLY 5.8 1.6 - - - +
157A SER* 4.4 16.6 + - - +
158A GLY 5.2 0.4 + - - -
160A HIS* 5.9 1.2 + - - -
461A HIS* 3.6 10.1 - - + +
462A LEU* 3.9 12.5 - - + +
496A TYR* 4.7 1.6 - - - -
497A ARG* 1.3 80.6 - - - +
499A ARG* 1.3 74.4 + - - +
500A PRO* 3.2 6.1 - - + +
----------------------------------------------------------
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