Contacts of the strand formed by residues 324 - 329 (chain A) in PDB entry 1IJH
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 324 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A GLY 3.9 3.1 - - - +
323A ASN* 1.3 83.3 - - - +
325A MET* 1.3 67.3 + - - +
326A THR* 4.2 0.4 + - - -
376A TYR 3.9 0.2 - - - +
377A LEU* 3.7 0.9 - - - -
378A ALA* 2.7 40.2 + - + +
380A THR* 4.7 0.7 - - + -
406A ASN* 4.2 5.8 - - - -
409A ALA* 3.6 37.7 - - + +
410A VAL* 3.7 23.6 - - + -
413A ALA* 4.1 14.8 - - + -
440A PHE* 3.9 32.8 - - + -
441A ALA 3.5 14.8 - - - +
442A ASP* 4.0 9.2 - - + -
444A PHE* 3.9 4.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 325 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A LEU* 4.4 20.2 - - + +
324A ILE* 1.3 73.7 - - - +
326A THR* 1.3 66.3 + - - +
363A ALA* 5.2 2.5 - - + -
375A LEU* 3.9 21.5 - - + -
376A TYR 3.2 23.1 - - - +
377A LEU* 3.7 35.2 - - + -
433A PHE* 3.6 20.4 - - + -
440A PHE* 3.3 2.8 - - - -
441A ALA* 2.8 46.3 + - + -
444A PHE* 3.4 21.6 - - + -
446A TYR* 4.3 14.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 326 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A ILE* 5.0 1.8 - - - +
325A MET* 1.3 78.0 - - - +
327A ALA* 1.3 66.8 + - - +
375A LEU* 3.6 5.1 - - - +
376A TYR* 2.9 38.0 + - + +
378A ALA* 5.7 0.7 - - + -
413A ALA* 5.4 2.7 - - + -
417A PHE* 3.8 39.0 - - + -
428A TYR* 3.7 12.3 - - + -
433A PHE* 4.4 3.4 - - - -
439A ALA 2.8 20.7 + - - -
440A PHE* 3.3 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 327 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A THR* 1.3 80.6 + - - +
328A ARG* 1.3 64.2 - - - +
373A VAL* 3.9 7.9 - - + -
374A SER 3.1 13.0 - - - +
375A LEU* 4.1 5.2 - - + -
376A TYR* 4.4 1.8 - - - -
428A TYR* 3.4 13.8 - - - +
429A ARG* 3.0 26.5 + - + +
432A LEU* 3.4 33.2 - - + -
433A PHE* 5.2 2.2 - - + -
439A ALA 4.1 2.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 328 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A SER* 4.7 0.4 + - - -
180A GLN* 2.9 38.8 + - - +
327A ALA* 1.3 78.3 - - - +
329A ALA* 1.3 62.9 + - - +
330A ASN* 3.7 5.4 + - - +
373A VAL* 3.6 4.2 - - - +
374A SER* 2.9 37.6 + - - +
376A TYR* 3.0 38.8 + - + -
417A PHE* 4.0 18.2 - - + -
420A ILE* 3.4 28.8 - - - +
421A ASN* 2.8 28.3 + - - +
424A ASN* 4.1 2.4 - - - +
426A THR* 2.9 21.6 + - - +
427A ILE 3.7 5.6 - - - +
428A TYR* 4.3 9.6 - - + -
429A ARG* 4.3 4.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 329 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A ARG* 1.3 71.6 - - - +
330A ASN* 1.3 64.9 + - - +
372A TRP* 4.1 4.0 - - + -
373A VAL* 5.0 0.7 - - - +
426A THR* 3.5 23.7 - - - +
427A ILE* 2.9 29.7 + - + +
428A TYR 4.7 1.1 - - - +
429A ARG* 3.9 26.9 - - - +
----------------------------------------------------------
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