Contacts of the strand formed by residues 369 - 376 (chain A) in PDB entry 1RP1
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 PHE 369 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A LYS* 3.2 4.6 - - - -
357A VAL 2.8 35.0 + - - +
366A THR* 4.1 7.0 - - - -
367A HIS* 3.2 35.2 - - + -
368A GLN* 1.3 76.1 - - - +
370A ASN* 1.3 67.6 + - - +
371A ILE* 3.2 5.9 + - - +
386A PHE* 3.4 56.5 - + + -
387A ASP 3.2 29.2 - - - -
388A ALA* 3.6 19.7 - - + -
389A LYS* 5.0 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 370 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A GLN* 3.4 28.6 + - - +
355A ALA 4.0 1.6 - - - -
356A LYS* 2.7 32.6 + - - +
368A GLN 4.3 0.5 + - - +
369A PHE* 1.3 73.4 - - - +
371A ILE* 1.3 64.4 + - - +
384A ASN* 3.5 15.9 + - - -
386A PHE* 5.4 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 371 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A VAL* 3.3 28.3 - - + -
344A ILE* 3.6 29.8 - - + -
354A GLN* 4.3 0.2 - - - -
355A ALA 2.9 11.7 + - - +
357A VAL* 3.8 18.6 - - + +
369A PHE 3.5 11.2 - - - +
370A ASN* 1.3 82.6 - - - +
372A PHE* 1.3 67.1 + - + +
382A HIS 4.0 16.8 - - - +
383A SER 4.2 5.3 - - - +
384A ASN* 3.3 34.3 + - + +
386A PHE* 3.8 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 372 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A GLY 3.8 0.9 - - - +
354A GLN* 2.9 5.6 + - - +
355A ALA* 2.8 37.9 + - + +
371A ILE* 1.3 84.9 - - + +
373A LYS* 1.3 80.7 + - - +
374A GLY* 4.0 5.2 - - - -
375A ILE 3.6 22.7 - - - -
376A LEU* 3.8 12.5 - - + +
382A HIS* 3.5 62.4 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 373 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A GLY 3.3 12.3 - - - +
354A GLN* 3.4 32.7 + - - +
372A PHE* 1.3 90.0 - - - +
374A GLY* 1.3 60.6 + - - +
406A ASN* 3.7 31.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 374 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A THR* 3.2 5.3 - - - -
353A GLY 2.8 34.5 + - - +
372A PHE* 4.0 6.8 - - - -
373A LYS* 1.3 79.1 - - - +
375A ILE* 1.3 66.2 + - - -
376A LEU* 3.4 0.9 + - - -
406A ASN* 5.5 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 375 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A ARG* 3.1 52.5 - - + +
351A ALA 3.5 7.2 - - - +
352A THR* 3.4 20.2 - - + -
372A PHE* 3.6 17.3 - - - -
374A GLY* 1.3 71.8 - - - -
376A LEU* 1.3 62.0 + - - +
377A LYS* 3.5 15.1 + - + +
382A HIS* 4.5 4.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 376 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A LEU* 3.7 22.4 - - + -
349A LYS 3.8 3.6 - - - +
350A ARG* 3.3 5.4 - - - -
351A ALA* 2.6 37.0 + - - +
352A THR 4.6 0.2 - - - -
353A GLY 3.9 24.5 - - - +
354A GLN 4.6 0.2 - - - +
355A ALA* 4.0 16.6 - - + +
372A PHE* 3.8 26.9 - - + -
374A GLY 4.0 5.6 - - - +
375A ILE* 1.3 72.1 - - - +
377A LYS* 1.3 59.2 + - - +
378A PRO 4.0 0.2 - - - -
402A TRP* 3.9 35.9 - - + -
415A VAL* 4.2 23.2 - - + +
----------------------------------------------------------
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