Contacts of the strand formed by residues 428 - 434 (chain A) in PDB entry 2R5N
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 LEU 428 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A MET* 4.6 4.7 - - - -
372A LEU* 4.3 13.2 - - + -
374A GLU* 2.8 24.7 + - + +
375A PHE* 3.3 16.8 - - + -
376A LEU 3.1 18.3 + - - -
427A PHE* 1.3 72.1 - - - +
429A PRO* 1.3 81.1 - - + +
430A TYR* 5.5 0.2 - - + -
454A ARG* 3.5 37.5 - - + +
456A VAL* 4.2 13.0 - - + +
507A VAL* 3.7 48.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 429 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A LEU* 3.1 14.8 - - + +
407A TYR* 5.6 0.4 - - - +
418A ALA* 3.7 36.1 - - + +
421A ILE* 4.0 15.9 - - + -
422A SER* 3.9 12.8 - - - +
427A PHE 3.8 7.4 - - - +
428A LEU* 1.3 91.6 - - + +
430A TYR* 1.3 60.7 + - - +
431A THR* 5.4 0.2 - - + -
454A ARG* 3.6 21.1 - - - +
455A GLN* 3.5 9.9 - - + -
456A VAL 3.1 19.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 430 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A ILE* 3.6 20.6 - - + +
375A PHE* 3.9 28.5 - + + -
376A LEU 3.3 5.5 + - - +
377A GLY* 3.2 22.4 - - - -
378A GLY 3.0 33.1 + - - -
388A THR* 2.7 43.0 + - + -
404A TYR* 4.3 0.7 - - - -
407A TYR* 4.8 1.4 + - - -
428A LEU* 5.5 0.2 - - + -
429A PRO* 1.3 73.1 - - - +
431A THR* 1.3 68.8 + - - +
455A GLN* 4.7 0.2 - - - -
456A VAL* 3.1 26.7 - - + +
458A VAL* 4.4 14.4 - - + -
503A TRP* 4.0 13.5 - + + -
679A EDO 2.8 31.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 431 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A GLY 3.5 7.0 - - - -
407A TYR* 4.3 6.5 - - + +
414A MET* 3.6 31.9 - - + +
415A THR* 4.6 5.0 + - - +
418A ALA* 3.5 22.4 - - + -
429A PRO* 5.4 0.2 - - + -
430A TYR* 1.3 78.5 - - - +
432A SER* 1.3 65.4 + - - +
455A GLN* 2.8 28.7 + - - +
456A VAL 3.0 6.0 + - - +
457A MET* 4.1 8.8 - - - +
458A VAL* 2.8 28.2 + - - +
459A TYR* 4.9 4.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 432 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A GLY 3.2 6.5 + - - -
379A SER* 3.5 1.1 - - - -
380A ALA 3.0 27.2 + - - -
386A ASN* 3.0 30.4 + - - +
388A THR* 3.3 25.5 - - - +
414A MET* 3.3 9.2 - - - +
431A THR* 1.3 81.0 - - - +
433A THR* 1.3 62.7 + - - +
458A VAL* 2.7 26.6 + - - +
459A TYR* 4.9 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 433 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A ALA* 4.5 3.6 - - - +
382A LEU* 3.8 12.7 - - - +
386A ASN* 3.3 15.2 + - - -
411A GLU* 3.7 29.3 + - + +
414A MET* 4.5 4.9 - - + -
432A SER* 1.3 76.2 + - - +
434A PHE* 1.3 85.3 + - - +
437A PHE* 3.8 24.2 - - - +
438A VAL* 4.8 0.4 - - - -
441A ALA* 6.2 1.1 - - + -
458A VAL 3.3 5.9 + - - +
459A TYR* 3.4 22.1 - - + -
460A THR 3.3 17.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 434 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A LEU* 3.7 29.0 - - + +
385A SER* 3.9 17.0 - - - -
386A ASN* 3.7 3.5 - - - +
433A THR* 1.3 87.3 + - - +
435A LEU* 1.3 66.3 + - - +
436A MET* 4.4 4.5 - - + +
437A PHE* 2.9 42.0 + + + -
460A THR* 3.4 9.6 - - - +
461A HIS* 3.4 56.1 - + + +
466A LEU* 6.3 0.7 - - + -
469A ASP* 5.0 0.9 - - - -
473A HIS* 4.1 15.7 - + + +
670A R5P 3.4 37.5 - - - -
672B TPP 4.2 0.9 - - - -
----------------------------------------------------------
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