Contacts of the strand formed by residues 414 - 421 (chain B) in PDB entry 2YA6
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 414 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B LEU* 3.8 22.4 - - + -
339B THR* 3.9 11.2 - - + -
345B ILE* 3.8 20.9 - - + -
405B LEU* 4.5 3.1 - - + -
406B VAL 3.4 3.4 - - - +
407B GLN* 3.9 20.2 - - + +
412B LYS 3.8 8.5 - - - +
413B ARG* 1.3 76.0 - - - +
415B PHE* 1.3 67.0 + - - +
525B TYR* 3.0 6.6 - - - +
526B SER* 2.7 42.3 + - - +
529B ASP* 3.7 33.7 - - - +
530B GLY 3.9 2.2 - - - +
533B TRP* 3.8 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 415 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404B VAL 3.5 0.9 - - - +
405B LEU* 3.2 12.5 - - - +
406B VAL* 2.7 56.5 + - + +
408B ASP* 4.1 7.6 - - + -
413B ARG* 3.6 44.0 - - + -
414B ILE* 1.3 74.1 - - - +
416B SER* 1.3 59.7 + - - +
417B ILE* 4.1 8.1 - - + -
523B MET* 3.8 31.4 - - + -
524B SER 3.5 2.2 - - - +
525B TYR* 3.9 8.5 - + + -
533B TRP* 4.4 0.7 - - - -
570B ILE* 4.1 16.4 - - + -
597B HIS 3.2 26.0 - - - -
598B GLY* 3.8 20.2 - - - -
601B TRP* 4.5 7.2 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 416 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B ILE* 3.8 11.7 - - - +
403B MET* 3.6 21.0 - - - +
404B VAL 3.4 4.7 - - - -
405B LEU* 3.9 9.4 - - - -
415B PHE* 1.3 72.5 - - - +
417B ILE* 1.3 62.1 + - - +
418B TYR* 3.3 23.4 - - - -
523B MET* 3.3 2.3 - - - -
524B SER* 2.7 38.3 + - - -
533B TRP* 3.8 20.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 417 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403B MET* 3.2 2.3 - - - -
404B VAL 2.8 38.9 + - - +
415B PHE* 4.7 6.5 - - + -
416B SER* 1.3 76.0 + - - +
418B TYR* 1.3 63.4 + - - +
521B LEU* 4.3 9.4 - - + -
522B TRP 3.3 10.1 - - - +
523B MET* 3.7 17.3 - - + -
539B ILE* 4.2 20.2 - - + -
553B VAL* 3.5 23.2 - - + +
572B ILE* 3.6 42.6 - - + -
592B ILE* 4.6 1.1 - - + -
601B TRP* 3.8 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 418 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363B MET* 3.6 28.5 - - + -
381B ILE* 4.5 3.6 - - + -
382B THR* 2.6 21.7 + - - -
400B ASN* 3.6 32.3 - - - -
401B ILE 4.4 0.2 - - - +
402B ASP 3.1 18.4 - - - +
403B MET* 4.0 1.8 - - + -
416B SER* 3.3 37.5 - - - -
417B ILE* 1.3 72.8 - - - +
419B ASP* 1.3 64.4 + - - +
521B LEU* 3.7 5.0 - - - +
522B TRP* 2.9 49.5 + + + +
524B SER* 2.5 30.3 + - - -
536B PRO* 3.8 12.0 - - - +
553B VAL* 4.3 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 419 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400B ASN* 3.0 17.9 + - - +
401B ILE* 3.0 43.4 + - + +
402B ASP* 4.0 6.2 - - - +
418B TYR* 1.3 77.2 - - - +
420B MET* 1.3 59.8 + - - +
421B PHE* 4.2 7.9 - - + -
519B SER* 6.0 0.2 - - - +
520B TYR 3.5 8.7 - - - +
521B LEU* 3.7 1.8 - - - +
550B PHE* 3.7 10.4 - - + -
551B LEU 5.3 0.2 - - - +
552B GLY* 3.1 14.3 - - - -
553B VAL* 3.0 27.6 + - - +
1777B DAN 3.4 26.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 420 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384B LEU* 4.2 6.7 - - + -
399B VAL 3.2 7.4 - - - +
400B ASN* 3.5 16.4 - - - +
419B ASP* 1.3 74.4 - - - +
421B PHE* 1.3 89.7 - - - +
422B PRO* 3.8 3.6 - - + -
504B TYR* 3.5 44.0 - - + -
515B ILE* 4.2 3.6 - - + -
520B TYR* 2.8 62.2 + - + +
522B TRP* 3.4 42.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 421 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398B PRO* 3.6 0.3 - - - +
399B VAL* 2.9 38.4 + - + -
401B ILE* 3.8 28.9 - - + -
419B ASP* 4.2 9.9 - - + -
420B MET* 1.3 89.8 - - - +
422B PRO* 1.3 75.3 - - + +
426B GLY* 3.7 31.2 - - - -
427B ILE* 3.6 20.4 - - + -
430B MET* 4.1 9.9 - - + -
518B ASP 3.7 15.0 - - - -
519B SER* 3.9 22.7 - - - -
550B PHE* 3.9 24.9 - + - -
1777B DAN 4.4 4.7 - - + -
----------------------------------------------------------
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