Contacts of the strand formed by residues 556 - 565 (chain B) in PDB entry 1PG4
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 GLY 556 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362B ARG* 3.5 16.5 - - - +
388B GLU* 4.3 4.3 - - - -
521B ASN 4.3 1.8 - - - -
551B PRO* 3.7 5.7 - - - +
552B HIS 3.0 30.3 + - - +
554B ILE 3.3 3.4 + - - -
555B LYS* 1.3 75.2 - - - +
557B GLN* 1.3 63.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 557 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519B VAL 4.6 1.4 - - - +
520B LEU* 3.5 14.3 - - + +
521B ASN* 2.9 45.3 + - + +
522B VAL* 3.5 26.9 - - + +
549B GLY* 3.7 28.1 + - - -
550B ILE* 3.1 11.6 - - - +
551B PRO* 5.2 0.4 - - + -
552B HIS* 4.1 3.8 - - - -
555B LYS* 2.9 11.8 + - - +
556B GLY* 1.3 80.4 - - - +
558B ALA* 1.3 62.7 + - - +
616B ARG* 5.8 4.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 558 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522B VAL* 5.1 0.4 - - - -
549B GLY* 3.4 6.6 - - - -
550B ILE* 2.8 50.3 + - + +
552B HIS* 4.0 24.8 - - + +
555B LYS* 4.8 2.2 - - + -
557B GLN* 1.3 74.9 - - - +
559B ILE* 1.3 64.8 + - - +
594B ASP* 3.3 23.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 559 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520B LEU* 4.4 5.8 - - + -
522B VAL* 3.7 27.8 - - + -
527B LEU* 4.1 0.9 - - + -
532B ILE* 4.1 13.5 - - + -
547B VAL* 3.8 25.1 - - + -
548B VAL 4.0 2.5 - - - -
549B GLY* 5.0 0.4 - - - -
550B ILE* 5.5 0.2 - - - -
558B ALA* 1.3 70.1 - - - +
560B TYR* 1.3 62.1 + - - +
561B ALA* 5.1 0.2 - - + -
590B LEU 3.8 9.0 - - - +
591B ALA* 3.4 36.8 - - - +
592B THR 3.7 6.1 - - - +
593B PRO* 3.7 27.1 - - + +
594B ASP* 2.8 39.2 + - - +
595B VAL* 3.1 6.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 560 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546B ALA 3.9 0.5 - - - +
547B VAL* 3.6 1.6 - - - -
548B VAL* 2.9 42.1 + - + +
550B ILE* 3.8 31.2 - - + -
558B ALA 3.5 0.6 + - - -
559B ILE* 1.3 73.5 - - - +
561B ALA* 1.3 61.1 + - - +
562B TYR* 3.5 35.1 + + - -
595B VAL* 3.5 30.9 - - + +
597B HIS* 2.9 41.1 + - + +
619B ALA* 3.8 16.4 - - + -
645B LYS* 3.3 34.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 561 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536B LEU* 3.9 27.8 - - + -
546B ALA 3.7 3.4 - - - +
547B VAL* 4.0 9.6 - - + -
559B ILE* 4.1 0.8 - - + -
560B TYR* 1.3 75.6 - - - +
562B TYR* 1.3 63.6 + - - +
563B VAL* 3.6 3.5 + - + +
593B PRO* 4.2 9.4 - - + -
595B VAL 2.9 15.1 + - - +
596B LEU* 3.5 16.3 - - + -
597B HIS 2.9 25.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 562 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545B ALA* 3.2 6.1 - - - +
546B ALA* 2.9 44.6 + - + +
548B VAL* 4.0 7.6 - - + -
560B TYR* 3.5 24.1 - + - -
561B ALA* 1.3 71.1 - - - +
563B VAL* 1.3 59.7 + - - +
597B HIS* 3.3 42.2 - + - -
599B THR* 4.1 4.7 - - + -
602B LEU* 3.7 19.8 - - + +
615B LEU* 2.6 67.6 + - + -
618B ILE* 3.8 8.3 - - + +
619B ALA* 3.4 15.2 + - - +
641B LEU* 4.2 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 563 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536B LEU* 4.5 15.0 - - + -
542B ILE* 3.7 39.5 - - + -
544B GLU 3.7 1.6 - - - -
545B ALA* 4.6 1.6 - - + -
561B ALA* 3.8 20.6 - - + +
562B TYR* 1.3 79.7 - - - +
564B THR* 1.3 68.7 + - - +
565B LEU* 3.9 2.9 + - + +
579B VAL* 5.0 0.4 - - + -
596B LEU* 4.3 14.8 - - + -
597B HIS 2.9 11.0 + - - +
598B TRP* 3.4 31.4 - - + +
599B THR* 3.0 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 564 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542B ILE* 3.8 3.1 - - - +
543B ALA* 2.9 33.1 + - + -
544B GLU* 2.9 27.2 + - + +
563B VAL* 1.3 72.5 - - - +
565B LEU* 1.3 65.8 + - - +
599B THR 2.9 15.1 + - - +
600B ASP* 3.4 27.7 - - + +
602B LEU* 3.6 25.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 565 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541B LYS* 3.5 16.4 - - + +
542B ILE* 4.1 16.6 - - + -
543B ALA* 4.4 2.5 - - - +
563B VAL* 3.9 2.8 + - + +
564B THR* 1.3 83.5 - - - +
566B ASN* 1.3 70.2 + - - +
567B HIS* 3.8 6.1 + - - -
569B GLU* 3.8 15.5 - - + +
571B PRO* 3.8 20.2 - - + -
575B LEU* 3.5 32.3 - - + -
598B TRP* 3.6 39.3 - - + -
599B THR 4.5 0.6 + - - -
600B ASP* 4.3 6.8 + - - +
----------------------------------------------------------
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