Contacts of the strand formed by residues 542 - 552 (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 ILE 542 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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536B LEU* 3.3 39.0 - - + +
537B VAL* 3.6 8.8 - - - +
539B HIS* 3.0 16.6 + - + +
541B LYS* 1.3 81.2 - - + +
543B ALA* 1.3 63.5 + - - +
544B GLU 3.6 24.0 - - - +
545B ALA* 4.7 2.0 - - + -
563B VAL* 3.7 26.7 - - + -
564B THR 3.8 2.7 - - - +
565B LEU* 4.1 8.3 - - + -
566B ASN* 3.8 4.8 + - - -
579B VAL* 4.0 30.5 - - + -
582B TRP* 5.9 0.4 - - + -
903B MG 2.4 30.1 - - - -
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Residues in contact with ALA 543 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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537B VAL* 3.8 14.6 - - - +
541B LYS 4.0 0.8 + - - -
542B ILE* 1.3 75.0 - - - +
544B GLU* 1.3 64.3 + - + +
564B THR* 2.9 20.8 + - + +
565B LEU 4.4 2.2 - - - +
566B ASN* 3.1 30.1 + - - +
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Residues in contact with GLU 544 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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537B VAL* 4.0 9.2 - - + -
542B ILE* 3.6 4.7 - - - +
543B ALA* 1.3 82.4 - - + +
545B ALA* 1.3 71.3 + - - +
563B VAL* 3.7 0.2 - - - -
564B THR* 2.9 37.4 + - + +
602B LEU* 3.5 22.6 - - + +
604B LYS* 2.9 41.9 + - - -
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Residues in contact with ALA 545 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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533B GLU* 3.7 21.3 - - - +
536B LEU* 3.9 38.1 - - + -
537B VAL* 3.9 12.4 - - + +
542B ILE* 4.7 1.3 - - + -
544B GLU* 1.3 84.5 - - - +
546B ALA* 1.3 61.4 + - - +
547B VAL 4.2 0.4 - - - -
562B TYR 3.2 12.1 - - - +
563B VAL* 4.6 3.8 - - + -
602B LEU* 4.5 4.9 - - - -
612B ARG* 4.8 1.7 + - - -
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Residues in contact with ALA 546 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533B GLU* 3.3 5.6 - - - -
545B ALA* 1.3 75.1 - - - +
547B VAL* 1.3 62.5 + - - +
548B VAL* 5.0 0.4 - - - -
562B TYR* 2.9 40.5 + - + -
602B LEU* 4.2 15.5 - - + +
610B ILE* 5.7 2.9 - - + -
612B ARG* 4.1 13.2 - - + +
615B LEU* 3.4 33.0 - - + -
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Residues in contact with VAL 547 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520B LEU* 4.1 17.7 - - + -
529B THR* 3.0 30.6 + - + +
532B ILE* 3.7 28.7 - - + -
533B GLU* 2.8 30.8 + - + -
536B LEU* 3.9 16.6 - - + -
546B ALA* 1.3 73.5 - - - +
548B VAL* 1.3 71.6 + - - +
559B ILE* 3.8 26.2 - - + -
560B TYR 3.6 3.6 - - - +
561B ALA* 4.0 8.3 - - + -
612B ARG* 3.8 4.5 - - - -
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Residues in contact with VAL 548 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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520B LEU* 4.3 6.7 - - - -
529B THR* 5.4 0.2 - - - -
546B ALA 4.9 0.9 - - - +
547B VAL* 1.3 84.0 - - - +
549B GLY* 1.3 63.3 + - - +
559B ILE* 3.9 2.3 - - - -
560B TYR* 2.9 43.7 + - + +
562B TYR* 4.0 9.9 - - + -
612B ARG* 4.2 15.9 - - + +
615B LEU* 4.0 13.9 - - + -
616B ARG* 3.9 36.8 - - + +
619B ALA* 3.8 29.4 - - + -
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Residues in contact with GLY 549 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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520B LEU* 3.6 20.6 - - - +
548B VAL* 1.3 75.2 - - - +
550B ILE* 1.3 65.2 + - - +
551B PRO* 4.8 0.5 - - - +
557B GLN* 3.7 26.6 + - - +
558B ALA 3.4 7.9 - - - -
616B ARG* 3.9 23.3 - - - +
620B ALA* 5.7 0.2 - - - +
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Residues in contact with ILE 550 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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548B VAL* 4.4 0.7 - - + -
549B GLY* 1.3 79.5 - - - +
551B PRO* 1.3 77.6 - - + +
557B GLN* 3.1 7.2 - - - -
558B ALA* 2.8 53.3 + - + +
559B ILE 5.5 0.2 - - - -
560B TYR* 3.8 27.8 - - + -
595B VAL* 4.8 10.3 - - + -
616B ARG 4.9 0.2 - - - +
619B ALA* 3.4 46.2 - - + +
620B ALA* 4.1 2.5 - - + +
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Residues in contact with PRO 551 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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549B GLY 4.8 0.7 - - - +
550B ILE* 1.3 99.7 - - + +
552B HIS* 1.3 60.7 + - - +
556B GLY 3.7 8.5 - - - +
557B GLN* 5.3 0.9 - - + -
620B ALA* 3.8 25.1 - - + +
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Residues in contact with HIS 552 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362B ARG* 5.1 0.2 + - - -
550B ILE* 6.2 0.2 - - - +
551B PRO* 1.3 77.3 + - - +
553B ALA* 1.3 67.3 + - - +
554B ILE* 3.3 21.3 - - + +
555B LYS* 3.0 56.6 - - + +
556B GLY* 3.0 30.1 + - - +
558B ALA* 4.0 30.0 - - + +
594B ASP* 6.3 0.4 - - - -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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