Contacts of the strand formed by residues 551 - 562 (chain B) in PDB entry 1PO3
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 551 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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546B TYR* 3.1 40.3 - - + -
548B ASP 3.4 8.1 + - - -
550B ALA* 1.3 80.4 - - + +
552B THR* 1.3 66.0 + - - +
553B ALA* 4.2 17.9 - - + -
590B ALA* 5.0 5.2 - - + -
591B ARG 3.7 9.6 - - - +
592B TYR* 4.6 7.0 - - - -
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Residues in contact with THR 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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546B TYR 3.2 15.6 + - - -
547B ASP* 3.4 22.0 + - - +
550B ALA 4.0 1.5 - - - -
551B LEU* 1.3 73.4 - - - +
553B ALA* 1.3 61.0 + - - +
590B ALA* 3.1 7.2 - - - +
591B ARG* 3.0 55.6 + - + +
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Residues in contact with ALA 553 (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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544B THR 4.4 0.2 - - - +
545B ARG* 4.7 0.2 - - - +
546B TYR* 2.6 49.0 + - + +
551B LEU* 4.2 15.9 - - + -
552B THR* 1.3 77.6 + - - +
554B GLU* 1.3 59.1 + - - +
588B THR* 6.0 0.2 - - - +
589B GLN 3.5 6.7 - - - +
590B ALA* 3.6 15.0 - - + +
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Residues in contact with GLU 554 (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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103B ALA* 5.8 1.4 - - - +
104B ARG 4.1 2.6 + - - +
105B ASP* 3.1 36.1 - - - +
128B PRO* 4.8 2.3 - - - +
196B ARG* 5.0 3.6 + - - -
544B THR* 3.5 12.6 - - - +
545B ARG* 3.2 34.5 + - + +
553B ALA* 1.3 76.3 - - - +
555B MET* 1.3 56.0 + - - +
587B GLU* 6.2 0.2 - - - +
588B THR* 2.7 26.9 + - - -
589B GLN* 3.1 44.0 + - + +
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Residues in contact with MET 555 (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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508B TYR* 4.9 2.5 + - - -
543B GLY* 3.6 0.9 - - - -
544B THR* 3.1 46.0 + - + +
554B GLU* 1.3 76.1 - - - +
556B GLY* 1.3 63.9 + - - +
557B LEU* 6.2 1.1 - - + -
586B LEU* 4.2 25.6 - - + -
587B GLU 3.2 11.9 - - - +
588B THR* 3.5 13.0 - - - +
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Residues in contact with GLY 556 (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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508B TYR* 4.8 6.3 - - - -
542B LEU 3.4 11.7 - - - -
543B GLY* 3.9 4.0 - - - -
555B MET* 1.3 78.7 - - - +
557B LEU* 1.3 64.8 + - - -
558B PHE* 4.3 0.4 + - - -
585B GLY 4.1 0.2 - - - +
586B LEU* 3.5 3.3 - - - +
587B GLU* 2.9 41.3 + - - +
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Residues in contact with LEU 557 (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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540B TRP 3.7 0.9 - - - +
541B GLU* 3.4 4.5 - - - +
542B LEU* 2.9 51.3 + - + +
555B MET* 6.2 1.3 - - + -
556B GLY* 1.3 74.8 - - - -
558B PHE* 1.3 61.2 + - - +
585B GLY 3.4 8.1 - - - +
586B LEU* 3.5 40.2 - - + -
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Residues in contact with PHE 558 (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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150B ARG* 3.5 62.4 - - + +
540B TRP 3.2 8.1 - - - +
541B GLU* 4.4 3.6 - - + -
557B LEU* 1.3 76.9 - - - +
559B LEU* 1.3 62.7 + - - +
560B ILE* 4.3 3.8 - - + -
583B HIS* 3.6 13.5 - - + -
584B THR* 3.2 17.2 - - - +
585B GLY* 2.9 63.3 + - - +
586B LEU 4.0 0.4 - - - -
587B GLU* 3.9 21.8 - - + -
613B VAL* 3.5 29.2 - - + -
614B ASN 5.3 0.2 - - - -
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Residues in contact with LEU 559 (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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538B ARG 4.0 0.3 - - - +
539B THR* 3.3 1.2 - - - +
540B TRP* 2.7 58.1 + - + +
558B PHE* 1.3 74.9 - - - +
560B ILE* 1.3 88.4 + - - +
561B ASN* 3.2 30.5 - - - +
582B ARG* 3.9 9.6 - - + -
583B HIS 3.4 2.5 - - - -
584B THR* 3.5 24.2 - - + -
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Residues in contact with ILE 560 (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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149B ILE* 5.4 0.2 - - + -
150B ARG* 3.6 45.3 - - + +
152B LEU* 5.6 4.0 - - + -
208B VAL* 4.1 32.3 - - + +
538B ARG 3.4 9.2 - - - +
539B THR* 3.6 17.0 - - + +
558B PHE* 4.3 3.8 - - + -
559B LEU* 1.3 81.9 - - - +
561B ASN* 1.3 68.7 + - - +
562B PHE* 4.1 15.9 - - + -
581B THR 3.7 1.0 - - - +
582B ARG* 3.3 5.0 - - - +
583B HIS* 2.6 53.1 + - + +
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Residues in contact with ASN 561 (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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536B LYS 3.8 0.5 - - - +
537B ALA* 3.1 27.2 - - - +
538B ARG* 3.2 17.4 + - + +
540B TRP* 5.5 5.2 - - + +
559B LEU* 3.2 28.6 - - - +
560B ILE* 1.3 73.6 - - - +
562B PHE* 1.3 61.8 + - - +
563B ASN 4.2 0.2 + - - -
580B LYS* 4.5 17.7 + - - +
581B THR 3.8 2.2 - - - +
582B ARG* 3.6 26.5 + - - +
618B ARG* 5.5 1.9 - - - +
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Residues in contact with PHE 562 (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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152B LEU* 3.8 13.2 - - + -
159B ARG* 3.8 11.9 - - - -
208B VAL* 3.4 45.3 - - + -
535B GLU* 3.6 28.3 - - + -
536B LYS 3.8 4.7 - - - -
537B ALA* 3.9 11.7 - - + -
560B ILE* 4.1 8.7 - - + -
561B ASN* 1.3 70.4 - - - +
563B ASN* 1.3 65.2 + - - +
564B ASN 3.1 23.1 + - - +
565B GLN* 3.0 21.8 - - + +
580B LYS* 2.8 33.2 - - - +
581B THR* 3.1 23.8 + - - +
583B HIS* 4.0 11.2 - + - -
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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