Contacts of the strand formed by residues 581 - 592 (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 THR 581 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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560B ILE 3.7 2.3 - - - +
561B ASN* 3.8 2.3 - - - +
562B PHE* 3.1 30.0 + - - +
565B GLN* 2.9 29.5 + - + +
578B ARG* 3.7 29.6 - - + -
579B GLY 3.4 12.3 - - - +
580B LYS* 1.3 83.2 - - - +
582B ARG* 1.3 58.9 + - - +
583B HIS* 3.1 12.2 + - - -
616B GLU 3.1 13.9 - - - +
617B ILE* 4.4 4.9 - - + -
618B ARG* 4.1 3.6 - - - +
628B VAL* 4.4 4.0 - - + -
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Residues in contact with ARG 582 (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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559B LEU* 3.9 23.3 - - + -
560B ILE 3.3 2.5 - - - -
561B ASN* 3.6 21.9 + - - +
581B THR* 1.3 72.3 - - - +
583B HIS* 1.3 64.9 + - - +
584B THR* 3.8 19.0 + - + +
614B ASN* 3.6 3.5 + - - +
615B ALA* 3.3 1.9 - - - -
616B GLU* 2.9 58.3 + - + +
618B ARG* 3.0 46.8 - - + +
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Residues in contact with HIS 583 (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 2.7 24.3 + - - +
151B GLY 3.5 15.7 - - - -
152B LEU* 3.2 23.0 - - + +
558B PHE* 3.6 8.1 - - + -
559B LEU* 3.4 2.6 - - - -
560B ILE* 2.6 56.2 + - + -
562B PHE* 4.0 10.3 - + - -
565B GLN* 3.1 25.7 + - - -
581B THR* 3.1 22.9 + - - -
582B ARG* 1.3 75.7 - - - +
584B THR* 1.3 60.3 + - - +
613B VAL* 6.2 0.2 - - + -
614B ASN 3.6 4.0 - - - -
615B ALA* 3.3 17.8 - - + +
628B VAL* 4.1 6.3 - - + -
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Residues in contact with THR 584 (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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558B PHE* 3.2 11.6 - - - +
559B LEU* 3.5 35.2 - - + -
582B ARG* 3.8 20.4 + - + +
583B HIS* 1.3 74.2 - - - +
585B GLY* 1.3 58.8 + - - +
612B TYR* 5.2 0.2 - - - -
614B ASN* 2.8 54.7 + - - +
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Residues in contact with GLY 585 (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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557B LEU* 3.4 9.7 - - - +
558B PHE* 2.9 47.8 + - - +
584B THR* 1.3 76.3 - - - +
586B LEU* 1.3 59.0 + - - -
612B TYR* 3.0 19.3 - - - -
614B ASN 4.6 0.2 - - - -
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Residues in contact with LEU 586 (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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555B MET* 4.2 22.0 - - + -
556B GLY 3.5 5.4 - - - +
557B LEU* 3.5 22.4 - - + -
585B GLY* 1.3 75.6 - - - -
587B GLU* 1.3 81.3 - - - +
588B THR* 4.1 15.9 - - + -
610B TYR* 5.1 8.7 - - + -
611B ALA* 3.2 5.0 - - - +
612B TYR* 2.7 50.4 + - + +
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Residues in contact with GLU 587 (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* 3.7 7.1 - - - +
128B PRO* 5.0 2.2 - - + -
129B GLY* 3.9 16.3 - - - +
150B ARG* 3.1 44.2 + - - +
196B ARG* 2.6 44.0 + - - +
554B GLU* 6.2 0.2 - - - +
555B MET* 3.2 1.6 - - - -
556B GLY* 2.9 39.6 + - - +
558B PHE* 3.9 15.8 - - + -
586B LEU* 1.3 79.8 - - - +
588B THR* 1.3 64.6 + - - +
610B TYR 4.0 4.9 - - - +
611B ALA* 4.4 2.2 - - + +
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Residues in contact with THR 588 (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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128B PRO* 4.2 4.9 - - - +
553B ALA* 6.0 0.3 - - - +
554B GLU* 2.7 22.3 + - - -
555B MET* 3.5 20.0 - - - +
586B LEU* 4.1 13.7 - - + -
587B GLU* 1.3 77.6 - - - +
589B GLN* 1.3 63.8 + - - +
609B SER* 3.3 2.3 - - - -
610B TYR* 2.7 60.8 + - + +
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Residues in contact with GLN 589 (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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105B ASP* 2.8 31.2 + - - +
128B PRO* 3.3 28.0 - - + +
553B ALA* 3.5 0.9 - - - +
554B GLU* 3.1 46.1 + - + +
588B THR* 1.3 81.2 + - - +
590B ALA* 1.3 66.8 + - - +
608B ALA 3.1 15.0 - - - +
609B SER* 3.6 13.0 - - - +
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Residues in contact with ALA 590 (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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551B LEU* 5.0 6.3 - - + -
552B THR* 3.1 17.0 - - - +
553B ALA* 3.6 12.3 - - + +
589B GLN* 1.3 80.9 + - - +
591B ARG* 1.3 60.9 + - - +
607B TYR* 3.1 4.7 - - - +
608B ALA* 2.8 33.8 + - + +
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Residues in contact with ARG 591 (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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111B ASP* 5.7 1.4 + - - -
114B LYS* 4.1 12.1 - - - +
550B ALA 3.6 1.8 - - - +
551B LEU* 3.7 4.9 - - - +
552B THR* 3.0 47.9 + - + +
590B ALA* 1.3 75.5 - - - +
592B TYR* 1.3 61.5 + - - +
605B SER* 3.9 22.4 + - - +
606B ILE 3.4 6.3 - - - +
607B TYR* 2.9 45.1 - - + +
641B ASP* 2.9 22.6 + - - +
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Residues in contact with TYR 592 (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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550B ALA 3.2 6.1 - - - -
551B LEU* 4.6 9.9 - - - +
591B ARG* 1.3 75.6 - - - +
593B ASP* 1.3 62.0 + - - +
594B LEU* 3.2 7.2 + - - -
605B SER* 3.5 9.1 + - - -
606B ILE* 2.8 36.8 + - - +
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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