Contacts of the strand formed by residues 535 - 547 (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 GLU 535 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159B ARG* 2.7 48.4 + - - +
206B GLN* 4.8 8.4 + - - +
515B PHE* 3.2 3.7 - - - -
516B GLY* 2.7 43.5 + - - +
519B GLN* 5.8 4.3 + - - -
522B GLN* 5.5 2.4 + - - -
534B PRO* 1.3 75.2 - - - +
536B LYS* 1.3 59.5 + - - +
537B ALA* 3.9 0.5 + - - +
562B PHE* 3.6 12.6 - - + -
563B ASN* 3.2 4.9 - - - +
564B ASN 3.4 22.7 - - - +
566B TYR* 3.0 36.4 + - + +
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Residues in contact with LYS 536 (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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514B SER 3.9 4.5 - - - +
515B PHE* 4.2 15.9 - - + -
534B PRO* 3.5 31.8 - - + +
535B GLU* 1.3 69.7 - - - +
537B ALA* 1.3 64.7 + - - +
561B ASN 3.8 0.5 - - - +
562B PHE* 3.8 0.9 - - - -
563B ASN* 2.3 69.3 + - + +
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Residues in contact with ALA 537 (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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208B VAL* 3.6 30.7 - - + -
513B GLY* 3.7 1.4 - - - -
514B SER* 2.9 39.6 + - - +
535B GLU 3.9 0.9 + - - +
536B LYS* 1.3 76.7 - - - +
538B ARG* 1.3 60.5 + - - +
560B ILE* 4.8 0.4 - - + -
561B ASN 3.1 13.5 - - - +
562B PHE* 3.9 17.7 - - + -
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Residues in contact with ARG 538 (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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491B PRO 5.2 0.6 + - - -
492B LEU* 4.8 0.8 - - - +
493B PRO* 2.5 55.3 + - - +
511B THR* 2.9 28.4 + - - +
512B GLU* 3.2 11.7 - - - +
513B GLY* 3.2 24.3 - - - +
537B ALA* 1.3 72.9 - - - +
539B THR* 1.3 64.1 + - - +
540B TRP* 2.9 36.2 - - + +
559B LEU 4.0 0.3 - - - +
560B ILE* 3.4 5.0 - - - +
561B ASN* 3.2 34.8 + - + +
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Residues in contact with THR 539 (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* 3.7 20.4 - - - +
196B ARG 4.9 4.0 - - - +
208B VAL* 4.5 13.4 + - - +
511B THR* 2.9 30.8 + - - -
512B GLU* 2.9 28.7 + - - +
514B SER* 4.6 4.0 + - - -
538B ARG* 1.3 78.2 + - - +
540B TRP* 1.3 67.2 + - - +
541B GLU* 4.4 8.5 - - + -
559B LEU 3.3 4.3 - - - +
560B ILE* 3.6 30.1 - - + +
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Residues in contact with TRP 540 (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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510B ASN 3.4 5.4 - - - -
511B THR* 3.6 31.4 - - + -
538B ARG* 2.9 27.8 - - + +
539B THR* 1.3 78.9 - - - +
541B GLU* 1.3 61.2 + - - +
557B LEU 3.7 0.9 - - - +
558B PHE* 3.2 4.7 - - - -
559B LEU* 2.7 64.0 + - + +
561B ASN* 5.5 4.7 - - - +
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Residues in contact with GLU 541 (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* 2.8 28.7 + - - +
150B ARG* 2.4 42.9 + - - +
196B ARG 3.3 5.4 - - - +
197B GLY* 2.8 12.8 - - - -
508B TYR* 4.4 6.5 - - + -
509B ALA* 2.9 7.3 - - - +
510B ASN* 2.6 75.3 + - - +
539B THR* 4.4 6.1 - - + -
540B TRP* 1.3 76.6 - - - +
542B LEU* 1.3 61.9 + - - +
543B GLY 4.2 0.4 - - - -
557B LEU 3.4 4.3 - - - +
558B PHE* 4.4 4.5 - - + -
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Residues in contact with LEU 542 (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* 3.5 12.8 - - - +
509B ALA* 4.2 11.9 - - + -
541B GLU* 1.3 76.3 - - - +
543B GLY* 1.3 60.0 + - - +
556B GLY* 3.4 1.0 - - - -
557B LEU* 2.9 49.7 + - + +
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Residues in contact with GLY 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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507B LEU* 3.5 6.1 - - - +
508B TYR* 2.6 65.0 + - - +
542B LEU* 1.3 78.4 - - - +
544B THR* 1.3 59.8 + - - -
555B MET 3.6 10.5 - - - -
556B GLY* 3.9 1.3 - - - -
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Residues in contact with THR 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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505B TRP* 2.6 35.1 + - + -
506B ASN 3.1 9.0 + - - -
507B LEU* 4.4 7.2 - - - -
508B TYR* 4.2 7.3 + - - -
543B GLY* 1.3 76.4 - - - -
545B ARG* 1.3 61.2 + - - +
546B TYR* 4.3 1.6 + - - +
553B ALA 4.9 0.2 - - - -
554B GLU* 3.5 5.1 - - - +
555B MET* 3.1 45.8 + - + +
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Residues in contact with ARG 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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97B VAL* 2.8 27.5 + - - +
98B PHE* 2.8 57.1 + - + +
100B HIS* 3.3 13.9 + - - +
102B GLY 2.6 30.9 + - - -
103B ALA* 5.5 0.2 - - - +
104B ARG 3.5 19.2 + - - +
505B TRP* 3.5 0.4 - - - -
506B ASN* 3.0 26.9 + - + +
508B TYR* 3.5 16.3 + - + -
544B THR* 1.3 76.3 + - - +
546B TYR* 1.3 63.7 + - - +
553B ALA 3.8 1.8 - - - -
554B GLU* 3.2 39.0 + - + +
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Residues in contact with TYR 546 (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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98B PHE* 4.5 0.7 - - - -
502B THR* 5.7 0.7 - - + -
504B SER* 3.6 23.5 + - - -
505B TRP* 4.3 28.0 - + + +
544B THR* 4.3 1.1 - - - +
545B ARG* 1.3 79.5 - - - +
547B ASP* 1.3 84.8 + - - +
548B ASP* 3.6 15.0 - - - -
551B LEU* 3.1 36.8 - - + -
552B THR* 3.2 5.2 + - - -
553B ALA* 2.6 43.2 + - + +
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Residues in contact with ASP 547 (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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98B PHE* 4.6 17.4 - - + -
504B SER* 3.1 26.9 + - - -
545B ARG 4.3 0.2 + - - -
546B TYR* 1.3 87.8 - - - +
548B ASP* 1.3 60.3 + - - +
549B GLY* 3.9 11.4 + - - -
551B LEU 3.8 3.1 - - - -
552B THR* 3.4 19.9 + - - +
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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