Contacts of the strand formed by residues 505 - 516 (chain A) 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 TRP 505 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98A PHE* 3.8 3.2 - - - -
501A LEU* 2.9 55.4 + - + +
502A THR* 3.2 20.2 + - + +
504A SER* 1.3 77.4 - - - +
506A ASN* 1.3 65.7 + - - +
507A LEU* 4.1 1.8 - - + +
544A THR* 2.7 35.2 + - + -
545A ARG 3.7 7.1 + - - -
546A TYR* 3.4 49.6 - + + +
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Residues in contact with ASN 506 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A PHE* 2.9 36.7 + - - +
99A GLU* 2.5 29.5 + - - -
498A LEU* 3.5 21.1 - - + +
499A TYR 3.3 4.7 - - - +
500A HIS* 3.6 24.0 - - - +
502A THR 4.1 4.2 - - - +
505A TRP* 1.3 80.6 - - - +
507A LEU* 1.3 63.5 + - - +
508A TYR* 4.9 1.1 - - + -
544A THR* 3.0 7.3 + - - -
545A ARG* 2.9 39.5 + - + +
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Residues in contact with LEU 507 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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497A VAL 4.0 0.2 - - - +
498A LEU* 2.8 5.7 - - - +
499A TYR* 2.7 47.7 + - + +
501A LEU* 3.5 39.0 - - + -
505A TRP* 4.1 1.6 - - + +
506A ASN* 1.3 79.9 - - - +
508A TYR* 1.3 61.9 + - - +
542A LEU* 6.6 0.7 - - + -
543A GLY 3.7 7.4 - - - +
544A THR* 3.8 15.3 - - - +
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Residues in contact with TYR 508 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A HIS 4.3 5.6 - - - -
101A ALA* 3.7 12.1 - - - -
102A GLY* 3.6 42.6 + - - -
103A ALA* 4.3 8.3 - - - +
497A VAL* 3.2 11.4 - - - +
498A LEU* 3.7 12.6 - - + -
506A ASN 4.9 0.7 - - - -
507A LEU* 1.3 78.2 - - - +
509A ALA* 1.3 71.1 + - - +
510A ASN* 4.4 1.3 - - - -
541A GLU* 4.2 11.8 - - + +
542A LEU* 3.4 9.6 - - - +
543A GLY* 2.8 68.5 + - - +
544A THR* 3.6 15.0 - - - -
545A ARG* 4.6 12.1 - - + -
554A GLU* 6.3 0.7 - - + -
555A MET 4.1 1.9 + - - -
556A GLY* 3.6 21.1 + - - -
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Residues in contact with ALA 509 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A ALA 4.5 1.2 - - - +
496A ASN* 3.8 0.2 - - - -
497A VAL* 3.0 45.7 + - + +
508A TYR* 1.3 80.3 - - - +
510A ASN* 1.3 66.2 + - - +
541A GLU 3.0 13.0 - - - +
542A LEU* 3.7 15.7 - - + -
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Residues in contact with ASN 510 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A ALA 3.0 20.2 + - - +
102A GLY* 3.3 5.5 - - - -
197A GLY 3.6 4.2 + - - -
495A LEU* 3.2 15.5 - - - +
496A ASN* 3.4 14.8 - - - +
497A VAL* 5.3 0.2 - - - -
508A TYR* 4.4 0.4 - - - -
509A ALA* 1.3 76.8 - - - +
511A THR* 1.3 68.1 + - - +
512A GLU* 2.5 25.1 - - - +
539A THR 4.5 0.2 - - - +
540A TRP* 3.3 5.4 - - - +
541A GLU* 2.8 73.5 + - - +
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Residues in contact with THR 511 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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494A ALA* 3.3 4.7 - - - -
495A LEU* 3.1 40.3 + - + +
510A ASN* 1.3 78.9 - - - +
512A GLU* 1.3 67.2 + - - +
538A ARG* 2.9 35.2 + - - +
539A THR 2.9 10.5 + - - -
540A TRP* 3.7 30.4 - - + -
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Residues in contact with GLU 512 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197A GLY* 3.1 10.0 - - - -
198A GLY* 2.3 42.9 + - - +
199A GLY 3.9 9.4 + - - +
201A VAL* 5.3 2.9 - - + -
207A SER* 5.5 3.8 - - - +
493A PRO 3.8 6.3 - - - -
494A ALA* 4.2 15.3 - - + -
495A LEU 5.2 0.2 - - - +
496A ASN* 4.6 4.7 - - - +
510A ASN* 2.5 25.7 - - - +
511A THR* 1.3 84.1 + - - +
513A GLY* 1.3 64.0 + - - +
538A ARG* 3.7 6.3 - - - -
539A THR* 3.1 35.6 + - - +
541A GLU* 5.0 0.3 - - - -
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Residues in contact with GLY 513 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A SER* 3.0 17.5 + - - -
208A VAL* 5.4 1.1 - - - -
492A LEU* 2.8 23.7 - - - +
493A PRO 3.7 9.3 + - - -
494A ALA* 5.3 0.4 - - - +
512A GLU* 1.3 78.3 - - - +
514A SER* 1.3 60.8 + - - -
537A ALA 3.4 12.6 - - - -
538A ARG* 4.3 11.0 - - - -
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Residues in contact with SER 514 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A PRO 3.4 14.6 - - - -
206A GLN* 4.4 1.1 - - - -
207A SER 3.8 0.7 - - - -
208A VAL* 2.8 52.0 - - - +
492A LEU* 3.0 11.7 - - - +
513A GLY* 1.3 74.5 - - - -
515A PHE* 1.3 65.7 + - - +
535A GLU 4.1 2.3 + - - -
536A LYS* 3.6 6.4 - - - +
537A ALA* 3.1 29.5 + - - +
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Residues in contact with PHE 515 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A PRO* 3.6 26.2 + - + +
206A GLN* 3.8 10.9 + - - +
471A ILE* 3.8 24.5 - - + -
488A TYR* 3.4 42.2 - + + -
489A ASN 4.5 4.0 - - - -
490A ALA* 3.6 31.6 - - + -
492A LEU* 4.8 5.1 - - + +
514A SER* 1.3 80.8 + - - +
516A GLY* 1.3 59.6 + - - +
517A THR* 3.4 24.1 + - + -
534A PRO* 3.7 20.2 - - + -
535A GLU 3.2 9.4 - - - -
536A LYS* 4.0 23.1 - - + -
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Residues in contact with GLY 516 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A PRO* 5.9 0.2 - - - -
206A GLN* 3.5 29.1 - - - -
515A PHE* 1.3 77.2 - - - +
517A THR* 1.3 68.1 + - - +
518A VAL* 3.5 1.6 + - - -
522A GLN* 5.7 0.3 + - - -
533A GLU* 4.4 2.3 - - - +
534A PRO* 3.9 4.7 - - - +
535A GLU* 3.2 33.3 + - - +
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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