Contacts of the strand formed by residues 551 - 562 (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 LEU 551 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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546A TYR* 3.4 29.8 - - + -
547A ASP* 3.5 4.0 + - - -
548A ASP* 2.5 43.7 + - - +
550A ALA* 1.3 79.0 - - + +
552A THR* 1.3 61.9 + - - +
553A ALA* 4.0 18.4 - - + -
590A ALA* 5.3 5.6 - - + -
591A ARG 3.7 9.2 - - - +
592A TYR* 3.4 30.7 - - + -
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Residues in contact with THR 552 (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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546A TYR 3.6 7.0 + - - -
547A ASP* 4.3 18.2 + - - +
550A ALA 5.6 1.3 - - - +
551A LEU* 1.3 74.3 - - - +
553A ALA* 1.3 63.4 + - - +
590A ALA* 3.4 2.3 - - - +
591A ARG* 3.0 56.1 + - + +
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Residues in contact with ALA 553 (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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545A ARG* 3.4 3.0 - - - +
546A TYR* 2.5 51.3 + - + +
551A LEU* 4.0 16.9 - - + +
552A THR* 1.3 78.5 + - - +
554A GLU* 1.3 63.5 + - - +
589A GLN 3.6 4.5 - - - +
590A ALA* 3.7 17.9 - - + -
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Residues in contact with GLU 554 (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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97A VAL* 5.4 0.2 - - - +
104A ARG 3.9 2.4 + - - +
105A ASP* 3.0 19.1 - - - +
128A PRO* 4.6 0.9 - - - +
196A ARG* 4.5 6.1 + - - -
508A TYR* 6.3 0.7 - - + -
544A THR* 3.3 13.7 - - - +
545A ARG* 3.0 37.9 + - + +
553A ALA* 1.3 78.6 - - - +
555A MET* 1.3 63.2 + - - +
587A GLU 5.6 2.4 - - - +
588A THR* 2.9 21.4 + - - -
589A GLN* 2.7 53.8 + - + +
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Residues in contact with MET 555 (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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508A TYR* 4.1 3.1 + - - -
543A GLY* 3.3 0.9 - - - -
544A THR* 2.8 50.5 + - + +
554A GLU* 1.3 78.5 - - - +
556A GLY* 1.3 61.4 + - - +
557A LEU* 5.9 1.3 - - + -
586A LEU* 4.3 26.7 - - + -
587A GLU 3.1 11.2 - - - +
588A THR* 3.6 15.5 - - - +
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Residues in contact with GLY 556 (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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508A TYR* 3.6 11.4 + - - -
542A LEU 3.2 9.6 - - - -
543A GLY* 3.5 5.6 - - - -
555A MET* 1.3 78.4 - - - +
557A LEU* 1.3 66.1 + - - +
558A PHE* 5.8 0.2 - - - -
586A LEU* 3.4 4.2 - - - +
587A GLU* 2.9 39.6 + - - +
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Residues in contact with LEU 557 (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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540A TRP 3.7 0.2 - - - +
541A GLU* 3.1 4.5 - - - +
542A LEU* 2.4 69.5 + - + +
555A MET* 6.1 1.1 - - + -
556A GLY* 1.3 69.6 - - - -
558A PHE* 1.3 62.7 + - - +
585A GLY 3.4 7.2 - - - +
586A LEU* 3.3 44.6 - - + -
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Residues in contact with PHE 558 (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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150A ARG* 3.3 58.8 - - + +
539A THR* 4.9 1.8 - - + -
540A TRP 3.0 9.4 - - - +
541A GLU* 4.6 5.2 - - + -
557A LEU* 1.3 76.5 - - - +
559A LEU* 1.3 67.4 + - - +
560A ILE* 4.0 8.1 - - + -
583A HIS* 3.4 17.5 - - + -
584A THR* 3.2 27.2 - - - +
585A GLY* 3.1 42.1 + - - +
586A LEU* 4.0 0.9 - - - -
587A GLU* 3.8 22.0 - - + -
612A TYR 4.5 2.2 - - - -
613A VAL* 3.7 17.0 - - + -
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Residues in contact with LEU 559 (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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538A ARG 3.6 0.7 - - - +
539A THR* 2.9 5.2 - - - +
540A TRP* 2.5 61.3 + - + +
558A PHE* 1.3 76.7 - - - +
560A ILE* 1.3 66.3 + - - +
561A ASN* 4.1 26.9 - - - +
582A ARG* 5.5 2.7 - - + -
583A HIS 3.4 4.7 - - - +
584A THR* 3.9 24.5 - - + -
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Residues in contact with ILE 560 (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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149A ILE* 5.5 0.4 - - + -
150A ARG* 3.5 43.1 - - + +
152A LEU* 4.9 7.4 - - + -
208A VAL* 3.7 31.0 - - + +
537A ALA* 4.7 1.3 - - + -
538A ARG 3.2 4.3 - - - +
539A THR* 3.3 27.6 - - + +
558A PHE* 4.0 4.9 - - + -
559A LEU* 1.3 79.7 - - - +
561A ASN* 1.3 62.8 + - - +
562A PHE* 3.9 11.2 - - + -
582A ARG* 3.6 4.7 - - - +
583A HIS* 2.8 57.5 + - + +
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Residues in contact with ASN 561 (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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536A LYS 3.8 0.9 - - - +
537A ALA* 2.9 28.5 - - - -
538A ARG* 2.7 19.9 + - + +
540A TRP* 4.7 12.3 - - - +
559A LEU* 4.1 18.5 - - - +
560A ILE* 1.3 74.9 - - - +
562A PHE* 1.3 60.5 + - - +
581A THR 4.0 1.8 - - - +
582A ARG* 4.0 16.8 - - - +
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Residues in contact with PHE 562 (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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152A LEU* 3.1 41.1 - - + -
159A ARG* 4.6 2.2 - - - -
208A VAL* 3.6 24.7 - - + -
535A GLU* 4.2 18.6 - - + -
536A LYS 3.8 2.5 - - - -
537A ALA* 4.0 8.5 - - + -
560A ILE* 3.9 15.0 - - + -
561A ASN* 1.3 74.1 - - - +
563A ASN* 1.3 64.5 + - - +
564A ASN 3.7 18.2 - - - +
565A GLN* 3.1 25.8 - - + +
580A LYS* 3.2 18.2 - - - +
581A THR* 3.1 23.4 + - - +
583A HIS* 3.2 24.7 - + - -
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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