Contacts of the helix formed by residues 535 - 550 (chain A) in PDB entry 1PG2
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 ASP 535 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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350A PHE* 4.8 0.3 - - - -
378A VAL* 3.9 14.2 - - - +
533A ARG 5.0 1.9 - - - +
534A ILE* 1.3 78.6 - - - +
536A MET* 1.3 63.3 + - - +
537A ARG* 2.9 41.3 + - + +
538A GLN* 3.0 42.3 + - - +
539A VAL* 3.6 3.1 + - - +
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Residues in contact with MET 536 (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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374A LEU* 5.5 0.4 - - + -
375A GLU* 3.3 54.5 - - + +
378A VAL* 3.9 25.8 - - + +
535A ASP* 1.3 71.1 - - - +
537A ARG* 1.3 59.8 + - + +
538A GLN 3.1 0.2 - - - -
539A VAL* 3.1 25.2 + - + +
540A GLU* 2.9 45.5 + - + +
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Residues in contact with ARG 537 (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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535A ASP* 2.9 17.6 + - + +
536A MET* 1.3 77.2 - - + +
538A GLN* 1.3 56.4 + - + +
540A GLU* 3.4 21.4 + - - +
541A ALA* 3.0 27.2 + - - +
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Residues in contact with GLN 538 (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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349A HIS* 4.0 22.3 + - + +
350A PHE* 3.6 20.6 - - + -
533A ARG 5.5 1.5 + - - -
534A ILE* 3.2 21.2 - - - +
535A ASP* 3.0 45.0 + - - +
537A ARG* 1.3 75.7 - - + +
539A VAL* 1.3 63.9 + - - +
541A ALA* 3.3 7.9 + - - +
542A LEU* 3.0 23.0 + - - +
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Residues in contact with VAL 539 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A PHE* 3.8 17.3 - - + -
374A LEU* 3.6 45.8 - - + +
377A PHE* 4.5 5.4 - - + -
378A VAL* 3.5 32.8 - - + -
535A ASP 3.6 0.4 + - - -
536A MET* 3.1 25.5 + - + +
538A GLN* 1.3 75.8 - - - +
540A GLU* 1.3 66.1 + - - +
542A LEU* 3.2 6.5 + - + +
543A VAL* 3.0 25.1 + - + +
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Residues in contact with GLU 540 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536A MET* 2.9 33.1 + - + +
537A ARG* 3.6 27.5 + - - +
539A VAL* 1.3 79.5 - - + +
541A ALA* 1.3 56.5 + - - +
543A VAL* 3.4 5.8 + - - +
544A GLU* 3.0 38.5 + - + +
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Residues in contact with ALA 541 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A HIS* 3.6 17.7 - - + +
537A ARG 3.0 17.4 + - - +
538A GLN* 3.6 7.2 - - - +
540A GLU* 1.3 78.7 - - - +
542A LEU* 1.3 55.8 + - - +
544A GLU* 3.4 5.3 + - - +
545A ALA* 2.9 32.1 + - - +
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Residues in contact with LEU 542 (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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341A ILE* 4.0 26.2 - - + -
345A THR* 3.9 20.4 - - + +
346A TRP* 3.7 42.0 - - + -
349A HIS* 3.6 33.8 + - + -
350A PHE* 3.8 11.7 - - + -
374A LEU* 5.0 9.9 - - + -
538A GLN 3.0 14.5 + - - +
539A VAL* 3.2 10.5 + - - +
541A ALA* 1.3 77.0 - - - +
543A VAL* 1.3 57.7 + - - +
545A ALA* 3.3 2.8 + - - +
546A SER* 2.9 32.6 + - - -
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Residues in contact with VAL 543 (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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329A ASN* 5.9 0.2 - - - +
337A ARG 3.2 25.6 - - - +
338A GLY* 3.6 15.9 - - - +
339A THR* 5.3 2.7 - - + -
341A ILE* 5.6 0.4 - - + -
374A LEU* 3.8 28.0 - - + -
539A VAL* 3.0 22.2 + - + +
540A GLU* 3.8 5.8 - - - +
542A LEU* 1.3 78.5 - - + +
544A GLU* 1.3 65.8 + - - +
546A SER* 3.2 3.6 + - - -
547A LYS* 3.0 32.6 + - - +
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Residues in contact with GLU 544 (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 GLU* 3.0 23.7 + - + +
541A ALA* 3.8 6.1 - - - +
543A VAL* 1.3 78.2 - - + +
545A ALA* 1.3 64.0 + - - +
547A LYS* 3.2 36.9 + - - +
548A GLU* 3.1 22.2 + - - +
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Residues in contact with ALA 545 (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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345A THR* 4.4 8.1 - - + -
349A HIS* 3.7 20.4 - - + +
541A ALA 2.9 18.5 + - - +
542A LEU 3.6 4.7 - - - +
544A GLU* 1.3 76.2 - - - +
546A SER* 1.3 60.5 + - - +
548A GLU* 3.3 8.6 + - - +
549A GLU* 3.0 31.0 + - + +
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Residues in contact with SER 546 (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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335A LYS* 4.5 3.1 - - - +
338A GLY* 3.4 28.2 - - - -
340A PHE 3.9 15.6 + - - +
341A ILE* 3.7 18.7 - - - +
345A THR* 4.0 12.8 - - - +
542A LEU 2.9 16.6 + - - -
543A VAL 3.2 0.6 + - - -
545A ALA* 1.3 74.3 - - - +
547A LYS* 1.3 64.0 + - - +
549A GLU* 3.6 20.5 + - - +
550A VAL* 3.7 10.2 + - - +
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Residues in contact with LYS 547 (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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335A LYS 4.1 8.7 - - - -
336A SER* 3.9 12.8 - - - +
337A ARG* 3.4 23.6 - - - +
338A GLY* 3.5 13.2 - - - +
543A VAL* 3.0 26.1 + - - +
544A GLU* 3.2 34.5 + - - +
546A SER* 1.3 76.2 - - - +
548A GLU* 1.3 63.4 + - - +
550A VAL* 3.2 21.1 + - - +
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Residues in contact with GLU 548 (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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544A GLU 3.1 8.4 + - - +
545A ALA* 3.3 12.5 + - - +
547A LYS* 1.3 80.9 - - - +
549A GLU* 1.3 61.0 + - + +
550A VAL 3.5 7.3 - - - +
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Residues in contact with GLU 549 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A PHE 5.0 2.4 - - - +
342A LYS* 4.2 26.8 + - - +
345A THR* 2.6 36.4 + - - +
348A ASN* 5.7 0.2 - - - +
545A ALA* 3.0 17.6 - - + +
546A SER* 3.8 15.6 + - - +
547A LYS 3.2 0.8 - - - -
548A GLU* 1.3 74.5 - - + +
550A VAL* 1.3 67.9 + - - +
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Residues in contact with VAL 550 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A LYS* 4.1 40.6 - - + +
336A SER* 5.9 0.4 - - - -
546A SER 3.7 5.4 + - - +
547A LYS 3.2 15.5 + - - +
548A GLU 3.5 8.3 - - - +
549A GLU* 1.3 85.3 - - - +
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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