Contacts of the helix formed by residues 548 - 562 (chain A) in PDB entry 1PMS
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 ALA 548 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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547A SER* 1.3 73.2 + - - +
549A GLU* 1.3 70.0 + - + +
551A LYS* 3.2 15.6 + - - +
552A ASN* 3.2 22.4 + - - +
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Residues in contact with GLU 549 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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547A SER* 4.5 0.8 - - - -
548A ALA* 1.3 82.0 - - + +
550A GLU* 1.3 52.5 + - + +
552A ASN* 4.7 3.8 - - - +
553A ASN* 2.4 56.3 + - - +
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Residues in contact with GLU 550 (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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463A MET* 6.4 0.9 - - + -
466A THR* 3.5 26.2 + - - +
467A LEU* 3.7 2.9 - - + +
545A ALA* 3.1 21.4 - - + +
546A LYS* 4.3 8.8 + - - +
547A SER* 2.6 33.8 + - - -
548A ALA 3.2 0.6 - - - -
549A GLU* 1.3 78.3 - - + +
551A LYS* 1.3 64.3 + - - +
553A ASN* 3.3 19.7 - - - +
554A TRP* 3.4 15.2 - - + +
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Residues in contact with LYS 551 (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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467A LEU* 5.3 0.4 - - - -
527A TYR* 3.5 34.7 - - - +
528A LYS 4.4 0.4 - - - +
529A HIS* 2.6 43.7 + - + +
530A ALA* 4.2 1.1 - - - +
531A PHE* 2.7 30.0 - - + -
543A PHE* 4.8 0.2 - - - -
544A SER* 4.2 7.9 + - - +
545A ALA* 3.1 39.7 + - - +
547A SER* 2.6 30.2 + - - +
548A ALA* 3.2 8.2 + - - +
549A GLU 3.1 0.6 - - - -
550A GLU* 1.3 76.1 - - - +
552A ASN* 1.3 62.2 + - - +
553A ASN 2.9 9.0 + - - -
554A TRP* 3.6 1.7 + - - +
555A MET 3.5 11.3 + - - -
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Residues in contact with ASN 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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520A ASP* 5.0 1.7 - - - +
529A HIS* 5.0 17.2 + - - -
531A PHE* 3.4 23.9 - - - -
548A ALA* 3.2 21.7 + - - +
549A GLU* 4.3 4.4 - - - +
551A LYS* 1.3 79.6 - - - +
553A ASN* 1.3 64.1 + - - +
555A MET* 3.9 12.3 - - + +
556A ALA* 3.2 23.4 + - - +
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Residues in contact with ASN 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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463A MET* 4.0 27.9 - - + +
549A GLU* 2.4 43.3 + - - +
550A GLU* 3.3 14.8 - - - +
551A LYS 2.9 2.0 - - - -
552A ASN* 1.3 78.2 - - - +
554A TRP* 1.3 67.1 + - - +
556A ALA* 3.0 15.0 + - - +
557A ALA* 3.0 12.1 + - - +
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Residues in contact with TRP 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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463A MET* 2.6 58.8 - - + +
465A GLY* 3.7 13.4 - - - +
466A THR 4.2 5.4 + - - +
467A LEU* 2.9 33.4 - - + +
478A ILE* 2.8 47.6 - - + -
479A PHE 3.3 7.2 - - - -
480A LEU* 3.3 36.3 - - + -
485A MET* 3.7 11.7 - - + -
543A PHE* 3.4 20.9 - + + -
550A GLU* 3.4 12.7 + - - +
553A ASN* 1.3 78.8 - - + +
555A MET* 1.3 63.7 + - - +
557A ALA* 3.1 8.2 + - - +
558A LEU* 3.0 24.0 + - + +
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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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518A ILE* 3.1 52.0 - - + +
519A ASN 5.5 0.7 - - - -
520A ASP* 4.5 15.3 - - + +
531A PHE* 3.0 48.0 - - + -
543A PHE* 4.1 2.3 - - - -
551A LYS 3.5 5.7 + - - +
552A ASN* 3.9 14.8 - - + +
553A ASN 3.1 0.6 - - - -
554A TRP* 1.3 79.9 - - - +
556A ALA* 1.3 64.7 + - + +
558A LEU* 3.4 5.0 + - - -
559A ILE* 3.4 10.0 + - + +
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Residues in contact with ALA 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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552A ASN 3.2 15.1 + - - +
553A ASN* 3.0 6.1 + - - +
555A MET* 1.3 81.2 - - + +
557A ALA* 1.3 55.1 + - - +
558A LEU 3.0 4.9 - - - -
559A ILE* 4.7 4.2 - - - +
560A SER* 2.6 42.4 + - - +
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Residues in contact with ALA 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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462A ILE* 3.7 15.4 - - + +
463A MET* 3.2 35.7 - - + -
480A LEU* 3.4 20.0 - - + +
482A ASP 5.3 0.3 - - - -
553A ASN 3.0 7.7 + - - +
554A TRP 3.1 4.2 + - - +
556A ALA* 1.3 76.4 - - - +
558A LEU* 1.3 58.4 + - - +
560A SER* 3.9 6.7 - - - -
561A LEU* 3.0 27.7 - - - +
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Residues in contact with LEU 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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480A LEU* 3.5 33.2 - - + -
485A MET* 5.9 0.7 - - + -
513A MET* 4.2 18.4 - - + +
516A VAL* 5.4 7.6 - - + +
518A ILE* 3.4 24.5 - - + +
533A ILE* 3.0 35.9 - - + -
543A PHE* 3.6 13.7 - - + -
554A TRP* 3.0 18.6 - - + +
555A MET* 3.6 0.7 - - - +
556A ALA 3.0 1.0 - - - -
557A ALA* 1.3 77.4 - - - +
559A ILE* 1.3 67.5 + - + +
560A SER 2.9 5.0 + - - -
561A LEU* 3.1 14.7 + - - +
562A GLN* 3.2 10.0 + - - +
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Residues in contact with ILE 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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516A VAL 5.2 0.4 - - - +
517A GLN* 4.4 9.9 - - + -
518A ILE* 2.9 50.7 - - + +
555A MET* 3.4 13.1 + - + +
556A ALA* 4.4 3.1 - - - +
558A LEU* 1.3 77.8 - - + +
560A SER* 1.3 60.8 + - - +
561A LEU 3.4 0.2 - - - -
562A GLN* 3.8 17.0 - - + +
563A TYR* 2.9 51.3 + - + +
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Residues in contact with SER 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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462A ILE* 4.9 4.0 - - - -
556A ALA* 2.6 28.7 + - - +
557A ALA* 3.8 5.5 - - - -
558A LEU 2.9 0.2 - - - -
559A ILE* 1.3 81.7 - - - +
561A LEU* 1.3 76.1 + - - +
563A TYR* 3.6 17.3 - - - +
564A ARG* 4.0 11.8 + - - -
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Residues in contact with LEU 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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460A GLU* 5.5 0.9 - - - +
462A ILE* 3.3 24.9 - - + -
482A ASP* 2.8 50.3 - - + +
483A GLY* 5.2 2.5 - - - -
513A MET 5.7 1.6 - - - +
514A ARG* 6.4 1.1 - - - -
557A ALA 3.0 20.0 - - - +
558A LEU* 3.1 6.3 + - - +
560A SER* 1.3 80.7 - - - +
562A GLN* 1.3 65.8 + - - +
564A ARG* 2.9 3.0 + - + -
565A SER* 2.3 56.3 + - - +
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Residues in contact with GLN 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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514A ARG 4.9 10.4 - - - +
516A VAL 3.5 10.6 - - - +
517A GLN* 3.3 39.7 + - - +
558A LEU 3.2 11.2 + - - +
559A ILE* 3.8 19.1 - - + +
560A SER 3.4 0.2 - - - -
561A LEU* 1.3 79.2 - - - +
563A TYR* 1.3 70.1 + - + +
564A ARG* 2.7 7.4 + - - +
565A SER 3.9 4.7 - - - -
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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