Contacts of the strand formed by residues 558 - 571 (chain A) in PDB entry 1HMU
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 VAL 558 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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399A ASN 5.5 0.2 - - - +
402A PRO* 3.4 20.9 - - + -
403A VAL* 3.3 19.0 - - + +
543A LYS* 3.1 23.4 - - - +
544A GLY 2.8 28.0 + - - +
545A ASN* 5.1 0.2 - - - -
546A TRP* 4.1 23.1 - - + +
556A ASP* 4.1 9.2 - - + +
557A GLU* 1.3 76.8 - - - +
559A SER* 1.3 63.2 + - - +
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Residues in contact with SER 559 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403A VAL* 4.7 4.0 - - - -
492A TRP* 4.9 4.8 - - - -
541A SER* 4.3 9.2 - - - -
542A GLN 3.4 9.9 - - - -
543A LYS* 3.5 7.8 - - - +
557A GLU* 3.3 22.7 + - - +
558A VAL* 1.3 77.7 + - - +
560A GLY* 1.3 58.1 + - - +
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Residues in contact with GLY 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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492A TRP* 3.7 17.6 - - - -
541A SER* 3.9 4.4 + - - -
542A GLN 2.9 29.1 + - - +
559A SER* 1.3 77.7 - - - +
561A ASP* 1.3 67.0 + - - -
562A VAL* 3.4 5.5 + - - +
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Residues in contact with ASP 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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492A TRP* 3.4 12.1 - - - -
493A LEU* 2.8 43.1 + - + +
506A ARG* 2.8 55.3 + - - +
539A THR 4.4 1.8 - - - +
540A GLN 3.7 4.3 - - - -
541A SER* 3.4 13.0 - - - -
560A GLY* 1.3 69.7 - - - -
562A VAL* 1.3 60.1 + - - +
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Residues in contact with VAL 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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400A ILE* 4.0 11.9 - - + -
403A VAL* 4.1 4.0 - - + -
490A GLN* 3.7 26.2 - - + -
491A SER 3.5 10.5 - - - +
492A TRP* 3.9 16.4 - - + -
493A LEU* 4.2 4.0 - - - -
538A SER* 3.2 15.1 + - - +
539A THR* 3.3 10.0 - - - -
540A GLN 2.9 13.7 + - - +
542A GLN* 3.6 41.8 - - + +
560A GLY 3.6 11.0 - - - +
561A ASP* 1.3 76.6 - - - +
563A PHE* 1.3 65.2 + - - +
564A LYS* 3.4 2.3 + - + +
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Residues in contact with PHE 563 (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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489A ASN* 4.2 11.0 - - + -
490A GLN* 3.2 3.8 - - - -
491A SER* 2.6 45.0 + - - +
493A LEU* 3.7 12.0 - - + +
497A VAL* 4.0 17.3 - - + -
520A LEU* 5.8 2.7 - - + -
522A HIS* 3.4 52.3 - + + +
527A TYR* 3.6 39.7 - + - -
537A LEU* 3.6 26.9 - - + -
538A SER 3.6 3.4 - - - -
539A THR* 4.7 0.2 - - + -
562A VAL* 1.3 70.3 - - - +
564A LYS* 1.3 57.8 + - - +
565A LEU* 4.1 22.9 - - + -
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Residues in contact with LYS 564 (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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405A GLU* 2.9 24.2 + - - +
408A LYS* 3.6 20.6 - - + -
487A THR* 5.1 1.1 - - + -
489A ASN 3.5 8.5 - - - +
490A GLN* 3.9 22.4 - - + +
537A LEU* 3.7 3.9 - - - +
538A SER* 2.8 51.3 + - - +
542A GLN* 2.7 34.5 + - - +
562A VAL* 3.4 1.1 + - + +
563A PHE* 1.3 73.7 - - - +
565A LEU* 1.3 61.2 + - - +
566A TRP* 3.5 32.2 - - + -
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Residues in contact with LEU 565 (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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487A THR* 3.6 2.5 - - - +
488A LEU* 2.7 61.0 + - + -
489A ASN 3.1 12.2 + - - +
520A LEU* 3.9 32.5 - - + -
527A TYR* 4.1 19.3 - - + -
529A PHE* 4.4 2.0 - - + -
535A LEU* 4.0 17.0 - - + -
536A SER 3.4 19.7 - - - +
537A LEU* 4.2 7.6 - - + -
563A PHE* 4.1 24.0 - - + -
564A LYS* 1.3 75.6 - - - +
566A TRP* 1.3 59.0 + - - +
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Residues in contact with TRP 566 (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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408A LYS* 3.5 22.1 - - + +
416A ASP* 5.0 3.0 + - - -
485A THR* 3.6 17.0 - - + +
486A THR 3.3 13.7 - - - +
487A THR* 3.6 15.0 - - - +
488A LEU* 4.0 2.7 - - - -
509A ILE* 5.3 8.5 - - + -
535A LEU* 3.5 7.8 - - - +
536A SER* 3.0 58.4 + - - -
537A LEU 5.3 0.4 - - - -
538A SER* 4.1 10.5 - - - -
564A LYS* 3.5 52.0 - - + -
565A LEU* 1.3 77.3 - - - +
567A ILE* 1.3 72.6 + - - +
568A ASN* 3.0 27.4 + - - -
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Residues in contact with ILE 567 (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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485A THR* 3.2 10.7 - - - -
486A THR* 2.8 36.7 + - - +
488A LEU* 3.8 22.4 - - + -
529A PHE* 4.5 5.8 - - + -
533A ALA* 4.1 16.4 - - + -
534A ASN 3.3 16.2 - - - +
535A LEU* 3.9 12.6 - - + -
566A TRP* 1.3 74.2 - - - +
568A ASN* 1.3 70.7 + - - +
569A HIS* 3.7 22.2 - - + +
577A GLN 5.4 0.7 - - - +
578A TYR* 3.7 28.9 - - + -
579A ALA 5.0 2.2 - - - +
580A TYR* 4.4 9.2 - - + -
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Residues in contact with ASN 568 (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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483A ASN* 3.4 22.1 + - - +
484A ILE 3.9 3.6 - - - -
511A THR* 4.2 8.9 - - - +
534A ASN* 2.8 48.5 + - + +
535A LEU 4.0 4.9 + - - -
536A SER* 2.9 29.3 + - - -
566A TRP* 3.0 21.6 + - - -
567A ILE* 1.3 76.8 - - - +
569A HIS* 1.3 63.4 + - - +
570A GLY* 3.4 2.0 - - - +
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Residues in contact with HIS 569 (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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476A ILE* 3.5 29.6 - - + +
484A ILE* 2.8 45.5 + - + +
485A THR 4.0 5.4 - - - -
486A THR* 2.7 32.6 + - - -
567A ILE* 3.7 19.6 - - + +
568A ASN* 1.3 73.3 - - - +
570A GLY* 1.3 62.7 + - - +
571A ALA 4.9 0.3 - - - +
573A PRO* 4.0 21.3 - - + +
576A ALA* 4.3 9.3 - - + +
577A GLN 3.6 19.3 + - - -
578A TYR* 3.9 7.0 - - + -
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Residues in contact with GLY 570 (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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483A ASN* 2.7 20.3 + - - -
484A ILE* 3.0 14.7 + - - +
568A ASN* 3.4 3.8 + - - +
569A HIS* 1.3 82.5 - - - +
571A ALA* 1.3 65.5 + - - -
573A PRO* 3.6 8.3 - - - +
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Residues in contact with ALA 571 (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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481A PRO 3.5 25.1 - - - +
482A GLU 3.5 11.9 - - - +
483A ASN* 3.8 4.8 + - + +
569A HIS 4.9 0.3 - - - +
570A GLY* 1.3 73.0 - - - -
572A ARG* 1.3 81.3 + - + +
573A PRO* 3.3 1.4 - - - +
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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