Contacts of the helix formed by residues 573 - 585 (chain A) in PDB entry 5HLB
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 MET 573 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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513A LYS* 3.4 1.0 - - - -
517A TYR* 4.2 0.3 + - - -
535A ASP* 3.4 27.4 - - - +
552A ASN* 4.1 10.5 - - - +
553A ASP* 6.1 1.1 - - - -
558A SER* 4.0 2.0 - - - +
563A VAL* 3.6 24.5 - - + -
567A ASP* 4.1 4.7 - - - +
568A ALA* 2.9 35.1 + - - +
571A ARG* 3.6 49.4 - - + +
572A SER* 1.3 71.0 - - - +
574A ASN* 1.4 58.1 + - - +
575A VAL 3.8 0.2 - - - -
576A PRO* 3.6 14.4 - - + -
577A THR* 2.5 33.1 + - - -
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Residues in contact with ASN 574 (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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513A LYS* 2.8 30.9 + - - +
550A PRO* 5.4 0.7 - - + -
551A GLN 3.1 28.0 + - - +
552A ASN* 3.3 8.9 + - - +
553A ASP* 4.1 11.2 - - - +
572A SER 3.3 4.9 + - - +
573A MET* 1.4 68.2 - - - +
575A VAL* 1.3 65.6 + - + +
577A THR* 3.1 13.7 + - - -
578A VAL* 3.1 15.3 + - - +
611A LEU* 3.6 30.1 - - + +
902A AZR 3.6 36.3 + - - +
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Residues in contact with VAL 575 (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* 3.4 20.4 - - - +
536A ALA 3.5 28.9 - - - +
538A ILE* 3.5 24.9 - - + +
550A PRO* 3.4 29.8 - - + +
551A GLN* 4.3 3.6 - - - -
552A ASN* 3.1 15.6 + - - +
557A TYR* 4.1 16.4 - - + -
574A ASN* 1.3 77.6 - - - +
576A PRO* 1.4 64.8 - - + +
578A VAL* 3.2 9.3 + - - -
579A ASN* 3.2 14.2 + - - +
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Residues in contact with PRO 576 (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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517A TYR* 4.4 2.0 - - - -
533A ILE* 3.3 24.5 - - + +
534A ALA 3.8 4.3 - - - +
535A ASP* 3.7 20.6 - - + +
552A ASN* 3.6 4.0 - - - +
563A VAL* 3.7 32.8 - - + -
568A ALA* 3.9 11.2 - - + -
573A MET* 3.6 26.2 - - + -
574A ASN 3.7 0.7 - - - -
575A VAL* 1.4 93.8 - - + +
577A THR* 1.4 54.3 + - - +
579A ASN* 4.1 0.7 - - - +
580A LEU* 3.2 23.9 + - - +
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Residues in contact with THR 577 (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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513A LYS* 3.5 21.5 - - + +
516A THR* 3.8 14.2 - - + +
517A TYR* 2.6 33.2 + - + -
573A MET 2.5 24.6 + - - -
574A ASN 3.1 6.5 + - - -
576A PRO* 1.4 73.9 - - - +
578A VAL* 1.4 61.1 + - - +
580A LEU* 4.6 1.6 - - - -
581A GLY* 3.0 25.1 + - - -
610A LEU* 3.8 26.6 - - + +
611A LEU* 4.0 7.0 - - + -
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Residues in contact with VAL 578 (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 ILE* 4.1 15.5 - - + -
540A LEU* 3.9 18.4 - - + -
548A TRP* 3.7 31.6 - - + -
550A PRO* 4.2 6.5 - - + -
574A ASN 3.1 12.1 + - - +
575A VAL 3.2 6.5 + - - +
577A THR* 1.4 72.8 - - - +
579A ASN* 1.4 55.2 - - - +
581A GLY 3.2 1.0 + - - -
582A MET* 2.7 54.9 + - + +
610A LEU* 3.9 12.5 - - + +
611A LEU* 3.7 18.6 - - + -
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Residues in contact with ASN 579 (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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533A ILE* 4.3 6.5 - - + -
534A ALA* 2.9 41.5 + - + +
536A ALA 4.8 2.2 + - - -
538A ILE* 3.4 27.4 - - - +
575A VAL* 3.2 17.7 + - - +
576A PRO 4.0 4.0 - - - +
578A VAL* 1.4 73.9 - - - +
580A LEU* 1.4 61.6 + - - +
582A MET* 3.7 4.8 + - - +
583A ALA* 3.1 24.6 + - - +
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Residues in contact with LEU 580 (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 THR* 4.0 15.5 - - + +
517A TYR* 3.7 36.6 - - + -
520A ALA* 3.8 22.9 - - + -
527A TYR* 3.7 36.8 - - + -
533A ILE* 4.1 23.9 - - + +
565A LEU* 4.2 3.4 - - + -
576A PRO 3.2 19.5 + - - +
577A THR* 4.0 3.8 - - - +
578A VAL 3.3 0.2 - - - -
579A ASN* 1.4 70.9 - - - +
581A GLY* 1.3 66.8 + - - +
583A ALA* 3.2 6.6 + - - +
584A LEU* 3.1 27.9 + - + +
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Residues in contact with GLY 581 (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 THR* 3.7 15.4 - - - +
577A THR 3.0 16.5 + - - -
578A VAL 3.6 2.9 - - - -
580A LEU* 1.3 76.5 - - - +
582A MET* 1.3 55.2 + - - +
584A LEU* 3.3 6.5 + - - +
585A GLY* 2.8 32.4 + - - +
586A LEU 4.1 0.7 + - - -
589A VAL* 4.5 2.3 - - - +
610A LEU* 3.8 20.6 - - - -
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Residues in contact with MET 582 (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 LEU* 4.2 18.2 - - + -
578A VAL* 2.7 36.8 + - + +
579A ASN* 4.2 4.7 - - - +
581A GLY* 1.3 71.9 - - - +
583A ALA* 1.3 60.1 + - - +
585A GLY* 3.5 11.7 + - - +
586A LEU* 4.3 17.3 - - + -
607A PRO* 3.8 33.7 - - + -
610A LEU* 3.9 16.6 - - - -
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Residues in contact with ALA 583 (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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527A TYR* 3.8 21.6 + - + +
579A ASN 3.1 18.9 + - - +
580A LEU* 3.2 7.6 + - - +
582A MET* 1.3 73.7 - - - +
584A LEU* 1.3 63.9 + - - +
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Residues in contact with LEU 584 (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 THR* 3.4 32.5 - - + +
519A THR* 4.0 14.4 - - + +
520A ALA* 3.7 24.2 - - + +
523A GLN* 3.8 18.4 - - - +
527A TYR* 3.5 30.3 - - + -
580A LEU* 3.1 21.1 + - + +
581A GLY 3.7 3.6 - - - +
583A ALA* 1.3 76.4 - - - +
585A GLY* 1.3 66.4 + - - +
588A ALA* 3.7 13.0 - - + +
589A VAL* 4.1 11.0 - - + -
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Residues in contact with GLY 585 (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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581A GLY 2.8 14.1 + - - +
582A MET* 3.5 10.7 + - - -
583A ALA 3.3 2.6 - - - -
584A LEU* 1.3 82.7 - - - +
586A LEU* 1.3 65.8 + - - +
587A PRO* 3.4 8.1 - - - -
588A ALA* 3.3 12.5 + - - +
589A VAL* 3.5 6.4 + - - +
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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