Contacts of the helix formed by residues 576 - 591 (chain A) in PDB entry 1LSH
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 ASN 576 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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540A VAL 5.9 1.6 - - - +
542A ILE 5.5 1.8 + - - -
544A SER* 2.6 29.0 + - - +
547A ARG* 3.9 10.5 - - - +
574A GLU* 2.8 29.6 + - - +
575A PRO* 1.3 73.6 - - + +
577A LEU* 1.3 60.0 + - - +
578A GLN* 2.8 36.9 + - - +
579A VAL* 3.0 14.5 + - + +
580A ALA 3.0 21.8 + - - -
650A PRO* 6.2 1.4 - - - +
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Residues in contact with LEU 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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574A GLU 5.0 6.5 - - - +
575A PRO 3.5 7.9 + - - +
576A ASN* 1.3 72.1 + - - +
578A GLN* 1.3 62.1 + - - +
580A ALA* 3.8 5.1 - - + +
581A SER* 2.8 32.2 + - - -
616A LEU* 4.4 22.4 - - + -
619A LEU* 4.3 12.2 - - + +
623A TYR* 3.9 31.0 - - + +
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Residues in contact with GLN 578 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544A SER* 4.3 16.2 - - - +
548A ILE* 3.8 3.5 - - + +
576A ASN* 2.8 11.1 + - - +
577A LEU* 1.3 78.6 - - - +
579A VAL* 1.3 62.1 + - - +
581A SER* 3.6 0.7 + - - -
582A PHE* 3.2 18.2 + - - +
622A ARG* 3.0 22.4 + - - +
623A TYR* 3.5 20.7 - - + -
624A SER* 2.6 54.8 + - - +
648A ASN* 3.3 20.2 - - - +
649A SER 4.4 9.9 + - - -
650A PRO* 4.7 17.1 - - + +
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Residues in contact with VAL 579 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537A PHE* 3.9 20.4 - - + -
544A SER* 3.8 25.6 - - - +
547A ARG* 3.6 53.4 - - + +
548A ILE* 4.2 11.7 - - + +
574A GLU* 4.3 4.0 - - + +
576A ASN* 3.0 22.0 + - - +
578A GLN* 1.3 75.0 - - - +
580A ALA* 1.3 62.4 + - - +
582A PHE* 3.2 2.3 + - - +
583A VAL* 3.0 30.8 + - + +
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Residues in contact with ALA 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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571A LEU* 3.8 15.0 - - + +
574A GLU* 3.9 17.9 - - + +
576A ASN 3.0 16.3 + - - +
577A LEU* 3.8 10.3 - - + +
579A VAL* 1.3 78.5 - - - +
581A SER* 1.3 63.2 + - - +
584A TYR* 3.0 27.9 + - - +
616A LEU* 3.8 28.2 - - + +
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Residues in contact with SER 581 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577A LEU 2.8 22.1 + - - -
578A GLN 3.7 3.4 - - - -
580A ALA* 1.3 72.7 - - - +
582A PHE* 1.3 63.9 + - - +
584A TYR* 4.0 1.2 - - - +
585A SER* 3.1 25.5 + - - -
616A LEU* 4.7 7.7 + - - +
619A LEU* 3.8 19.5 - - - +
623A TYR* 3.4 11.9 - - - +
624A SER 2.7 20.6 + - - -
625A LYS* 3.2 22.3 + - - +
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Residues in contact with PHE 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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548A ILE* 3.6 37.2 - - + -
551A CYS* 3.9 14.6 - - + -
552A ILE* 3.6 16.6 - - + -
578A GLN 3.2 14.8 + - - +
579A VAL 3.6 3.6 - - - +
580A ALA 3.2 0.2 - - - -
581A SER* 1.3 80.6 - - - +
583A VAL* 1.3 60.8 + - + +
585A SER* 3.0 5.4 + - - -
586A GLN* 3.0 48.7 + - - +
624A SER* 3.5 8.7 - - - -
625A LYS 3.5 34.1 - - - -
626A ALA* 3.7 3.5 - - + +
645A PHE* 3.4 34.3 - + + -
646A ARG 4.0 8.7 - - - -
647A ILE* 4.9 0.4 - - + -
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Residues in contact with VAL 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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537A PHE* 3.4 30.3 - - + -
548A ILE* 6.1 0.7 - - + -
551A CYS* 3.7 17.0 - - + -
555A PHE* 4.1 15.9 - - + -
567A VAL* 3.6 27.1 - - + -
571A LEU* 3.9 11.2 - - + -
579A VAL* 3.0 18.9 + - + +
582A PHE* 1.3 78.5 - - + +
584A TYR* 1.3 64.6 + - - +
586A GLN* 3.4 1.1 + - - +
587A MET* 3.1 32.5 + - + +
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Residues in contact with TYR 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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571A LEU* 4.1 8.0 - - + +
580A ALA 3.0 20.5 + - - +
581A SER 4.1 1.8 - - - +
583A VAL* 1.3 77.3 - - - +
585A SER* 1.3 57.7 + - - +
587A MET* 3.4 8.6 + - + +
588A ARG* 2.9 78.6 + - + +
609A ILE* 4.3 7.9 - - + +
612A LEU* 3.9 33.0 + - + -
613A GLY 3.5 19.9 + - - -
614A SER* 3.3 15.7 - - - -
616A LEU* 3.7 29.6 - - + -
617A ASP* 3.5 33.7 - - + -
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Residues in contact with SER 585 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581A SER 3.1 15.8 + - - -
582A PHE 3.0 12.1 + - - -
583A VAL 3.3 0.2 - - - -
584A TYR* 1.3 75.5 - - - +
586A GLN* 1.3 58.8 + - - +
588A ARG* 4.0 0.5 - - - +
589A SER* 2.8 32.7 + - - -
617A ASP* 5.0 1.6 - - - -
625A LYS* 3.4 17.0 - - - -
626A ALA 3.1 27.8 + - - -
1505B ARG* 3.7 23.4 + - - +
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Residues in contact with GLN 586 (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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551A CYS* 2.7 41.4 + - - -
552A ILE* 4.1 6.1 - - - +
555A PHE* 3.0 32.9 - - + +
556A GLU 5.4 0.2 + - - -
582A PHE* 3.0 29.9 + - - +
583A VAL 3.8 4.9 - - - +
585A SER* 1.3 76.4 + - - +
587A MET* 1.3 59.2 + - - +
589A SER* 3.8 2.3 - - - -
590A LEU* 2.8 48.6 + - + +
626A ALA* 3.6 20.9 - - + -
628A HIS* 6.5 0.2 - - + -
645A PHE* 3.6 20.6 - - + -
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Residues in contact with MET 587 (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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555A PHE* 3.5 25.4 - - + -
564A VAL* 4.0 22.4 - - - +
567A VAL* 4.8 1.3 - - - -
568A ALA* 4.1 23.3 - - + -
571A LEU* 3.7 29.6 - - + -
583A VAL* 3.1 21.6 + - + +
584A TYR* 3.9 13.9 - - + +
586A GLN* 1.3 78.3 - - - +
588A ARG* 1.3 63.2 + - - +
591A SER* 2.9 25.6 + - - -
605A CYS* 3.5 17.7 - - - +
608A ALA* 4.2 5.8 - - + -
609A ILE* 3.9 15.3 - - + +
612A LEU* 4.9 4.3 - - + -
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Residues in contact with ARG 588 (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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584A TYR* 2.9 66.5 + - + +
587A MET* 1.3 76.0 - - - +
589A SER* 1.3 60.9 - - - +
591A SER* 2.7 19.9 + - - -
592A ARG* 3.7 9.9 - - - +
609A ILE* 3.2 33.7 - - + +
614A SER* 4.0 10.9 - - - -
617A ASP* 3.1 16.8 + - - -
1503B THR* 5.7 0.6 + - - -
1505B ARG* 3.4 48.5 + - - +
1506B ARG* 5.3 6.3 - - - +
1524B LEU* 4.0 22.8 - - - +
1525B LEU 5.1 0.2 - - - +
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Residues in contact with SER 589 (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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585A SER 2.8 19.9 + - - -
586A GLN* 3.8 3.6 - - - -
588A ARG* 1.3 75.6 - - - +
590A LEU* 1.3 65.3 + - - +
592A ARG* 3.1 18.4 + - - +
593A SER 3.8 2.4 + - - -
626A ALA 4.0 7.0 - - - -
627A VAL* 4.3 0.2 - - - -
628A HIS* 2.8 43.4 + - - +
1505B ARG* 4.1 3.1 - - - +
1526B PRO* 2.5 32.2 + - - +
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Residues in contact with LEU 590 (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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555A PHE* 4.0 29.8 - - + +
586A GLN* 2.8 29.0 + - + +
587A MET 4.0 2.0 - - - +
589A SER* 1.3 72.4 - - - +
591A SER* 1.3 68.1 + - - +
592A ARG 3.0 2.5 - - - -
593A SER* 2.9 15.2 + - - +
598A PHE* 4.5 15.3 - - + -
601A VAL* 3.9 23.8 - - + -
602A ALA* 3.2 14.6 - - - +
605A CYS* 4.0 9.4 - - - -
628A HIS* 3.4 43.1 - - + +
643A ASP* 5.0 1.8 - - - +
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Residues in contact with SER 591 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587A MET 2.9 15.8 + - - -
588A ARG* 2.7 22.0 + - - -
590A LEU* 1.3 77.3 - - - +
592A ARG* 1.3 73.0 + - - +
593A SER 3.2 1.5 + - - +
602A ALA* 3.8 19.3 - - - +
605A CYS* 4.2 1.3 - - - +
606A SER* 4.0 22.0 - - - -
609A ILE* 3.6 18.2 - - - +
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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
------------------------------------------------------------
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