Contacts of the helix formed by residues 579 - 595 (chain B) in PDB entry 2L1L
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 GLY 579 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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577B HIS 3.2 0.8 + - - -
578B ASP* 1.3 70.2 - - - +
580B VAL* 1.3 63.4 + - - +
581B GLN* 3.3 7.2 + - - +
582B ASP* 3.1 21.7 + - - +
583B MET* 2.9 21.4 + - - +
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Residues in contact with VAL 580 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A ILE* 4.1 4.9 - - + -
538B ALA* 4.0 24.5 - - + +
541B ALA* 5.9 1.3 - - + -
542B SER* 6.2 1.1 - - - -
545B MET* 4.6 9.6 - - + -
572B PHE* 3.8 24.7 - - + -
575B GLU* 3.6 35.2 - - + -
577B HIS* 3.1 27.7 + - + +
578B ASP 3.4 0.6 + - - +
579B GLY* 1.3 75.3 - - - +
581B GLN* 1.3 51.9 + - - +
583B MET* 3.0 9.3 + - - +
584B ALA* 2.7 33.3 + - - +
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Residues in contact with GLN 581 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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572B PHE 4.1 12.6 - - - +
573B MET* 4.4 12.8 - - - +
575B GLU 2.8 29.8 + - - +
576B THR* 3.8 7.9 - - - +
577B HIS 2.8 31.1 + - - -
578B ASP* 5.3 0.9 - - - -
579B GLY 4.0 5.2 + - - +
580B VAL* 1.3 76.0 - - - +
582B ASP* 1.3 65.2 + - - +
584B ALA* 3.4 2.8 + - - +
585B CYS* 3.0 30.7 + - - -
624B ASP* 4.9 8.5 - - - +
625B LEU* 6.3 0.4 - - - -
626B GLN* 4.1 14.0 + - - +
629B GLN* 3.3 25.3 - - - +
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Residues in contact with ASP 582 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579B GLY* 3.1 21.6 + - - +
581B GLN* 1.3 76.0 - - - +
583B MET* 1.3 63.7 + - - +
585B CYS* 3.5 3.1 + - - +
586B ASP* 2.5 38.6 + - - +
626B GLN* 5.3 0.3 - - - +
628B GLN* 5.5 5.2 + - - -
629B GLN* 3.8 24.8 - - - +
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Residues in contact with MET 583 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542B SER* 3.6 37.5 - - - +
545B MET* 3.5 28.0 - - + -
546B TYR* 4.9 16.6 - - + -
579B GLY 2.9 11.2 + - - +
580B VAL* 3.3 12.6 - - - +
582B ASP* 1.3 75.8 - - - +
584B ALA* 1.3 64.5 + - - +
586B ASP* 3.3 14.1 + - + +
587B THR* 3.0 38.3 + - - +
590B LYS* 5.4 4.3 - - - +
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Residues in contact with ALA 584 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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545B MET* 4.2 2.6 - - - -
569B LEU* 3.7 42.1 - - + +
572B PHE* 3.9 20.4 - - + +
573B MET* 4.1 11.2 - - + +
580B VAL 2.7 18.8 + - - +
581B GLN 3.6 5.2 - - - +
582B ASP 3.3 0.2 - - - -
583B MET* 1.3 73.7 - - - +
585B CYS* 1.3 62.0 + - - +
588B PHE* 3.1 23.0 + - - +
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Residues in contact with CYS 585 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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573B MET* 4.3 11.4 - - - -
581B GLN 3.0 22.1 + - - +
582B ASP* 4.0 3.8 - - - +
584B ALA* 1.3 74.3 - - - +
586B ASP* 1.3 67.4 + - - +
588B PHE* 3.1 10.8 + - - +
589B ILE* 3.1 22.9 + - - +
625B LEU* 3.7 29.8 - - - -
629B GLN* 3.7 30.7 - - + +
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Residues in contact with ASP 586 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582B ASP* 2.5 35.3 + - - +
583B MET* 3.7 13.5 - - + +
585B CYS* 1.3 78.2 - - - +
587B THR* 1.3 58.6 + - - +
589B ILE* 2.9 30.4 - - - +
590B LYS* 3.2 26.5 + - - +
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Residues in contact with THR 587 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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545B MET* 3.6 36.4 + - - +
546B TYR* 4.8 0.9 - - - -
548B VAL* 4.3 11.0 - - + -
549B GLY* 4.4 9.0 - - - -
565B VAL* 5.5 0.4 - - + -
569B LEU* 3.9 29.2 - - + -
583B MET* 3.0 25.6 + - - +
586B ASP* 1.3 73.8 - - - +
588B PHE* 1.3 66.2 + - - +
589B ILE 3.2 0.3 + - - -
590B LYS* 3.2 13.4 + - - +
591B ILE* 3.0 25.0 + - + +
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Residues in contact with PHE 588 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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566B VAL* 3.8 19.5 - - + -
569B LEU* 4.2 13.4 - - + +
570B PHE* 3.6 39.5 - + - -
573B MET* 5.7 7.9 - - - -
584B ALA 3.1 19.9 + - - +
585B CYS* 3.1 10.3 + - - +
587B THR* 1.3 77.9 - - - +
589B ILE* 1.3 64.6 + - + +
591B ILE* 2.9 28.6 - - + +
592B ALA* 3.0 21.6 + - + +
599B PHE* 5.4 5.8 - + - -
614B ILE* 5.3 7.2 - - + -
621B ILE* 6.2 0.2 - - + -
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Residues in contact with ILE 589 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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585B CYS 3.1 8.3 + - - +
586B ASP* 2.9 31.6 - - - +
588B PHE* 1.3 80.1 - - + +
590B LYS* 1.3 73.1 + - + +
592B ALA* 3.4 8.0 + - + +
593B GLN* 3.0 45.6 + - + +
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Residues in contact with LYS 590 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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546B TYR* 5.5 14.4 - - + +
549B GLY* 4.4 23.6 - - - +
550B GLN* 4.5 17.5 - - - +
583B MET* 5.4 4.0 - - - +
586B ASP* 3.2 38.3 + - - +
587B THR* 3.2 12.6 + - - +
589B ILE* 1.3 82.7 - - + +
591B ILE* 1.3 56.8 + - - +
593B GLN* 3.3 8.4 + - - +
594B LYS* 3.0 45.1 + - + +
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Residues in contact with ILE 591 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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548B VAL* 5.4 0.2 - - + -
549B GLY* 5.8 4.0 - - - -
552B PRO* 6.3 0.4 - - - -
555B LEU* 3.6 23.3 - - + -
562B LEU* 3.4 34.3 - - + -
565B VAL* 4.5 15.3 - - + -
566B VAL* 3.8 19.5 - - + -
569B LEU* 4.6 5.8 - - + -
587B THR* 3.0 13.1 + - + +
588B PHE* 2.9 41.7 - - + +
590B LYS* 1.3 77.3 - - - +
592B ALA* 1.3 56.6 + - - +
594B LYS* 4.9 3.1 - - - -
595B CYS* 2.8 40.0 + - + +
599B PHE* 4.8 3.6 - - + -
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Residues in contact with ALA 592 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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588B PHE* 3.0 27.9 + - + +
589B ILE* 3.9 11.4 - - + +
591B ILE* 1.3 80.5 - - + +
593B GLN* 1.3 69.2 + - - +
596B ARG* 3.2 25.1 + - - +
599B PHE* 4.1 18.4 - - + -
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Residues in contact with GLN 593 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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589B ILE* 3.0 42.9 + - + +
590B LYS* 3.6 5.8 - - - +
592B ALA* 1.3 79.5 - - - +
594B LYS* 1.3 91.1 + - + +
595B CYS 3.1 0.5 + - - -
596B ARG* 3.3 15.0 + - - +
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Residues in contact with LYS 594 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552B PRO* 3.5 40.9 - - + +
556B ARG* 5.7 6.1 - - - +
590B LYS* 3.0 27.4 + - + +
591B ILE* 4.4 2.5 - - - +
593B GLN* 1.3 106.1 + - + +
595B CYS* 1.3 57.3 + - - +
596B ARG 3.6 0.2 - - - -
598B HIS* 5.5 0.5 - - - -
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Residues in contact with CYS 595 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552B PRO* 5.8 3.1 - - + +
555B LEU* 5.6 2.7 - - + -
556B ARG* 5.5 6.5 - - + -
562B LEU* 3.9 19.3 - - + -
591B ILE* 2.8 42.6 + - + +
594B LYS* 1.3 74.4 - - + +
596B ARG* 1.3 65.9 + - - +
597B ARG 3.0 4.8 + - - -
598B HIS* 3.0 30.7 + - + +
599B PHE* 3.3 34.9 + - - -
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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