Contacts of the helix formed by residues 509 - 531 (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 HIS 509 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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507B ALA 5.7 0.9 - - - -
508B MET* 1.3 74.3 - - - +
510B GLU* 1.3 67.8 + - - +
511B GLU* 2.7 8.2 + - + +
512B ASP* 2.7 33.8 + - - +
513B GLU* 2.9 8.7 + - - -
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Residues in contact with GLU 510 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508B MET 3.6 3.0 + - - -
509B HIS* 1.3 70.2 - - - +
511B GLU* 1.3 56.6 + - - +
513B GLU* 3.2 13.5 - - + +
514B LYS* 3.0 27.4 + - + +
553B ARG* 4.3 39.0 + - + +
554B PHE* 5.9 2.0 - - - +
557B ALA* 5.1 12.9 - - - +
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Residues in contact with GLU 511 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509B HIS* 2.7 8.9 + - + +
510B GLU* 1.3 74.0 - - - +
512B ASP* 1.3 67.9 + - - +
514B LYS* 3.5 16.5 + - - +
515B ARG* 3.4 32.8 + - + +
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Residues in contact with ASP 512 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508B MET* 3.5 26.2 - - + +
509B HIS* 2.7 35.8 + - - +
511B GLU* 1.3 73.2 - - - +
513B GLU* 1.3 65.0 + - - +
515B ARG* 3.3 14.9 + - - +
516B PHE* 3.0 25.1 + - - +
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Residues in contact with GLU 513 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504B ILE* 5.1 1.9 - - - +
505B SER* 4.1 0.7 - - - -
506B GLY* 3.3 21.5 + - - -
508B MET* 3.2 44.8 - - + +
509B HIS 2.9 16.9 + - - +
510B GLU* 3.2 14.6 - - + +
512B ASP* 1.3 76.5 - - - +
514B LYS* 1.3 62.7 + - - +
516B PHE* 3.2 6.2 + - - +
517B LEU* 2.9 28.0 + - - +
551B TYR* 3.2 39.7 + - + -
554B PHE* 5.1 5.6 - - + -
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Residues in contact with LYS 514 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A LEU* 5.0 10.0 - - + +
510B GLU 3.0 13.7 + - - +
511B GLU* 3.6 21.5 - - - +
512B ASP 3.3 0.4 - - - -
513B GLU* 1.3 76.0 - - - +
515B ARG* 1.3 76.4 + - - +
517B LEU* 3.3 1.9 + - - +
518B VAL* 2.9 35.0 + - + +
554B PHE* 3.9 28.9 - - + -
558B HIS* 4.1 21.5 - - + +
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Residues in contact with ARG 515 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511B GLU* 3.4 22.9 + - - +
512B ASP* 3.3 14.6 + - - +
514B LYS* 1.3 96.1 - - - +
516B PHE* 1.3 58.2 + - - +
518B VAL* 2.8 27.1 - - + +
519B THR* 2.9 15.6 + - - -
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Residues in contact with PHE 516 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504B ILE* 5.0 17.3 - - + -
508B MET* 4.4 23.1 - - + -
512B ASP 3.0 18.3 + - - +
513B GLU* 3.6 7.4 - - - +
514B LYS 3.1 0.2 - - - -
515B ARG* 1.3 76.7 - - - +
517B LEU* 1.3 64.4 + - + +
519B THR* 3.2 7.6 + - - -
520B VAL* 2.9 55.2 + - + +
551B TYR* 5.1 9.9 - + - -
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Residues in contact with LEU 517 (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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513B GLU 2.9 17.3 + - - +
514B LYS 3.8 2.7 - - - +
516B PHE* 1.3 77.2 - - + +
518B VAL* 1.3 65.6 + - - +
520B VAL* 3.1 23.7 - - + +
521B ILE* 3.2 25.2 + - + +
547B ILE* 3.6 31.4 - - + -
548B VAL* 5.5 4.5 - - + -
551B TYR* 3.6 33.7 - - + -
554B PHE* 3.4 48.7 - - + -
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Residues in contact with VAL 518 (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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10A LEU* 3.4 33.2 - - + -
514B LYS* 2.9 18.0 + - + +
515B ARG* 2.8 36.1 - - + +
517B LEU* 1.3 76.5 - - - +
519B THR* 1.3 59.6 - - - +
521B ILE* 5.5 0.7 - - - -
522B LYS* 3.0 59.4 + - + +
554B PHE* 5.1 7.3 - - + -
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Residues in contact with THR 519 (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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515B ARG 2.9 13.8 + - - -
516B PHE* 3.2 11.8 + - - -
517B LEU 3.2 0.2 - - - -
518B VAL* 1.3 81.1 - - - +
520B VAL* 1.3 66.6 + - + +
521B ILE 3.6 0.2 + - - -
522B LYS* 4.4 3.6 - - - +
523B ASP* 3.6 22.0 + - + +
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Residues in contact with VAL 520 (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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516B PHE* 2.9 54.9 + - + +
517B LEU* 3.1 31.6 - - + +
519B THR* 1.3 78.7 - - + +
521B ILE* 1.3 74.6 + - + +
523B ASP* 3.8 2.8 + - - +
524B LEU* 3.3 24.3 + - - +
547B ILE* 4.6 7.0 - - + -
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Residues in contact with ILE 521 (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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14A LEU* 5.5 2.5 - - + -
517B LEU* 3.2 34.3 + - + +
518B VAL 4.9 0.2 - - - +
520B VAL* 1.3 89.4 - - + +
522B LYS* 1.3 58.7 + - - +
523B ASP 3.1 1.8 - - - -
524B LEU* 4.2 6.5 - - + -
525B LEU* 2.9 29.7 + - + +
544B ILE* 3.4 40.4 - - + -
547B ILE* 4.1 17.5 - - + -
548B VAL* 4.7 12.8 - - + +
554B PHE* 6.2 0.4 - - + -
561B PHE* 5.0 21.8 - - + -
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Residues in contact with LYS 522 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LEU* 3.8 29.0 - - + +
13A LYS* 5.4 15.3 - - + +
518B VAL* 3.0 48.2 + - + +
519B THR* 4.4 4.9 - - - +
520B VAL 3.6 0.2 - - - -
521B ILE* 1.3 77.4 - - - +
523B ASP* 1.3 57.7 + - + +
525B LEU* 3.7 11.3 - - + +
526B GLY* 3.2 19.4 + - - -
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Residues in contact with ASP 523 (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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519B THR* 3.6 16.8 + - + +
520B VAL 4.3 2.4 - - - +
521B ILE 3.1 0.4 - - - -
522B LYS* 1.3 80.7 - - + +
524B LEU* 1.3 59.9 + - - +
525B LEU 3.4 0.2 - - - -
526B GLY* 3.6 2.6 - - - +
527B LEU* 2.8 30.0 + - - +
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Residues in contact with LEU 524 (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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520B VAL 3.3 18.7 + - - +
521B ILE* 3.9 8.5 - - + +
523B ASP* 1.3 72.3 - - - +
525B LEU* 1.3 55.6 + - - +
527B LEU* 3.1 12.4 + - + +
528B CYS* 2.8 35.3 + - - +
540B ILE* 3.5 40.5 - - + +
543B ASN* 3.3 21.3 - - + +
544B ILE* 3.3 44.6 - - + +
547B ILE* 5.3 2.5 - - + -
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Residues in contact with LEU 525 (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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13A LYS* 3.2 40.8 - - + +
14A LEU* 3.5 32.3 - - + +
16A GLY 3.3 23.3 - - - +
17A LEU* 4.0 15.7 - - + -
521B ILE* 2.9 24.7 + - + +
522B LYS* 3.7 9.9 - - + +
524B LEU* 1.3 75.8 - - - +
526B GLY* 1.3 62.3 + - - +
528B CYS* 3.2 14.7 + - - +
529B GLU* 3.2 22.1 + - - +
544B ILE* 5.1 4.5 - - + +
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Residues in contact with GLY 526 (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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522B LYS 3.2 13.9 + - - -
523B ASP* 3.4 5.5 + - - -
524B LEU 3.2 0.2 - - - -
525B LEU* 1.3 80.3 - - - +
527B LEU* 1.3 62.0 + - - +
529B GLU* 3.6 12.2 + - - +
530B GLN* 3.2 20.5 + - - +
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Residues in contact with LEU 527 (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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523B ASP* 2.8 22.4 + - - +
524B LEU* 3.5 15.3 - - + +
526B GLY* 1.3 75.2 - - - +
528B CYS* 1.3 64.2 + - - +
530B GLN* 3.0 30.4 + - - +
531B LYS* 2.9 47.3 + - + +
540B ILE* 3.5 26.9 - - + -
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Residues in contact with CYS 528 (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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17A LEU* 3.5 40.4 - - + -
18A ASP 4.0 10.9 - - - +
524B LEU 2.8 20.0 + - - +
525B LEU* 3.2 10.5 + - - +
527B LEU* 1.3 75.9 - - - +
529B GLU* 1.3 62.8 + - + +
531B LYS* 3.3 16.2 - - - +
537B LYS* 3.9 29.6 - - - +
540B ILE* 3.6 21.5 - - + +
541B ALA 4.8 1.1 - - - -
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Residues in contact with GLU 529 (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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13A LYS 5.0 0.7 - - - +
16A GLY* 3.0 39.6 - - - +
17A LEU* 4.7 4.3 - - - -
18A ASP* 5.1 11.7 - - - +
525B LEU* 3.2 22.3 + - - +
526B GLY* 3.9 10.4 - - - +
528B CYS* 1.3 77.2 - - - +
530B GLN* 1.3 63.5 + - - +
531B LYS 4.1 2.8 - - - +
532B ARG* 5.9 0.2 - - - +
537B LYS* 5.3 3.5 + - - +
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Residues in contact with GLN 530 (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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526B GLY 3.2 14.1 + - - +
527B LEU* 3.0 35.1 + - - +
529B GLU* 1.3 78.4 - - - +
531B LYS* 1.3 80.2 + - + +
532B ARG* 3.5 10.6 + - - +
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Residues in contact with LYS 531 (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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527B LEU* 2.9 46.5 + - + +
528B CYS 3.3 15.0 - - - +
529B GLU 4.1 1.4 - - - +
530B GLN* 1.3 87.9 - - + +
532B ARG* 1.3 61.0 + - - +
536B ASN* 3.9 28.0 - - + +
537B LYS* 3.3 15.3 - - - +
540B ILE* 5.1 8.1 - - + -
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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
------------------------------------------------------------
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