Contacts of the helix formed by residues 515 - 528 (chain A) in PDB entry 1LW0
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 SER 515 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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361A HIS* 4.5 7.6 - - - -
476A LYS* 5.8 2.4 - - - +
479A LEU* 5.6 2.0 - - - +
513A SER* 2.7 14.5 + - - -
514A GLU* 1.3 80.6 - - - +
516A GLU* 1.3 64.0 + - - +
517A LEU* 3.2 16.5 + - - +
518A VAL* 3.4 18.7 + - - +
519A ASN* 2.7 26.7 + - - -
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Residues in contact with GLU 516 (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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514A GLU 3.9 2.0 + - - -
515A SER* 1.3 71.8 + - - +
517A LEU* 1.3 67.8 + - - +
519A ASN* 3.2 10.6 + - + +
520A GLN* 2.9 49.1 + - + +
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Residues in contact with LEU 517 (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 LYS* 3.4 40.8 - - + +
479A LEU* 3.6 27.8 - - + +
480A GLN* 3.7 24.9 - - + +
483A TYR* 3.9 22.9 - - + -
515A SER* 3.2 8.0 + - - +
516A GLU* 1.3 80.1 + - - +
518A VAL* 1.3 64.7 + - + +
520A GLN* 2.9 37.6 + - - +
521A ILE* 3.0 15.5 + - + +
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Residues in contact with VAL 518 (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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361A HIS* 4.1 16.6 - - + +
479A LEU* 4.5 23.1 - - + -
505A ILE* 4.6 13.5 - - + -
510A PRO* 4.7 9.2 - - + -
513A SER* 3.3 28.0 - - - +
515A SER* 3.4 17.9 + - - +
517A LEU* 1.3 78.0 - - - +
519A ASN* 1.3 67.1 + - - +
521A ILE* 2.6 25.5 + - + +
522A ILE* 2.7 30.2 + - + +
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Residues in contact with ASN 519 (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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334A GLN* 4.5 7.1 + - - -
511A ASP 4.3 4.0 - - - +
512A GLN* 3.8 8.8 - - - -
513A SER* 2.8 40.9 + - - -
515A SER 2.7 23.8 + - - -
516A GLU* 3.2 12.7 + - + +
518A VAL* 1.3 78.5 - - - +
520A GLN* 1.3 56.3 + - - +
522A ILE* 3.1 10.7 + - - +
523A GLU* 2.8 34.1 + - - +
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Residues in contact with GLN 520 (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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480A GLN* 4.9 3.0 + - - -
483A TYR* 3.6 37.4 + - + +
516A GLU* 2.9 38.5 + - + +
517A LEU* 2.9 34.0 + - - +
518A VAL 2.8 1.6 + - - -
519A ASN* 1.3 71.7 - - + +
521A ILE* 1.3 66.8 + - - +
523A GLU* 3.1 10.4 + - - +
524A GLN* 3.0 23.6 + - - +
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Residues in contact with ILE 521 (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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479A LEU* 3.4 46.9 - - + +
482A ILE* 4.6 5.2 - - + -
483A TYR* 3.9 26.2 - - + +
486A LEU* 3.3 21.3 - - + -
506A ILE* 4.3 16.4 - - + -
517A LEU* 3.0 15.7 + - + +
518A VAL* 2.6 19.2 + - + +
520A GLN* 1.3 70.1 - - - +
522A ILE* 1.3 59.8 + - + +
524A GLN* 2.8 24.5 + - - +
525A LEU* 2.8 25.3 + - + +
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Residues in contact with ILE 522 (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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427A TYR* 4.0 7.6 - - + +
510A PRO* 3.5 30.3 - - + +
511A ASP* 3.5 37.5 - - - +
512A GLN* 3.6 9.0 - - - +
518A VAL* 2.7 42.7 + - + +
519A ASN* 3.3 14.4 - - - +
521A ILE* 1.3 72.7 - - + +
523A GLU* 1.3 65.7 + - - +
525A LEU* 3.3 10.9 + - + +
526A ILE* 3.0 43.8 + - + +
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Residues in contact with GLU 523 (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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519A ASN* 2.8 16.5 + - - +
520A GLN* 3.3 13.9 - - - +
521A ILE 3.0 0.2 - - - -
522A ILE* 1.3 81.2 - - - +
524A GLN* 1.3 64.8 + - + +
526A ILE* 3.5 14.1 + - - +
527A LYS* 3.1 31.7 + - + +
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Residues in contact with GLN 524 (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 TYR* 3.6 15.1 - - + -
486A LEU* 3.7 29.5 + - + -
487A GLN* 3.2 50.9 + - - +
520A GLN 3.0 13.8 + - - +
521A ILE 2.8 8.6 + - - +
523A GLU* 1.3 79.4 - - - +
525A LEU* 1.3 54.9 + - - +
527A LYS* 2.7 34.9 + - - +
528A LYS* 3.1 18.2 + - - +
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Residues in contact with LEU 525 (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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427A TYR* 3.5 53.7 - - + +
429A LEU* 4.8 7.2 - - + -
486A LEU* 4.0 23.8 - - + -
506A ILE* 4.0 19.7 - - + -
521A ILE* 2.8 28.1 + - + +
522A ILE* 3.4 12.1 - - + +
524A GLN* 1.3 76.5 - - - +
526A ILE* 1.3 64.4 + - - +
528A LYS* 3.1 22.0 + - - +
531A VAL* 4.2 22.8 - - + +
533A LEU* 5.7 1.8 - - + -
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Residues in contact with ILE 526 (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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426A TRP* 3.6 59.5 - - + +
427A TYR* 3.7 19.0 - - + +
511A ASP* 5.8 1.1 - - + -
522A ILE* 3.0 32.1 + - + +
523A GLU* 3.9 14.6 - - - +
525A LEU* 1.3 77.8 - - - +
527A LYS* 1.3 69.8 + - + +
528A LYS 3.4 6.6 + - - +
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Residues in contact with LYS 527 (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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491A LEU* 4.7 9.1 - - - +
523A GLU* 3.1 22.0 - - + +
524A GLN* 2.7 25.4 + - - +
526A ILE* 1.3 81.5 - - + +
528A LYS* 1.3 62.0 + - + +
529A GLU* 5.3 1.0 - - - +
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Residues in contact with LYS 528 (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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486A LEU* 2.5 47.5 + - + -
489A SER* 2.6 26.3 + - - -
490A GLY 3.1 24.0 + - - +
491A LEU* 3.9 9.9 - - + +
493A VAL* 4.0 8.3 - - + -
524A GLN* 3.1 19.0 + - - +
525A LEU* 3.1 10.3 + - - +
526A ILE 3.4 8.1 - - - +
527A LYS* 1.3 85.1 - - + +
529A GLU* 1.3 64.8 + - - +
530A LYS 4.2 0.7 - - - +
531A VAL* 3.4 30.5 - - + -
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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