Contacts of the helix formed by residues 487 - 501 (chain B) in PDB entry 1HWL
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 THR 487 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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482B GLU* 5.0 1.4 - - - +
485B ILE* 2.9 18.7 + - + +
486B GLU* 1.3 83.4 - - + +
488B HIS* 1.3 68.5 + - - +
489B GLU* 3.8 9.4 + - - +
490B ARG* 3.2 36.3 + - + +
491B GLY* 3.2 16.8 + - - -
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Residues in contact with HIS 488 (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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482B GLU* 3.1 35.8 - - + +
485B ILE 5.9 0.4 + - - -
487B THR* 1.3 73.8 + - - +
489B GLU* 1.3 61.5 + - - +
491B GLY* 2.8 18.9 + - - -
492B VAL* 3.0 14.1 + - - +
519B TYR* 3.7 17.9 - - + -
520B SER* 3.5 37.1 + - - -
523B MET* 3.6 28.1 - - + +
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Residues in contact with GLU 489 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487B THR* 3.7 5.6 + - - +
488B HIS* 1.3 77.4 - - - +
490B ARG* 1.3 62.8 + - - +
492B VAL* 3.2 5.6 + - - +
493B SER* 3.0 21.7 + - - -
514B TYR* 4.1 20.6 - - + +
515B ARG* 3.6 34.9 + - - +
516B ASP* 2.8 35.5 + - - +
517B TYR 3.9 8.9 + - - +
519B TYR* 4.2 13.5 - - + -
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Residues in contact with ARG 490 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463B SER* 3.4 19.2 - - - +
464B ASP* 3.0 47.2 + - - +
467B ILE* 3.5 21.0 - - - +
485B ILE* 3.9 15.2 - - + +
486B GLU* 5.3 7.5 + - - +
487B THR* 3.2 31.0 + - + +
488B HIS 3.1 0.6 - - - -
489B GLU* 1.3 76.0 - - - +
491B GLY* 1.3 64.2 + - - +
493B SER* 3.2 8.7 + - - -
494B ILE* 3.1 27.1 + - + +
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Residues in contact with GLY 491 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481B LEU* 3.3 16.0 - - - +
482B GLU* 3.9 12.6 - - - -
485B ILE* 3.6 21.5 - - - +
487B THR 3.2 10.9 + - - -
488B HIS 2.8 8.6 + - - -
490B ARG* 1.3 76.9 - - - +
492B VAL* 1.3 61.3 + - - +
494B ILE* 3.3 2.3 + - - -
495B ARG* 3.1 20.9 + - - +
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Residues in contact with VAL 492 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482B GLU* 3.8 8.2 + - - +
488B HIS 3.0 16.6 + - - +
489B GLU* 3.4 8.1 - - - +
491B GLY* 1.3 76.3 - - - +
493B SER* 1.3 61.9 + - - +
495B ARG* 3.4 4.3 + - - +
496B ARG* 3.0 29.2 + - - +
514B TYR* 3.8 22.9 - - + -
519B TYR* 3.9 33.0 - - + +
523B MET* 5.6 0.7 - - - -
530B VAL* 3.8 19.7 - - + +
531B ILE 3.7 28.9 - - - -
532B GLY 3.8 2.2 - - - +
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Residues in contact with SER 493 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464B ASP* 4.1 6.2 + - - -
489B GLU 3.0 12.6 + - - -
490B ARG* 3.5 14.6 - - - -
492B VAL* 1.3 77.5 - - - +
494B ILE* 1.3 61.6 + - - +
496B ARG* 3.3 7.9 + - - +
497B GLN* 3.1 41.4 + - - +
514B TYR* 3.8 29.1 + - - -
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Residues in contact with ILE 494 (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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464B ASP* 4.2 28.9 - - + +
467B ILE* 3.6 36.6 - - + +
468B ILE* 4.3 15.3 - - + +
481B LEU* 4.0 18.8 - - + -
485B ILE* 3.3 25.4 - - + -
490B ARG* 3.1 16.8 + - + +
491B GLY 3.8 3.8 - - - +
493B SER* 1.3 74.3 - - - +
495B ARG* 1.3 67.2 + - - +
497B GLN* 3.1 10.0 + - - +
498B LEU* 2.9 33.4 + - + +
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Residues in contact with ARG 495 (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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540A VAL* 6.2 0.4 - - - -
478B ALA* 3.3 30.7 + - + +
479B TYR* 3.7 17.6 + - - +
481B LEU* 3.5 22.5 - - + +
482B GLU* 3.0 37.6 + - - -
491B GLY 3.1 14.1 + - - +
492B VAL* 3.7 5.4 - - - +
494B ILE* 1.3 75.7 - - - +
496B ARG* 1.3 58.1 + - - +
498B LEU* 3.3 8.8 + - + +
499B LEU* 2.9 33.2 + - + +
523B MET* 5.1 1.6 - - - +
529B ASN* 3.4 33.6 - - - +
530B VAL* 3.0 39.6 + - - +
531B ILE* 4.0 12.3 - - + -
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Residues in contact with ARG 496 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492B VAL* 3.0 21.9 + - - +
493B SER* 3.4 9.0 - - - +
494B ILE 3.1 0.2 - - - -
495B ARG* 1.3 76.0 - - - +
497B GLN* 1.3 54.0 + - + +
499B LEU* 3.3 3.5 + - - +
500B SER* 2.8 38.6 + - - +
509B LEU* 2.9 49.1 + - + +
510B GLN* 4.7 4.0 + - - +
512B LEU* 2.7 33.1 + - - +
514B TYR* 3.5 43.8 - - - +
531B ILE* 2.9 41.5 + - + +
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Residues in contact with GLN 497 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464B ASP* 3.0 33.5 + - - +
468B ILE* 3.4 29.0 - - + +
493B SER* 3.1 30.2 + - - +
494B ILE* 3.1 9.4 + - - +
496B ARG* 1.3 72.5 - - + +
498B LEU* 1.3 67.6 + - - +
500B SER* 3.4 15.6 + - - -
501B LYS* 3.5 16.5 + - - +
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Residues in contact with LEU 498 (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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468B ILE* 4.1 26.0 - - + -
471B VAL* 3.9 37.7 - - + -
472B ASN* 4.2 16.6 - - - +
478B ALA* 4.6 17.7 - - + -
481B LEU* 4.6 7.0 - - + -
494B ILE* 2.9 33.4 + - + +
495B ARG* 3.6 13.0 - - - +
497B GLN* 1.3 76.7 - - - +
499B LEU* 1.3 63.1 + - - +
501B LYS* 3.4 18.0 + - - +
502B LYS* 3.9 19.2 + - - +
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Residues in contact with LEU 499 (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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540A VAL* 3.9 29.8 - - + -
552A GLN* 3.6 42.6 - - + +
820A MET* 4.4 9.2 - - - -
495B ARG* 2.9 19.7 + - + +
496B ARG 3.6 4.0 - - - +
498B LEU* 1.3 75.5 - - - +
500B SER* 1.3 59.9 + - - +
502B LYS* 2.8 32.0 + - + +
503B LEU* 3.4 17.7 - - + +
509B LEU* 4.0 17.7 - - + -
531B ILE* 4.1 14.4 - - + -
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Residues in contact with SER 500 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496B ARG* 2.8 25.3 + - - +
497B GLN* 3.6 8.8 - - - -
498B LEU 3.4 0.4 - - - -
499B LEU* 1.3 76.4 - - - +
501B LYS* 1.3 61.2 + - - +
502B LYS 3.2 0.7 + - - -
503B LEU* 3.3 19.6 + - - -
506B PRO* 3.3 45.2 + - - +
509B LEU* 3.7 15.4 - - - +
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Residues in contact with LYS 501 (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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468B ILE* 6.3 4.3 - - + +
497B GLN 3.5 11.8 + - - +
498B LEU* 3.4 12.0 + - - +
499B LEU 3.1 1.0 - - - -
500B SER* 1.3 76.6 - - - +
502B LYS* 1.3 61.5 + - + +
503B LEU 3.4 3.4 - - - +
506B PRO* 5.3 5.6 - - + +
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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