Contacts of the helix formed by residues 487 - 502 (chain B) in PDB entry 3THW
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 GLU 487 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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368B ASN* 5.4 0.9 + - - -
378B PHE* 3.6 23.7 - - + -
395B SER* 3.4 28.5 - - - +
486B LEU* 1.3 84.5 - - - +
488B LYS* 1.3 75.1 + - - +
489B PRO* 3.6 2.9 - - + -
490B VAL* 3.7 17.7 - - + +
491B ILE* 3.2 14.7 - - - +
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Residues in contact with LYS 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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365B ASN* 4.0 18.8 - - + +
378B PHE* 5.1 1.3 - - + -
456B TYR* 3.5 55.0 + - + +
487B GLU* 1.3 81.5 + - - +
489B PRO* 1.3 72.9 - - + +
491B ILE* 3.3 15.4 + - - +
492B CYS* 3.5 11.3 - - - -
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Residues in contact with PRO 489 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363B SER* 3.4 14.7 + - - +
364B GLU* 4.7 2.7 - - - +
365B ASN* 4.6 8.1 - - + +
378B PHE* 3.5 37.0 - - + +
379B ILE 4.0 1.6 - - - +
380B GLY* 3.7 29.6 - - - +
487B GLU* 3.7 1.8 - - + -
488B LYS* 1.3 93.5 - - + +
490B VAL* 1.3 60.8 + - + +
491B ILE 3.0 5.8 - - - -
492B CYS* 2.9 29.9 + - - +
493B SER* 2.9 16.1 + - - -
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Residues in contact with VAL 490 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380B GLY* 4.0 11.0 - - - -
381B ILE 4.8 1.6 - - - +
382B VAL* 3.4 14.8 - - + +
393B PHE* 5.0 10.8 - - + -
394B ASP 4.2 5.6 - - - +
395B SER* 3.4 35.4 - - - +
486B LEU* 3.7 33.2 - - + -
487B GLU* 3.7 18.2 - - + +
489B PRO* 1.3 74.0 - - - +
491B ILE* 1.3 61.5 + - + +
493B SER* 3.4 9.0 - - - -
494B LEU* 3.0 28.5 + - + +
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Residues in contact with ILE 491 (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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456B TYR* 4.1 26.0 - - + +
459B ALA* 4.4 2.0 - - + -
460B PHE* 4.2 31.9 - - + +
463B VAL* 4.1 22.4 - - + -
484B VAL* 4.9 7.9 - - + +
485B ASN* 5.0 5.4 - - - +
486B LEU* 4.0 23.3 - - + +
487B GLU 3.2 19.3 - - - +
488B LYS 3.4 6.1 - - - +
489B PRO 3.0 0.4 - - - -
490B VAL* 1.3 82.7 - - + +
492B CYS* 1.3 56.2 + - - +
494B LEU* 3.5 9.4 - - + +
495B ALA* 2.7 33.1 + - - +
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Residues in contact with CYS 492 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363B SER* 3.3 15.5 - - - +
365B ASN* 6.3 2.5 - - - -
453B TYR 4.2 2.8 - - - +
454B PHE* 3.0 37.0 - - + +
456B TYR* 4.2 20.9 - - - -
459B ALA* 3.8 7.0 - - - -
488B LYS* 3.5 18.2 - - - -
489B PRO* 2.9 14.5 + - - +
491B ILE* 1.3 79.4 - - - +
493B SER* 1.3 56.3 + - - +
495B ALA* 3.5 2.1 + - - +
496B ALA* 3.0 27.5 + - - +
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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
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361B CYS* 3.6 26.3 - - - -
363B SER* 3.7 15.0 - - - -
380B GLY 3.1 18.1 + - - -
382B VAL* 3.4 14.4 - - - +
454B PHE* 4.5 0.4 - - - -
489B PRO 2.9 15.9 + - - -
490B VAL* 3.4 9.5 - - - -
492B CYS* 1.3 73.9 - - - +
494B LEU* 1.3 59.4 + - - +
496B ALA* 3.8 1.6 - - - -
497B ILE* 3.0 33.6 + - - +
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Residues in contact with LEU 494 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382B VAL* 3.8 19.3 - - + +
391B VAL* 5.8 0.4 - - + -
463B VAL* 4.2 24.0 - - + -
467B TYR* 4.4 16.8 - - + +
484B VAL* 4.8 13.7 - - + -
486B LEU* 5.6 4.7 - - + -
490B VAL* 3.0 21.5 + - + +
491B ILE* 3.1 10.5 + - + +
493B SER* 1.3 75.9 - - - +
495B ALA* 1.3 61.9 + - - +
497B ILE* 3.3 5.6 + - + +
498B ILE* 2.9 41.2 + - + +
510B LEU* 4.9 11.4 - - + -
516B PHE* 4.5 23.6 - - + -
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Residues in contact with ALA 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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453B TYR* 4.4 5.6 - - - +
459B ALA* 3.5 39.3 - - + +
462B ALA* 4.3 12.6 - - + +
463B VAL* 3.8 10.7 - - + +
491B ILE 2.7 21.3 + - - +
492B CYS 3.8 1.1 - - - +
494B LEU* 1.3 73.6 - - - +
496B ALA* 1.3 61.4 + - - +
498B ILE* 3.5 7.0 + - - +
499B LYS* 3.3 22.7 + - - +
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Residues in contact with ALA 496 (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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361B CYS* 4.2 3.6 - - - -
418B LEU* 3.6 6.7 - - + +
449B MET* 3.8 15.2 - - - +
453B TYR* 4.4 7.1 + - - +
454B PHE* 3.4 40.2 - - + -
492B CYS 3.0 18.3 + - - +
493B SER 4.0 4.0 - - - +
494B LEU 3.3 0.2 - - - -
495B ALA* 1.3 76.5 - - - +
497B ILE* 1.3 62.1 + - - +
499B LYS* 3.8 3.4 + - - +
500B TYR* 3.4 21.1 + - - +
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Residues in contact with ILE 497 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359B LEU* 4.1 16.8 - - + -
361B CYS* 3.7 25.4 - - + -
382B VAL* 3.9 18.8 - - + +
384B VAL* 4.0 24.0 - - + -
418B LEU* 4.2 8.5 - - + -
493B SER 3.0 25.7 + - - +
494B LEU* 3.5 7.4 - - + +
495B ALA 3.2 0.2 - - - -
496B ALA* 1.3 75.5 - - - +
498B ILE* 1.3 61.1 + - - +
500B TYR* 3.1 3.2 + - + +
501B LEU* 2.8 38.4 + - + +
510B LEU* 3.6 27.4 - - + -
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Residues in contact with ILE 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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462B ALA* 5.4 1.1 - - + +
463B VAL* 4.4 19.7 - - + +
466B PHE* 3.6 60.8 - - + -
467B TYR* 4.8 4.5 - - + +
494B LEU* 2.9 25.7 + - + +
495B ALA* 3.9 5.6 - - - +
496B ALA 3.4 0.4 - - - -
497B ILE* 1.3 73.5 - - - +
499B LYS* 1.3 65.9 + - - +
501B LEU* 3.8 1.4 - - - +
502B LYS* 3.0 43.6 + - + +
507B GLU* 4.7 2.2 - - + +
510B LEU* 3.5 22.2 - - + -
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Residues in contact with LYS 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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449B MET* 3.9 22.7 - - + -
453B TYR* 3.4 61.9 + - + -
495B ALA 3.3 15.2 + - - +
496B ALA* 3.9 4.5 - - - +
497B ILE 3.4 0.2 - - - -
498B ILE* 1.3 78.3 - - - +
500B TYR* 1.3 62.3 + - - +
502B LYS* 3.7 19.8 - - - +
503B GLU* 3.7 20.2 + - - +
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Residues in contact with TYR 500 (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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294B LYS* 4.3 2.9 - - - -
326B THR* 4.1 4.3 - - - +
329B THR* 5.2 2.5 - - + -
359B LEU* 4.2 18.4 - - + -
416B GLU* 2.7 29.0 + - - -
418B LEU* 3.8 20.4 - - + -
445B ARG* 4.3 0.9 + - - -
447B GLU* 3.6 35.6 - - + +
449B MET* 4.0 17.5 - - + -
496B ALA 3.4 11.8 + - - +
497B ILE* 3.1 7.6 + - + +
498B ILE 3.0 0.6 - - - -
499B LYS* 1.3 77.5 - - - +
501B LEU* 1.3 71.0 + - + +
502B LYS 3.1 4.5 - - - -
503B GLU* 3.1 41.2 + - - +
504B PHE* 3.3 41.2 - + - -
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Residues in contact with LEU 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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329B THR* 4.9 7.9 - - + -
359B LEU* 4.1 15.9 - - + -
384B VAL* 4.2 19.5 - - + -
386B PRO* 5.0 3.8 - - + -
497B ILE* 2.8 30.4 + - + +
498B ILE* 4.2 3.1 - - - +
500B TYR* 1.3 89.4 - - + +
502B LYS* 1.3 62.3 + - - +
503B GLU 3.2 0.2 - - - -
504B PHE* 3.5 9.8 + - + -
505B ASN 3.3 2.1 + - - -
506B LEU* 2.8 55.6 + - + +
507B GLU* 3.2 13.8 + - + +
509B MET* 4.2 15.7 - - + -
510B LEU* 4.4 9.9 - - + -
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Residues in contact with LYS 502 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466B PHE* 4.3 19.8 - - - -
498B ILE* 3.0 40.4 + - + +
499B LYS* 3.7 12.3 - - - +
501B LEU* 1.3 76.4 - - - +
503B GLU* 1.3 63.4 + - + +
505B ASN* 3.1 17.3 + - - +
507B GLU* 3.5 30.2 + - + +
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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