Contacts of the helix formed by residues 493 - 507 (chain O) in PDB entry 6LTJ
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 ASP 493 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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261M ARG* 5.0 8.8 - - + +
280M GLU* 4.3 8.0 - - - +
281M TRP* 3.5 4.5 - - - +
282M ASP* 2.9 37.5 + - + +
288M ASN* 3.2 25.3 + - - +
457O LYS* 3.3 26.5 + - + -
465O TYR* 4.4 1.0 + - - -
492O GLY* 1.3 70.3 - - - +
494O VAL* 1.3 67.9 + - - +
495O CYS* 3.4 5.5 + - - +
496O ALA* 3.2 19.9 + - + +
497O ILE* 3.1 20.6 + - - +
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Residues in contact with VAL 494 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279M PHE* 3.6 16.8 - - + -
280M GLU 3.0 22.7 + - - +
281M TRP* 3.5 29.6 - - + -
293M PHE* 4.0 14.8 - - + -
487O ARG* 3.4 37.9 - - + -
492O GLY 3.2 6.6 + - - +
493O ASP* 1.3 74.0 + - - +
495O CYS* 1.3 61.9 + - - +
497O ILE* 3.4 7.9 + - - +
498O MET* 2.9 29.5 + - - +
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Residues in contact with CYS 495 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281M TRP* 3.4 41.1 - - - -
288M ASN* 3.1 33.9 - - - +
289M SER 4.4 4.0 - - - -
293M PHE* 4.4 11.2 - - - -
493O ASP* 3.2 2.5 + - - +
494O VAL* 1.3 82.0 - - - +
496O ALA* 1.3 59.6 + - - +
498O MET* 3.7 13.6 - - - +
499O ARG* 2.8 42.0 + - - +
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Residues in contact with ALA 496 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448O GLU* 3.6 22.7 - - - +
449O PHE* 4.0 13.7 - - + -
457O LYS* 3.7 21.5 - - + +
465O TYR* 5.0 5.2 - - + -
493O ASP* 3.2 18.6 + - + +
495O CYS* 1.3 79.0 - - - +
497O ILE* 1.3 57.0 + - - +
499O ARG* 3.2 6.8 + - - +
500O VAL* 2.9 35.4 + - - +
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Residues in contact with ILE 497 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465O TYR* 3.8 24.0 - - + +
469O MET* 3.3 25.2 - - + +
483O SER* 4.6 3.1 - - - +
486O CYS* 3.9 6.1 - - + -
487O ARG* 3.8 32.8 - - + +
490O LEU* 3.2 38.4 - - + +
492O GLY 3.5 22.0 - - - +
493O ASP 3.1 7.5 + - - +
494O VAL* 3.6 7.6 - - - +
495O CYS 3.3 0.2 - - - -
496O ALA* 1.3 74.8 - - - +
498O MET* 1.3 58.8 + - - +
500O VAL* 3.3 3.6 + - - -
501O HIS* 2.9 24.9 + - - +
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Residues in contact with MET 498 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292M LYS* 4.6 3.1 - - + +
293M PHE* 3.2 47.8 - - + +
296M LYS* 3.8 34.1 - - + -
483O SER* 3.1 29.4 - - - +
487O ARG* 5.2 3.4 - - - -
494O VAL* 2.9 27.8 + - + +
495O CYS* 3.8 11.7 - - - +
497O ILE* 1.3 76.6 - - + +
499O ARG* 1.3 57.8 + - - +
501O HIS* 3.4 3.2 + - - +
502O ALA* 2.9 29.3 + - - +
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Residues in contact with ARG 499 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285M GLU* 3.9 3.0 + - - -
287M GLU* 3.4 36.1 + - - +
288M ASN* 3.1 28.3 + - - -
446O LEU* 3.9 16.7 - - + +
448O GLU* 2.7 41.5 + - - +
457O LYS* 3.7 5.5 - - - +
495O CYS* 2.8 23.9 + - - +
496O ALA* 3.5 16.1 - - - +
497O ILE 3.2 0.2 - - - -
498O MET* 1.3 74.7 - - - +
500O VAL* 1.3 64.8 + - - +
502O ALA* 3.3 6.7 + - + +
503O PHE* 2.9 25.3 + - - +
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Residues in contact with VAL 500 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446O LEU* 3.9 14.6 - - + +
449O PHE* 3.6 30.7 - - + -
462O TYR* 4.0 12.1 - - + -
465O TYR* 4.4 8.3 - - + -
466O ARG* 4.0 31.0 - - + +
469O MET* 3.7 19.7 - - + -
496O ALA 2.9 17.8 + - - +
497O ILE* 3.6 7.0 - - - +
499O ARG* 1.3 75.0 - - - +
501O HIS* 1.3 58.3 + - - +
503O PHE* 3.3 2.6 + - - +
504O LEU* 2.9 30.6 + - + +
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Residues in contact with HIS 501 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296M LYS* 6.2 4.3 - - + -
300M GLU* 4.6 1.3 + - - -
469O MET* 3.5 17.9 - - + -
480O TYR* 4.0 5.4 + - - -
481O LEU* 2.9 30.1 + - + -
482O THR 3.8 1.3 - - - -
483O SER* 3.7 38.2 + - - +
486O CYS* 4.0 9.7 - - - -
497O ILE 2.9 17.4 + - - +
498O MET 3.7 4.3 - - - +
500O VAL* 1.3 78.0 - - - +
502O ALA* 1.3 65.1 + - + +
504O LEU* 3.4 4.5 + - - +
505O GLU* 2.9 35.2 + - - +
510O ILE* 4.3 14.5 - - + +
511O ASN* 3.5 15.4 + - - -
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Residues in contact with ALA 502 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296M LYS* 6.1 5.4 - - - -
498O MET 2.9 18.2 + - - +
499O ARG* 3.7 8.1 - - + +
501O HIS* 1.3 81.4 - - + +
503O PHE* 1.3 57.0 + - - +
505O GLU* 3.4 6.3 + - - +
506O GLN* 2.9 31.4 + - - +
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Residues in contact with PHE 503 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432O TRP* 3.8 13.0 - + - -
441O ILE* 4.2 3.6 - - + -
442O GLU* 3.4 38.4 - - + -
445O ALA* 3.4 34.1 - - + -
446O LEU* 4.0 18.2 - - + -
462O TYR* 3.8 11.2 - + - -
499O ARG 2.9 13.2 + - - +
500O VAL 3.4 8.3 - - - +
501O HIS 3.2 0.2 - - - -
502O ALA* 1.3 72.7 - - - +
504O LEU* 1.3 83.0 + - + +
506O GLN* 2.9 23.6 + - - +
507O TRP* 3.1 50.0 + + - -
509O LEU* 5.0 1.1 - - + -
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Residues in contact with LEU 504 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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433O PHE* 5.2 1.3 - - + -
442O GLU* 5.7 0.2 - - - +
462O TYR* 5.6 0.2 - - - +
466O ARG* 3.6 43.1 - - + +
469O MET* 3.8 27.4 - - + -
470O ILE* 4.3 13.5 - - + -
500O VAL* 2.9 22.3 + - + +
501O HIS* 3.9 3.6 - - - +
503O PHE* 1.3 89.4 - - + +
505O GLU* 1.3 58.7 + - - +
507O TRP 3.7 0.7 + - - -
508O GLY 3.6 1.2 + - - -
509O LEU* 2.8 59.2 + - + +
510O ILE* 3.2 15.9 + - + -
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Residues in contact with GLU 505 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296M LYS* 5.5 4.0 + - - -
480O TYR* 3.0 40.9 + - - -
501O HIS* 2.9 26.1 + - - +
502O ALA* 3.9 6.6 - - - +
504O LEU* 1.3 75.2 - - - +
506O GLN* 1.3 65.7 + - - +
507O TRP 3.2 0.4 - - - -
508O GLY* 3.2 11.4 + - - -
510O ILE* 3.5 27.6 - - + +
511O ASN* 3.4 11.8 + - + +
519O ARG* 4.5 9.2 + - - +
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Residues in contact with GLN 506 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1824L VAL* 2.6 45.5 + - - +
1825L VAL* 4.4 4.0 - - - +
1826L ASP 5.1 1.0 - - - +
429O TYR* 4.9 2.1 + - - -
502O ALA 2.9 19.0 + - - +
503O PHE* 2.9 10.0 + - - +
505O GLU* 1.3 77.5 - - - +
507O TRP* 1.3 71.9 + - + +
508O GLY 3.3 3.5 + - - -
58R GLU* 4.8 1.7 - - - +
60R ARG* 3.7 42.9 + - - +
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Residues in contact with TRP 507 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1824L VAL* 3.5 30.5 - - + -
1825L VAL* 3.4 32.5 - - + -
427O PRO* 4.5 0.5 - - - +
429O TYR* 3.6 35.7 - + + -
430O ALA* 3.2 22.8 - - - +
432O TRP* 3.8 19.7 - + + -
441O ILE* 3.8 34.3 - - + +
445O ALA* 5.5 0.4 - - - +
503O PHE* 3.1 53.2 + + - +
504O LEU 4.3 0.2 - - - +
505O GLU 3.2 0.2 - - - -
506O GLN* 1.3 85.9 - - + +
508O GLY* 1.3 55.9 + - - +
509O LEU* 2.8 29.5 + - + +
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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