Contacts of the helix formed by residues 518 - 536 (chain B) in PDB entry 6T2C
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 ASN 518 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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517B ASN* 1.3 82.3 + - - +
519B GLU* 1.3 64.9 + - - +
520B SER* 3.0 14.0 + - - -
521B ALA* 2.7 43.0 + - - +
522B ASP* 2.8 21.1 + - - +
559B TYR* 2.9 14.3 + - - -
657B TYR* 5.4 2.6 + - - -
664B HIS 3.9 11.2 - - - +
665B SER* 4.0 9.2 + - - +
666B TRP* 3.7 41.9 + - + +
668B PRO* 6.0 0.2 - - - +
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Residues in contact with GLU 519 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518B ASN* 1.3 77.9 - - - +
520B SER* 1.3 58.8 + - - +
523B MET* 3.0 21.8 + - - +
555B TYR* 2.9 26.1 + - - +
559B TYR* 3.5 30.1 - - - +
572B ARG* 3.3 21.7 + - - -
592B ALA* 3.3 24.0 - - + +
664B HIS* 3.3 34.9 + - + +
666B TRP* 3.2 30.1 + - - +
51C MET* 5.2 0.9 - - - +
93C PRO* 5.5 1.0 - - - +
96C VAL* 5.8 0.7 - - - +
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Residues in contact with SER 520 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518B ASN* 3.0 2.2 + - - -
519B GLU* 1.3 79.7 - - - +
521B ALA* 1.3 62.7 + - - +
523B MET* 3.3 7.1 + - - +
524B SER* 3.0 24.9 + - - -
590B LEU* 6.6 0.2 - - - -
609B VAL* 5.1 9.1 - - - +
657B TYR* 5.4 0.2 - - - -
659B ALA* 4.3 10.4 - - - +
660B VAL 4.1 11.8 + - - -
662B THR* 4.6 10.8 + - - -
664B HIS* 4.2 4.2 + - - -
665B SER* 3.5 26.5 + - - -
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Residues in contact with ALA 521 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517B ASN* 3.7 17.3 - - + -
518B ASN* 2.7 35.3 + - - +
520B SER* 1.3 73.8 - - - +
522B ASP* 1.3 57.6 + - - +
524B SER* 3.4 1.4 + - - -
525B ILE* 2.9 35.8 + - + +
657B TYR* 4.0 36.0 - - + +
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Residues in contact with ASP 522 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514B VAL* 4.1 12.0 - - + -
515B ALA* 2.9 21.5 + - - +
516B GLY 2.7 22.7 + - - -
517B ASN* 2.7 23.6 + - - +
518B ASN 2.8 12.4 + - - +
519B GLU 3.4 2.5 + - - +
520B SER 3.4 0.2 - - - -
521B ALA* 1.3 77.0 - - - +
523B MET* 1.3 59.6 + - - +
525B ILE* 4.0 3.1 - - - +
526B GLY* 3.0 23.9 + - - -
551B PHE* 3.4 11.3 - - - -
555B TYR* 4.3 0.9 - - + -
559B TYR* 2.3 35.1 + - + +
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Residues in contact with MET 523 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519B GLU 3.0 16.5 + - - +
520B SER* 3.6 8.7 - - - +
521B ALA 3.3 0.2 - - - -
522B ASP* 1.3 77.2 - - - +
524B SER* 1.3 62.2 + - - +
526B GLY* 3.4 0.9 + - - -
527B THR* 3.1 25.3 + - - +
551B PHE* 4.1 18.0 - - - -
552B ILE* 4.3 7.4 - - + -
555B TYR* 3.6 36.0 - - + +
591B VAL* 4.0 16.2 - - + -
599B TYR* 3.7 37.2 - - + +
608B GLU* 3.4 30.5 - - + +
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Residues in contact with SER 524 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520B SER 3.0 16.3 + - - -
523B MET* 1.3 76.5 - - - +
525B ILE* 1.3 59.4 + - - +
527B THR* 2.9 20.1 + - - -
528B THR* 2.9 22.6 + - - +
599B TYR* 5.6 1.1 - - - -
607B PRO* 5.5 9.3 - - - +
657B TYR* 3.4 27.6 - - - +
658B ASP 3.7 9.2 + - - -
659B ALA* 4.0 16.4 - - - +
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Residues in contact with ILE 525 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515B ALA* 4.6 19.1 - - + +
517B ASN* 4.0 22.2 - - - +
521B ALA 2.9 24.2 + - - +
522B ASP* 4.0 4.9 - - - +
523B MET 3.3 0.2 - - - -
524B SER* 1.3 75.6 - - - +
526B GLY* 1.3 58.7 + - - +
528B THR* 3.0 8.4 + - - +
529B VAL* 2.9 40.2 + - + +
657B TYR* 3.7 33.7 - - + +
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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
----------------------------------------------------------
513B GLY 5.6 2.7 - - - -
522B ASP 3.0 16.9 + - - -
523B MET 3.9 0.9 - - - -
525B ILE* 1.3 79.7 - - - +
527B THR* 1.3 61.7 + - - +
529B VAL* 3.3 6.8 + - - +
530B ILE* 3.0 32.1 + - - +
551B PHE* 4.0 23.1 - - - -
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Residues in contact with THR 527 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523B MET* 3.1 17.1 + - - +
524B SER* 2.9 20.8 + - - -
526B GLY* 1.3 74.3 - - - +
528B THR* 1.3 59.3 + - - +
530B ILE* 3.4 5.9 + - + +
531B LYS* 3.0 27.2 + - - +
551B PHE* 4.9 6.7 - - + -
599B TYR* 3.6 42.8 + - + -
604B LEU* 3.6 37.3 + - + +
606B ILE 5.3 0.5 + - - -
607B PRO* 6.1 0.5 - - - +
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Residues in contact with THR 528 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524B SER* 2.9 26.7 + - - +
525B ILE* 3.0 13.2 + - - +
527B THR* 1.3 78.7 + - - +
529B VAL* 1.3 57.6 + - - +
531B LYS* 3.4 17.0 + - - +
532B THR* 2.9 35.8 + - - +
604B LEU 4.9 6.1 - - - +
605B HIS* 5.6 4.5 - - - +
657B TYR* 5.2 7.7 + - - -
658B ASP* 5.1 10.8 - - - +
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Residues in contact with VAL 529 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510B PRO* 5.3 4.3 - - + -
511B SER 6.0 0.9 - - - +
512B PHE* 4.0 24.9 - - + -
525B ILE* 2.9 32.7 + - + +
526B GLY* 3.7 6.7 - - - +
528B THR* 1.3 76.3 - - - +
530B ILE* 1.3 60.8 + - - +
532B THR* 3.1 8.7 + - - +
533B ASN* 3.0 35.8 + - - +
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Residues in contact with ILE 530 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512B PHE* 3.7 27.1 - - + -
526B GLY 3.0 19.6 + - - +
527B THR* 3.9 6.5 - - + +
528B THR 3.4 0.2 - - - -
529B VAL* 1.3 75.1 - - - +
531B LYS* 1.3 58.4 + - - +
533B ASN* 3.4 3.0 + - - +
534B MET* 3.0 28.5 + - + +
539B LEU* 4.6 7.4 - - + -
544B ALA* 4.3 25.8 - - + +
547B ALA* 3.9 11.7 - - + +
548B ILE* 3.9 33.7 - - + +
551B PHE* 4.5 11.4 - - + -
604B LEU* 3.9 17.3 - - + -
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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 THR 3.0 16.6 + - - +
528B THR* 3.6 14.5 - - - +
529B VAL 3.2 0.2 - - - -
530B ILE* 1.3 76.3 - - - +
532B THR* 1.3 76.4 + - - +
534B MET* 3.1 7.6 + - - +
535B ILE* 3.0 37.7 + - + +
604B LEU* 4.1 14.3 - - + +
605B HIS* 4.1 25.2 - - + +
230C GLU* 4.4 9.9 + - - +
233C HIS* 3.4 39.4 - - + +
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Residues in contact with THR 532 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528B THR* 2.9 20.1 + - - +
529B VAL* 3.1 17.2 + - - +
531B LYS* 1.3 90.3 - - - +
533B ASN* 1.3 59.9 + - - +
535B ILE* 4.3 9.6 - - + +
536B ASN* 2.9 43.8 + - - +
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Residues in contact with ASN 533 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507B MET* 5.1 3.8 - - - +
509B LEU* 5.9 1.6 - - - -
510B PRO* 3.5 24.2 - - - +
512B PHE* 3.5 27.1 - - - -
529B VAL* 3.0 22.9 + - - +
530B ILE* 3.8 4.9 - - - +
532B THR* 1.3 78.3 + - - +
534B MET* 1.3 64.2 + - - +
537B ASN* 3.3 42.8 + - + +
539B LEU* 3.4 29.6 + - + +
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Residues in contact with MET 534 (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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530B ILE 3.0 18.7 + - - +
531B LYS 3.1 7.4 + - - +
533B ASN* 1.3 76.1 - - - +
535B ILE* 1.3 63.5 + - - +
538B ASP* 4.4 3.6 + - - -
539B LEU* 3.8 33.6 + - + +
541B PRO* 4.6 9.0 - - + -
544B ALA* 3.7 32.8 - - + -
601B LEU* 4.4 23.3 - - + -
604B LEU* 4.5 7.0 - - - -
233C HIS* 3.3 48.4 - - + +
234C LEU* 5.5 0.7 - - - -
237C GLY* 6.1 1.0 - - - -
238C THR* 6.0 0.7 - - - +
240C TRP* 5.3 5.8 - - + -
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Residues in contact with ILE 535 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B ASN* 5.4 7.3 + - - +
531B LYS* 3.0 37.7 + - + +
532B THR* 3.8 9.4 - - + +
534B MET* 1.3 79.4 - - - +
536B ASN* 1.3 77.2 + - - +
538B ASP* 4.6 3.1 + - - +
229C VAL 5.1 5.2 - - - +
230C GLU 5.3 1.3 - - - +
232C LEU* 4.0 24.0 - - + +
233C HIS* 3.7 31.0 - - + +
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Residues in contact with ASN 536 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B GLY* 4.2 30.8 - - - -
276B ASN 5.6 0.2 - - - +
504B ASN* 4.0 6.5 + - - -
532B THR* 2.9 28.9 + - - +
535B ILE* 1.3 92.7 - - - +
537B ASN* 1.3 72.4 + - - +
538B ASP* 3.2 17.5 + - - +
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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
------------------------------------------------------------
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