Contacts of the helix formed by residues 501 - 523 (chain B) in PDB entry 6WG4
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 501 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500B ALA* 1.3 80.1 - - - +
502B GLY* 1.3 64.1 + - - +
504B ALA* 4.1 2.8 - - - +
505B ILE* 3.2 33.9 + - + +
556B ASN* 3.3 33.0 - - - +
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Residues in contact with GLY 502 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500B ALA 3.1 0.6 + - - -
501B THR* 1.3 83.5 - - - +
503B LYS* 1.3 60.9 + - - +
505B ILE* 3.8 4.4 + - - +
506B LEU* 3.3 31.5 + - - +
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Residues in contact with LYS 503 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500B ALA 3.0 10.2 + - - +
502B GLY* 1.3 72.2 - - - +
504B ALA* 1.3 57.8 + - - +
505B ILE 3.2 2.2 - - - -
506B LEU* 3.1 14.9 + - + +
507B ASN* 2.7 71.3 + - - +
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Residues in contact with ALA 504 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
658A ASP* 3.7 22.0 - - - +
500B ALA* 2.6 31.0 + - + +
501B THR* 4.2 2.7 - - - +
503B LYS* 1.3 72.0 - - - +
505B ILE* 1.3 57.6 + - - +
507B ASN* 4.0 7.6 - - - +
508B GLY 3.0 14.2 + - - -
583B GLY* 3.2 1.1 - - - -
584B GLU* 2.8 36.3 + - + +
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Residues in contact with ILE 505 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501B THR* 3.2 23.7 + - + +
502B GLY* 3.9 5.4 - - - +
503B LYS 3.2 0.4 - - - -
504B ALA* 1.3 76.1 - - + +
506B LEU* 1.3 70.3 + - + +
508B GLY* 3.0 2.6 + - - -
509B ILE* 3.0 32.3 + - + +
556B ASN* 3.6 42.8 - - + +
559B PHE* 3.6 37.7 - - + +
584B GLU* 3.9 22.0 - - + +
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Residues in contact with LEU 506 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502B GLY 3.3 16.7 + - - +
503B LYS* 3.1 20.9 + - + +
505B ILE* 1.3 89.1 - - + +
507B ASN* 1.3 64.1 + - - +
509B ILE* 3.3 17.5 + - + +
510B ASP* 3.1 28.6 + - - +
559B PHE* 5.3 10.1 - - + -
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Residues in contact with ASN 507 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
658A ASP* 5.4 1.2 + - - -
503B LYS* 2.7 60.8 + - - +
504B ALA* 4.0 3.4 - - - +
506B LEU* 1.3 72.6 - - - +
508B GLY* 1.3 53.5 + - - +
510B ASP* 3.3 7.2 + - - +
511B SER* 2.7 37.1 + - - -
582B PRO* 3.6 25.6 - - + +
583B GLY* 3.8 15.9 - - - -
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Residues in contact with GLY 508 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504B ALA 3.0 12.9 + - - -
505B ILE 3.0 8.0 + - - -
507B ASN* 1.3 74.4 - - - +
509B ILE* 1.3 58.5 + - - +
511B SER* 3.8 0.9 - - - -
512B ILE* 2.9 35.0 + - - +
576B PHE* 4.3 1.8 - - - -
582B PRO 4.0 8.1 - - - -
583B GLY* 3.7 2.6 - - - -
584B GLU 3.9 1.8 - - - -
585B VAL* 3.6 25.0 - - - +
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Residues in contact with ILE 509 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505B ILE* 3.0 26.0 + - + +
506B LEU* 3.6 17.0 - - + +
507B ASN 3.3 0.2 - - - -
508B GLY* 1.3 75.7 - - - +
510B ASP* 1.3 65.3 + - - +
512B ILE* 3.3 3.1 + - - +
513B ASN* 2.9 42.2 + - - +
532B TYR* 6.1 0.2 - - - +
535B ILE* 4.2 28.5 - - + -
559B PHE* 4.4 16.6 - - + +
561B HIS* 4.0 26.4 - - + +
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Residues in contact with ASP 510 (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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506B LEU* 3.1 17.6 + - - +
507B ASN* 3.8 7.2 - - - +
509B ILE* 1.3 81.7 - - - +
511B SER* 1.3 61.7 + - - +
513B ASN* 3.3 12.6 + - - +
514B LYS* 2.9 42.7 + - - +
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Residues in contact with SER 511 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507B ASN 2.7 18.2 + - - -
510B ASP* 1.3 73.6 - - - +
512B ILE* 1.3 57.8 + - - +
514B LYS* 3.2 11.7 + - - +
515B VAL* 3.0 30.3 + - - +
576B PHE* 3.4 24.5 - - - -
581B LEU* 3.5 17.9 - - - +
582B PRO* 2.5 37.1 + - - +
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Residues in contact with ILE 512 (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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508B GLY 2.9 16.1 + - - +
509B ILE 3.7 3.1 - - - +
511B SER* 1.3 72.8 - - - +
513B ASN* 1.3 69.2 + - - +
515B VAL* 3.2 7.2 + - - +
516B LEU* 2.9 43.1 + - + +
532B TYR* 3.8 20.4 - - + +
561B HIS* 3.7 20.2 - - + +
572B ILE* 3.9 17.0 - - + -
576B PHE* 4.0 7.0 - - + -
585B VAL* 3.6 25.4 - - + -
587B PHE* 3.7 28.3 - - + -
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Residues in contact with ASN 513 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509B ILE* 2.9 34.8 + - - +
510B ASP* 3.5 14.1 + - - +
512B ILE* 1.3 80.5 - - - +
514B LYS* 1.3 61.9 + - - +
516B LEU* 4.0 7.4 - - - +
517B ASP* 3.0 26.4 + - - +
532B TYR* 4.8 8.3 + - - -
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Residues in contact with LYS 514 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510B ASP* 2.9 30.0 + - - +
511B SER* 3.3 13.5 - - - +
512B ILE 3.1 0.2 - - - -
513B ASN* 1.3 76.2 - - - +
515B VAL* 1.3 62.2 + - - +
517B ASP* 3.3 4.9 + - - +
518B HIS* 3.0 25.2 + - - +
521B ARG* 5.1 1.6 + - - -
579B MET* 5.8 4.3 - - + -
581B LEU* 4.6 17.8 - - + +
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Residues in contact with VAL 515 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511B SER 3.0 15.7 + - - +
512B ILE* 3.2 9.6 + - - +
514B LYS* 1.3 75.3 - - - +
516B LEU* 1.3 58.9 + - + +
518B HIS* 3.5 6.2 + - - +
519B PHE* 3.0 57.1 + - + -
572B ILE* 4.1 18.8 - - + +
575B GLU* 3.9 17.9 - - + -
576B PHE* 3.9 21.5 - - + +
579B MET* 4.6 4.0 - - - -
581B LEU* 3.6 18.8 - - + -
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Residues in contact with LEU 516 (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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512B ILE* 2.9 35.4 + - + +
513B ASN* 4.1 6.5 - - - +
515B VAL* 1.3 75.4 - - + +
517B ASP* 1.3 60.9 + - - +
519B PHE* 3.3 6.8 + - + +
520B ARG* 2.8 28.3 + - - +
528B VAL* 4.1 22.4 - - + -
529B GLN* 4.1 20.6 - - + +
532B TYR* 3.5 52.7 - - + -
572B ILE* 5.0 5.6 - - + -
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Residues in contact with ASP 517 (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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513B ASN 3.0 19.0 + - - +
514B LYS* 3.8 4.9 - - - +
516B LEU* 1.3 74.3 - - - +
518B HIS* 1.3 54.0 + - - +
520B ARG* 3.0 24.1 + - - +
521B ARG* 2.7 68.4 + - - +
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Residues in contact with HIS 518 (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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514B LYS 3.0 17.2 + - - +
515B VAL 3.6 4.0 - - - +
517B ASP* 1.3 75.9 - - - +
519B PHE* 1.3 79.4 + + - +
521B ARG* 3.4 23.3 + - - +
522B LYS* 3.1 61.0 + - + +
524B ILE* 4.4 9.0 - - + +
575B GLU* 3.7 24.2 + - + -
579B MET* 4.0 21.2 - - + +
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Residues in contact with PHE 519 (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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515B VAL* 3.0 41.1 + - + -
516B LEU* 3.3 11.0 + - + +
518B HIS* 1.3 84.7 - + - +
520B ARG* 1.3 63.2 + - - +
522B LYS 3.5 0.2 + - - -
523B GLY 3.2 17.7 + - - -
524B ILE* 3.2 33.4 + - + +
525B ASN* 3.2 34.5 - - + -
528B VAL* 3.8 34.3 - - + -
529B GLN* 3.5 11.0 + - + -
571B LYS* 4.3 13.0 - - + -
572B ILE* 4.9 0.7 - - - -
575B GLU* 3.9 35.4 - - + -
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Residues in contact with ARG 520 (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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516B LEU 2.8 13.8 + - - +
517B ASP* 3.0 25.1 + - - +
519B PHE* 1.3 78.3 - - - +
521B ARG* 1.3 65.8 + - - +
522B LYS 3.4 0.3 + - - -
523B GLY* 3.5 8.5 + - - -
529B GLN* 3.4 25.7 + - - +
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Residues in contact with ARG 521 (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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514B LYS 5.1 1.2 + - - -
517B ASP* 2.7 47.5 + - - +
518B HIS* 3.7 30.9 + - - +
520B ARG* 1.3 76.3 - - + +
522B LYS* 1.3 86.0 + - + +
523B GLY 3.6 0.5 + - - -
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Residues in contact with LYS 522 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518B HIS* 3.1 43.2 + - + +
521B ARG* 1.3 101.5 - - + +
523B GLY* 1.3 64.3 + - - +
524B ILE* 3.4 25.6 + - + +
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Residues in contact with GLY 523 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519B PHE 3.2 6.0 + - - -
520B ARG 3.5 6.3 + - - -
521B ARG 3.3 4.2 + - - -
522B LYS* 1.3 80.1 - - - +
524B ILE* 1.3 61.0 + - - +
526B GLN* 5.7 4.3 - - - -
529B GLN* 5.1 3.8 - - - -
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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