Contacts of the helix formed by residues 518 - 531 (chain W) in PDB entry 5IY6
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 ARG 518 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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503W ALA* 3.9 24.2 - - + +
514W ILE* 3.0 36.7 + - + +
515W ALA 3.4 3.3 + - - +
517W ILE* 1.3 99.6 - - + +
519W ASN* 1.3 70.6 + - - +
520W TYR 2.8 4.8 + - - -
521W GLY 3.1 0.5 + - - -
522W ASN* 3.1 18.9 + - - +
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Residues in contact with ASN 519 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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495W ILE 4.1 9.5 + - - +
496W GLY* 3.8 16.6 - - - -
497W ARG* 4.8 2.1 + - - -
501W GLN* 3.0 37.1 + - - +
503W ALA 4.9 6.0 + - - +
504W ILE* 5.4 9.4 - - + -
515W ALA 4.2 0.8 + - - -
518W ARG* 1.3 77.8 - - - +
520W TYR* 1.4 59.8 + - - +
522W ASN* 4.5 4.2 + - - +
523W LEU* 2.9 63.0 + - + +
621W PHE* 3.9 3.2 - - - -
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Residues in contact with TYR 520 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503W ALA 5.4 0.9 - - - -
504W ILE* 4.0 31.6 - - + +
506W SER* 4.6 8.7 + - - -
509W GLU* 5.0 7.4 + - + +
515W ALA* 3.5 24.7 + - + +
516W VAL* 3.4 14.8 - - - +
518W ARG 2.8 5.7 + - - -
519W ASN* 1.4 77.0 - - - +
521W GLY* 1.3 59.1 + - - +
524W LEU* 3.5 9.7 - - - +
544W TYR* 3.1 39.2 - + - -
548W THR* 4.7 7.6 - - + +
621W PHE* 3.2 38.4 - + + -
622W GLY* 3.7 26.8 - - - -
680W ALA* 3.4 21.1 + - + -
681W ASP* 3.8 15.2 + - - -
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Residues in contact with GLY 521 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516W VAL 2.7 21.4 + - - -
517W ILE* 4.3 3.8 - - - -
518W ARG 3.1 0.8 + - - -
520W TYR* 1.3 71.7 - - - +
522W ASN* 1.3 60.5 + - - +
524W LEU* 3.4 5.5 - - - +
525W LEU* 3.2 22.2 + - - +
548W THR* 4.7 6.5 - - - +
560W ASN* 4.2 8.5 - - - -
561W ILE* 3.7 26.3 - - - +
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Residues in contact with ASN 522 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517W ILE 3.7 10.4 + - - +
518W ARG* 3.1 21.1 + - - +
519W ASN* 4.5 3.6 + - - -
521W GLY* 1.3 69.4 - - - +
523W LEU* 1.3 53.8 + - - +
525W LEU* 3.1 13.1 + - - +
526W GLU* 2.7 43.1 + - - +
560W ASN* 4.6 6.7 - - - +
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Residues in contact with LEU 523 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494W ILE* 4.0 28.7 - - + -
496W GLY* 6.2 2.7 - - - +
497W ARG* 3.1 34.3 - - - +
519W ASN* 2.9 47.9 + - + +
522W ASN* 1.3 70.5 - - - +
524W LEU* 1.3 57.7 + - - +
526W GLU* 3.2 7.7 + - + +
527W MET* 2.8 65.6 + - + +
621W PHE* 4.3 4.3 - - + -
712W GLU* 6.0 0.4 - - + -
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Residues in contact with LEU 524 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520W TYR 3.5 12.3 + - - +
521W GLY 3.4 7.6 - - - +
523W LEU* 1.3 76.1 - - - +
525W LEU* 1.3 54.0 + - - +
527W MET* 3.4 3.3 + - + +
528W SER* 2.8 50.7 + - - +
535W ILE* 6.3 1.1 - - + -
537W ALA* 4.4 14.6 - - + -
539W PHE* 4.1 20.6 - - + -
548W THR* 5.1 0.4 - - - -
549W VAL* 4.9 4.0 - - + -
561W ILE* 3.4 28.3 - - + -
565W LYS* 4.5 10.5 - - + -
595W ILE* 5.4 3.6 - - + -
597W LEU* 5.2 1.1 - - + -
619W ILE* 5.5 5.2 - - + -
621W PHE* 3.5 39.4 - - + -
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Residues in contact with LEU 525 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521W GLY 3.2 9.5 + - - +
522W ASN* 3.1 17.1 + - - +
524W LEU* 1.3 80.6 - - - +
526W GLU* 1.3 63.6 + - - +
528W SER* 3.7 7.0 - - - +
529W ALA* 3.1 35.7 + - + +
560W ASN 5.4 1.8 - - - +
561W ILE* 4.3 17.7 - - + -
562W GLN 4.1 11.9 - - - +
563W ARG* 3.9 39.0 - - + +
565W LYS* 5.3 0.2 - - - -
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Residues in contact with GLU 526 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497W ARG* 2.8 43.8 + - - -
522W ASN* 2.7 27.7 + - - +
523W LEU* 3.7 10.9 - - + +
525W LEU* 1.3 73.8 - - - +
527W MET* 1.3 57.1 + - - +
529W ALA* 4.2 2.0 - - - +
530W VAL* 3.0 51.3 + - + +
711W ASP* 5.2 1.4 - - - +
713W GLY* 6.0 1.7 - - - -
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Residues in contact with MET 527 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494W ILE* 4.0 10.1 - - + -
523W LEU* 2.8 43.9 + - + +
524W LEU* 3.7 3.6 - - - +
526W GLU* 1.3 72.2 - - - +
528W SER* 1.3 55.4 + - - +
530W VAL* 4.1 6.5 - - - -
531W VAL* 2.7 51.0 + - + +
535W ILE* 5.5 2.0 - - + -
619W ILE* 3.7 44.0 - - + -
621W PHE* 5.6 0.4 - - - -
678W VAL* 4.3 13.9 - - + -
712W GLU* 4.0 27.1 - - + -
713W GLY* 4.7 11.4 - - - +
716W VAL* 5.6 5.4 - - + -
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Residues in contact with SER 528 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524W LEU* 2.8 33.7 + - - +
525W LEU* 3.7 6.9 - - - +
527W MET* 1.3 77.4 - - - +
529W ALA* 1.4 60.8 + - - +
531W VAL 3.0 23.3 - - - +
532W PRO* 3.7 5.9 - - - +
535W ILE* 4.9 6.5 - - - -
563W ARG* 5.7 0.3 - - - +
565W LYS* 3.2 19.2 + - - -
589W GLU* 4.8 7.9 - - - +
595W ILE* 3.6 31.2 - - - +
619W ILE* 6.5 0.7 - - - -
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Residues in contact with ALA 529 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525W LEU* 3.1 29.6 + - + +
526W GLU* 4.2 2.5 - - - +
528W SER* 1.4 77.3 + - - +
530W VAL* 1.3 64.6 + - + +
532W PRO* 4.3 9.5 - - - +
563W ARG* 4.3 29.5 + - - +
589W GLU* 5.4 4.0 - - - -
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Residues in contact with VAL 530 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526W GLU* 3.0 40.4 + - + +
527W MET* 3.7 5.8 - - - +
529W ALA* 1.3 78.1 - - + +
531W VAL* 1.3 74.6 + - + +
532W PRO* 3.1 14.0 - - - +
713W GLY* 4.9 14.1 - - - +
717W ALA* 6.4 0.9 - - + -
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Residues in contact with VAL 531 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527W MET* 2.7 30.5 + - + +
528W SER 3.0 11.2 - - - +
530W VAL* 1.3 81.3 - - + +
532W PRO* 1.4 59.3 - - + +
533W ASP* 3.0 12.2 + - + +
535W ILE* 3.4 25.5 - - + +
617W ALA* 5.5 1.8 - - + -
713W GLY* 4.3 5.6 - - - +
716W VAL* 3.6 26.0 - - + -
717W ALA* 5.1 7.9 - - + +
720W PHE* 3.7 33.9 - - + -
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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