Contacts of the helix formed by residues 519 - 527 (chain I) in PDB entry 6PSU
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 519 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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517I GLN 3.1 4.4 + - - -
518I ASN* 1.3 82.7 - - - +
520I PRO* 1.3 82.1 - - - +
521I LEU* 4.3 3.1 - - - +
522I SER* 2.8 31.3 + - - +
523I GLU* 3.0 19.1 - - - +
686I GLN 3.5 11.9 + - - -
687I ARG* 4.6 3.2 - - - +
689I ALA* 3.3 19.7 + - - +
691I PRO* 5.3 1.3 - - - -
714I VAL* 5.6 0.7 - - - -
765I ILE* 5.6 0.6 - - - +
787I PRO* 6.1 0.9 - - - -
788I SER* 3.5 17.7 + - - -
796I LEU* 3.1 33.8 - - - +
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Residues in contact with PRO 520 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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519I ASN* 1.3 94.6 - - - +
521I LEU* 1.3 62.9 + - - +
523I GLU* 3.4 11.0 - - + +
524I ILE* 3.0 27.2 + - - +
708I VAL* 4.3 7.9 - - - +
712I SER* 4.1 18.3 - - - +
714I VAL* 4.1 17.3 - - + -
787I PRO* 3.3 29.8 - - + +
788I SER* 3.8 3.6 - - - -
789I THR* 4.2 7.0 - - + -
794I LEU* 3.4 23.3 - - + -
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Residues in contact with LEU 521 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519I ASN* 3.4 1.5 - - - +
520I PRO* 1.3 80.2 - - - +
522I SER* 1.3 57.8 + - - +
524I ILE* 3.5 10.3 - - + +
525I THR* 2.8 48.8 + - - +
663I VAL 4.4 2.0 - - - +
664I GLY* 4.1 20.2 - - - +
667I LEU* 3.2 35.4 - - + -
683I ALA 5.2 0.2 - - - +
686I GLN* 3.8 18.6 - - + +
687I ARG* 3.6 35.0 - - + +
708I VAL* 4.3 4.0 - - + -
794I LEU* 4.2 12.6 - - + +
796I LEU* 4.4 11.0 - - + -
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Residues in contact with SER 522 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516I ASP* 3.3 24.2 + - - +
518I ASN* 3.2 14.3 + - - -
519I ASN* 2.8 46.9 + - - +
520I PRO 3.2 0.2 - - - -
521I LEU* 1.3 80.0 - - - +
523I GLU* 1.3 58.8 + - - +
525I THR* 3.8 1.6 - - - -
526I HIS* 2.9 28.2 + - - +
687I ARG* 4.0 25.6 + - - +
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Residues in contact with GLU 523 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142I GLU* 5.4 0.9 - - - +
515I MET* 3.6 23.1 - - - +
516I ASP 3.4 14.4 - - - +
517I GLN* 3.4 27.7 + - - +
519I ASN 3.0 18.5 - - - +
520I PRO* 3.4 9.3 - - + +
522I SER* 1.3 80.0 + - - +
524I ILE* 1.3 57.0 + - - +
525I THR 3.1 0.4 - - - -
526I HIS* 3.7 4.3 - - - +
527I LYS* 2.9 49.5 + - - +
712I SER* 4.7 8.6 - - - -
713I GLY* 4.8 4.2 + - - -
714I VAL* 3.8 23.7 - - - +
765I ILE* 6.1 0.3 - - - +
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Residues in contact with ILE 524 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27I LEU* 3.8 17.9 - - + -
28I LEU* 3.5 23.3 - - + -
520I PRO 3.0 17.6 + - - +
521I LEU* 3.5 16.8 - - + +
523I GLU* 1.3 76.7 - - - +
525I THR* 1.3 63.0 + - - +
527I LYS* 4.1 3.1 - - - -
528I ARG* 3.1 27.9 - - - +
663I VAL* 4.4 7.9 - - + +
708I VAL* 4.3 20.6 - - + +
711I ASP* 3.5 44.2 - - + +
712I SER* 3.7 9.4 - - - +
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Residues in contact with THR 525 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521I LEU* 2.8 32.6 + - - +
522I SER 3.8 2.5 - - - -
524I ILE* 1.3 79.4 + - - +
526I HIS* 1.3 64.0 + - - +
527I LYS 3.2 1.8 - - - -
528I ARG* 3.5 21.3 + - - +
529I ARG* 3.9 11.6 + - - +
562I GLU* 3.0 31.6 - - - +
574I SER* 4.9 5.3 - - - -
662I SER* 5.3 0.9 - - - +
663I VAL* 4.1 6.1 - - + +
664I GLY* 4.0 13.5 + - - -
687I ARG* 3.7 17.5 - - - +
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Residues in contact with HIS 526 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144I VAL* 3.4 27.4 - - + +
146I VAL* 3.9 9.7 - - + +
513I GLN* 2.5 34.3 + - + +
514I PHE 3.0 28.6 + - - -
515I MET* 3.8 1.5 - - + -
516I ASP* 3.7 18.9 + - + +
522I SER 2.9 17.4 + - - +
523I GLU* 4.0 6.1 - - - +
525I THR* 1.3 78.9 - - - +
527I LYS* 1.3 62.4 + - - +
528I ARG 3.4 0.2 - - - -
529I ARG* 3.7 35.6 + - - +
687I ARG* 4.7 7.6 - - - +
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Residues in contact with LYS 527 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28I LEU* 3.3 40.0 - - + +
30I ILE* 4.7 3.0 - - - +
31I GLN* 3.7 34.2 + - + +
133I ASN* 2.9 38.0 + - - +
134I GLY 4.6 1.1 - - - +
135I THR* 4.3 9.5 - - - +
144I VAL* 3.9 19.3 - - + -
145I ILE 4.7 1.7 - - - +
146I VAL* 5.4 1.2 - - - -
147I SER 5.5 0.5 + - - -
515I MET* 4.3 17.0 - - - +
523I GLU* 2.9 47.0 + - - +
524I ILE* 4.5 0.9 - - - +
525I THR 3.2 0.2 - - - -
526I HIS* 1.3 80.4 - - - +
528I ARG* 1.3 57.7 + - - +
529I ARG 3.3 5.4 + - - +
712I SER* 5.7 1.2 - - - +
713I GLY 5.3 3.4 - - - +
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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