Contacts of the strand formed by residues 520 - 524 (chain X) in PDB entry 3I39
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 VAL 520 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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404X VAL 4.8 0.2 - - - +
461X ALA* 5.3 0.4 - - + -
465X LEU* 4.3 5.2 - - + -
471X VAL* 3.4 33.4 - - + +
473X ALA* 3.8 20.0 - - + -
481X LEU* 4.1 7.2 - - + -
486X PHE* 3.1 37.0 + - + +
487X MET* 3.5 34.2 - - + +
518X PRO* 3.6 17.7 - - - +
519X PRO* 1.3 82.3 - - - +
521X LEU* 1.3 66.0 + - - +
522X HIS 3.7 2.4 + - - -
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Residues in contact with LEU 521 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407X PHE* 4.0 32.5 - - + -
412X ILE* 4.0 32.5 - - + -
470X LEU* 4.3 24.5 - - + -
471X VAL 3.0 11.0 + - - +
472X VAL* 3.2 18.8 - - + +
473X ALA 3.0 24.3 + - - -
504X LEU* 5.0 2.5 - - + -
517X LEU* 4.2 24.9 - - + -
518X PRO* 4.1 16.8 - - + +
519X PRO 5.8 0.2 - - - -
520X VAL* 1.3 74.8 - - - +
522X HIS* 1.3 62.6 + - - +
523X MET* 3.4 1.8 + - + +
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Residues in contact with HIS 522 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298X ASN* 2.8 26.7 + - + -
301X LEU* 4.1 8.1 - - + +
302X MET* 3.5 8.3 - - - +
403X VAL* 5.0 1.6 - - + -
404X VAL 5.1 0.2 + - - -
405X ALA* 3.7 32.3 - - + -
407X PHE* 3.0 30.9 + - - +
473X ALA 3.6 3.4 - - - -
478X ALA* 3.4 18.8 - - + +
482X MET* 3.4 25.8 - - + +
487X MET* 4.1 16.4 - - + -
520X VAL 3.7 4.0 + - - -
521X LEU* 1.3 69.9 - - - +
523X MET* 1.3 58.5 + - - +
524X GLY* 3.0 45.4 + - - -
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Residues in contact with MET 523 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302X MET* 3.5 4.2 - - - +
407X PHE 3.4 17.9 - - - +
409X THR* 3.5 24.9 - - - +
412X ILE* 3.8 23.3 - - + -
442X LEU* 5.6 0.2 - - - -
472X VAL* 3.7 32.3 - - + -
473X ALA 2.9 11.3 + - - +
474X THR* 4.1 13.0 - - + -
521X LEU 3.8 12.6 - - - +
522X HIS* 1.3 71.2 - - - +
524X GLY* 1.3 57.3 + - - +
528X ASP* 3.3 5.4 - - - +
531X ARG* 3.1 52.1 + - + +
532X ALA* 3.7 12.1 - - + +
535X LEU* 4.5 9.2 - - + -
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Residues in contact with GLY 524 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298X ASN* 4.0 2.6 + - - -
302X MET* 3.6 15.9 - - - -
473X ALA 3.8 1.4 + - - -
474X THR* 3.1 5.2 - - - -
475X GLY* 2.9 22.7 + - - -
522X HIS* 3.0 23.2 + - - -
523X MET* 1.3 79.5 - - - +
525X SER* 1.3 63.5 + - - -
528X ASP* 3.5 7.2 - - - -
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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