Contacts of the strand formed by residues 509 - 514 (chain D) in PDB entry 5U03
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 MET 509 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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402D MET* 4.3 4.6 - - + +
458D GLN* 3.5 19.1 - - - +
483D GLU* 3.6 12.9 + - - +
484D VAL* 4.0 27.5 - - + +
489D LYS* 3.3 36.1 - - + -
499D PHE* 3.6 29.6 - - + -
501D GLY 3.5 1.6 - - - +
502D GLN* 3.6 20.6 - - + +
506D GLY 4.0 7.4 - - - +
507D GLU 3.3 25.8 + - - +
508D ARG* 1.4 85.7 - - - +
510D GLU* 1.3 61.7 + - - +
511D ILE 5.1 0.2 - - - +
524D GLN* 3.4 18.9 - - - +
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Residues in contact with GLU 510 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402D MET* 3.7 4.4 - - - +
449D ARG* 4.0 6.9 + - - -
455D THR* 3.6 35.0 - - + +
478D HIS* 3.3 26.5 + - + -
480D HIS* 2.9 22.3 + - - -
483D GLU* 4.7 0.2 - - - +
501D GLY 2.8 9.6 + - - +
502D GLN 4.4 9.6 - - - -
503D ASP* 4.4 4.5 - - - +
508D ARG* 4.5 7.8 - - - +
509D MET* 1.3 79.8 - - - +
511D ILE* 1.3 60.0 + - + +
523D VAL* 3.2 8.5 - - - +
524D GLN* 3.1 28.2 + - - +
525D TYR* 3.4 29.3 + - + +
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Residues in contact with ILE 511 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402D MET* 4.2 2.2 - - - -
455D THR* 4.6 0.7 - - + -
457D PHE* 4.2 23.1 - - + -
464D MET* 4.6 14.4 - - + -
468D TYR* 5.2 0.4 - - + -
474D LEU* 4.4 14.1 - - + -
499D PHE* 3.5 6.9 - - - +
500D VAL* 2.8 37.6 + - + -
501D GLY* 3.1 25.3 + - - +
510D GLU* 1.3 85.9 - - + +
512D VAL* 1.4 70.5 + - - +
513D GLU* 4.3 11.2 - - + +
521D VAL* 5.7 0.4 - - + -
522D GLY 3.5 6.5 - - - +
523D VAL* 4.3 4.7 - - + -
525D TYR* 3.6 32.8 - - + +
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Residues in contact with VAL 512 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402D MET* 3.8 24.2 - - + -
405D ALA* 6.1 3.4 - - + -
406D VAL* 5.1 4.9 - - + -
497D LEU* 3.5 36.8 - - + -
498D LYS 3.2 20.2 - - - +
499D PHE* 4.0 13.2 - - + -
511D ILE* 1.4 76.0 - - - +
513D GLU* 1.4 63.0 + - - +
514D LEU 4.2 0.7 - - - +
520D PHE* 5.8 4.0 - - + +
521D VAL* 3.3 8.2 - - - +
522D GLY* 3.0 40.1 + - - +
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Residues in contact with GLU 513 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461D ASN 5.0 0.9 - - - +
462D SER* 2.6 30.5 + - - -
463D VAL* 3.2 28.0 + - - +
464D MET* 3.0 23.2 + - + +
498D LYS* 2.8 33.6 + - - +
500D VAL* 3.8 19.1 - - + +
511D ILE* 4.3 6.5 - - + -
512D VAL* 1.4 80.4 - - - +
514D LEU* 1.3 64.8 + - - +
515D GLU* 3.5 12.4 + - - +
520D PHE 3.9 3.6 - - - -
521D VAL* 3.8 15.0 - - + -
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Residues in contact with LEU 514 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389D ARG* 3.6 34.8 - - + -
392D LYS* 5.5 2.5 - - - +
409D PHE* 3.8 22.4 - - + -
496D GLY 3.5 17.0 - - - +
497D LEU* 3.7 22.1 - - + +
512D VAL* 4.2 0.8 - - - +
513D GLU* 1.3 73.1 - - - +
515D GLU* 1.3 71.0 + - - +
516D ASP 3.9 0.5 + - - -
517D HIS* 4.0 25.4 + - + +
520D PHE* 3.0 43.7 + - + +
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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