Contacts of the strand formed by residues 449 - 457 (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 ARG 449 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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436D MET 6.0 0.4 - - - +
437D PRO* 5.8 0.6 - - - +
438D GLU* 3.2 39.4 + - + +
447D THR 3.6 2.8 + - - -
448D MET* 1.3 69.9 - - - +
450D LEU* 1.3 61.5 + - - +
453D ARG* 3.3 36.1 - - - +
454D ARG 4.1 6.5 + - - +
478D HIS* 3.0 32.4 + - + -
479D ARG* 3.1 5.9 + - - -
480D HIS* 2.8 55.9 + - - +
481D ARG* 4.7 0.4 - - - +
503D ASP* 3.8 27.7 + - - +
504D VAL* 5.1 1.2 - - - +
505D GLU* 4.8 6.7 + - - -
508D ARG* 3.8 36.5 - - - +
510D GLU* 4.0 2.4 + - - -
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Residues in contact with LEU 450 (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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60D VAL* 4.0 9.9 - - + -
64D GLY* 3.2 38.4 - - - +
66D GLU* 3.5 19.7 - - + +
448D MET* 3.3 14.2 + - + +
449D ARG* 1.3 76.5 - - - +
451D GLY* 1.3 64.9 + - - +
453D ARG* 2.8 27.9 + - - +
478D HIS* 3.1 11.9 - - - +
479D ARG* 3.4 39.5 - - + +
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Residues in contact with GLY 451 (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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60D VAL* 3.8 18.8 - - - +
62D ASP 5.2 0.2 - - - -
64D GLY* 4.1 9.2 - - - -
450D LEU* 1.3 81.5 - - - +
452D LYS* 1.3 62.7 + - - -
453D ARG* 3.3 6.7 + - - +
477D ARG* 4.5 0.4 - - - -
478D HIS* 2.7 39.0 + - - +
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Residues in contact with LYS 452 (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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60D VAL* 4.9 0.6 - - - +
61D LEU 4.7 2.0 + - - -
62D ASP* 4.3 29.2 + - + +
81D ARG* 5.9 1.2 - - - +
451D GLY* 1.3 67.7 - - - -
453D ARG* 1.3 65.7 + - - +
475D GLU* 3.4 43.3 + - + +
476D GLU 3.2 16.6 - - - +
477D ARG* 3.6 29.9 - - - +
530D LEU* 5.2 6.8 - - - +
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Residues in contact with ARG 453 (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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438D GLU* 2.7 42.2 + - - -
440D ASN* 5.6 1.4 - - - +
448D MET 4.9 0.4 + - - -
449D ARG* 3.3 31.6 - - - +
450D LEU 2.8 36.4 + - - +
451D GLY* 3.4 12.4 - - - +
452D LYS* 1.3 83.1 - - - +
454D ARG* 1.3 62.1 + - - +
455D THR 3.9 0.2 + - - -
475D GLU* 3.2 6.8 - - - -
476D GLU 3.0 28.8 + - - +
478D HIS* 3.5 23.1 + - + +
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Residues in contact with ARG 454 (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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449D ARG* 4.1 10.0 + - - -
453D ARG* 1.3 75.6 - - - +
455D THR* 1.3 62.7 + - - +
456D LEU* 3.9 21.1 - - + -
473D TYR* 3.5 51.1 + - + -
474D LEU 3.5 3.4 - - - +
475D GLU* 2.8 30.0 + - + +
503D ASP* 4.2 1.0 - - - -
504D VAL* 3.7 33.7 + - + +
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Residues in contact with THR 455 (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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453D ARG 4.6 0.5 + - - -
454D ARG* 1.3 73.0 + - - +
456D LEU* 1.3 66.0 + - - +
473D TYR* 3.3 4.9 - - - +
474D LEU* 2.8 56.8 + - + +
476D GLU* 5.2 1.4 - - - +
478D HIS* 3.5 28.4 + - - -
501D GLY* 4.0 5.2 - - - -
502D GLN 3.2 20.4 - - - +
503D ASP* 4.8 0.2 - - - +
510D GLU* 3.6 26.6 + - + +
511D ILE* 4.6 4.0 - - + -
525D TYR* 4.6 4.6 - - + -
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Residues in contact with LEU 456 (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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454D ARG* 3.9 17.0 - - + -
455D THR* 1.3 77.5 - - - +
457D PHE* 1.4 69.1 + - - +
458D GLN 3.7 0.2 + - - -
472D ASP 4.3 3.4 - - - +
473D TYR* 3.6 22.7 - - + -
474D LEU* 4.9 0.2 - - - -
501D GLY* 3.5 4.2 - - - -
502D GLN* 2.7 48.5 + - + +
503D ASP 4.3 2.0 - - - +
504D VAL* 3.9 40.2 - - + +
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Residues in contact with PHE 457 (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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456D LEU* 1.4 78.9 - - - +
458D GLN* 1.3 61.3 + - - +
459D THR 3.3 6.7 - - - +
462D SER* 4.3 2.5 - - - -
464D MET* 4.5 1.8 - - + -
465D ARG* 3.4 58.6 + - + +
468D TYR* 3.8 20.2 - + + -
471D ALA* 3.0 32.8 - - + -
472D ASP 3.3 20.3 + - - +
473D TYR* 3.9 7.9 - - - -
474D LEU* 3.7 22.9 - - + -
500D VAL* 3.6 20.4 - - + -
502D GLN* 5.3 1.7 + - - -
511D ILE* 4.2 19.5 - - + -
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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