Contacts of the strand formed by residues 509 - 513 (chain D) in PDB entry 4L28
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 ALA 509 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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488D LYS 3.2 8.5 - - - +
490D ILE* 4.4 9.4 - - + -
499D LEU* 3.7 27.4 - - + -
502D ILE* 4.4 14.6 - - + -
503D LEU* 4.6 2.7 - - + -
508D PHE* 1.3 76.0 - - - +
510D LEU* 1.3 63.1 + - - +
511D VAL* 3.7 1.0 + - - +
533D VAL* 3.4 1.9 - - - -
534D VAL* 2.8 47.0 + - + +
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Residues in contact with LEU 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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447D PRO* 4.5 12.3 - - + -
455D ILE* 3.5 41.1 - - + -
457D GLY 4.6 3.8 - - - +
458D MET* 4.1 11.9 - - - -
487D PHE* 3.8 23.8 - - + -
488D LYS 2.9 11.4 + - - +
489D GLN* 3.3 5.1 - - + -
490D ILE* 2.9 25.2 + - - -
508D PHE* 4.7 8.7 - - + -
509D ALA* 1.3 74.5 - - - +
511D VAL* 1.3 62.6 + - - +
512D VAL* 3.5 13.5 + - + +
530D VAL* 4.6 4.3 - - + -
532D GLY 3.5 2.9 - - - +
533D VAL* 3.5 32.5 - - + -
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Residues in contact with VAL 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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414D VAL* 3.9 9.6 - - + -
419D LEU* 3.6 25.8 - - + -
490D ILE* 3.2 25.8 - - + +
491D ARG 4.5 0.2 - - - -
492D LEU* 3.6 39.3 - - + +
510D LEU* 1.3 71.9 - - - +
512D VAL* 1.3 64.1 + - - +
530D VAL* 3.4 1.7 - - - -
531D PHE* 2.9 29.4 + - + -
532D GLY 2.6 25.5 + - - +
534D VAL* 4.1 13.2 - - + -
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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
----------------------------------------------------------
455D ILE* 4.2 9.0 - - + -
489D GLN* 4.1 22.7 - - + +
490D ILE 3.1 13.8 + - - +
491D ARG* 4.3 15.8 - - - +
492D LEU* 4.8 4.8 + - - +
510D LEU* 3.8 18.8 - - + +
511D VAL* 1.3 81.7 - - - +
513D HIS* 1.3 76.6 + - - +
528D GLN* 3.7 20.2 - - + +
529D MET 3.2 12.3 - - - +
530D VAL* 4.0 18.2 - - + -
531D PHE* 4.5 3.1 - - - +
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Residues in contact with HIS 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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492D LEU* 5.2 7.7 - - + +
512D VAL* 1.3 87.5 + - - +
514D GLU* 1.3 84.3 + - + +
527D ARG 3.4 10.7 - - - +
528D GLN* 3.5 2.4 - - - -
529D MET* 3.0 20.1 + - + +
531D PHE* 3.2 30.3 - + + -
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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