Contacts of the helix formed by residues 485 - 493 (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 ASN 485 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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431D PRO* 2.9 36.5 + - - +
432D VAL 2.8 13.7 + - - +
434D VAL* 3.8 20.5 - - + +
483D GLU 3.5 0.4 + - - -
484D VAL* 1.3 73.9 - - - +
486D PRO* 1.3 70.7 - - - +
487D VAL* 2.9 36.3 + - - +
488D TRP* 2.9 29.5 + - + +
489D LYS 3.0 9.4 + - - -
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Residues in contact with PRO 486 (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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434D VAL* 5.1 1.1 - - + -
436D MET* 4.6 8.5 - - + -
484D VAL 3.1 10.5 - - - +
485D ASN* 1.3 88.7 - - - +
487D VAL* 1.3 66.3 + - + +
488D TRP 3.0 1.3 + - - -
489D LYS* 3.3 25.9 + - + +
490D LYS* 3.3 17.3 + - - +
507D GLU* 3.9 24.7 - - - +
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Residues in contact with VAL 487 (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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485D ASN* 2.9 26.0 + - - +
486D PRO* 1.3 82.4 - - + +
488D TRP* 1.3 88.5 + - + +
490D LYS* 3.3 35.4 - - - +
491D CYS* 3.9 0.5 - - - -
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Residues in contact with TRP 488 (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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410D SER* 5.8 1.1 - - - +
416D TRP* 3.4 40.4 - + + -
429D SER 4.2 5.8 - - - -
430D HIS* 3.4 33.8 - + + -
431D PRO* 3.1 48.2 + - + +
432D VAL* 4.1 13.2 - - + -
484D VAL* 6.1 0.4 - - + -
485D ASN* 2.9 18.4 + - + +
487D VAL* 1.3 102.8 - - + +
489D LYS* 1.3 58.5 + - - +
490D LYS* 3.1 2.5 - - - -
491D CYS* 2.7 33.0 + - - +
492D LEU* 2.9 21.1 + - + +
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Residues in contact with LYS 489 (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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458D GLN* 4.4 11.0 + - - -
484D VAL* 4.2 7.6 - - + -
485D ASN 3.0 8.2 + - - +
486D PRO* 3.6 24.7 - - + +
488D TRP* 1.3 74.5 - - - +
490D LYS* 1.3 54.3 + - - +
492D LEU* 2.7 34.4 + - - +
493D GLU* 2.7 48.0 + - - +
499D PHE* 4.0 15.5 - - + -
507D GLU 5.7 1.1 - - - +
509D MET* 3.3 46.0 - - + -
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Residues in contact with LYS 490 (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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486D PRO 3.3 8.1 + - - +
487D VAL* 3.3 36.7 - - - +
488D TRP* 6.1 0.2 - - - -
489D LYS* 1.3 77.5 - - - +
491D CYS* 1.3 67.8 + - - +
493D GLU* 3.8 16.2 + - - +
494D GLU* 2.9 16.6 - - - +
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Residues in contact with CYS 491 (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 LEU* 4.5 7.0 - - + +
416D TRP* 3.7 24.7 - - + -
487D VAL 3.9 7.9 - - - -
488D TRP* 2.7 40.7 + - - +
490D LYS* 1.3 83.1 - - - +
492D LEU* 1.3 58.6 + - - +
494D GLU* 3.0 27.2 - - - +
495D GLN* 3.5 11.8 + - - +
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Residues in contact with LEU 492 (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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406D VAL* 3.9 20.0 - - + -
409D PHE* 3.6 36.8 - - + -
410D SER* 4.2 5.8 - - - +
414D LEU* 3.7 21.3 - - + -
432D VAL* 5.8 1.3 - - + -
484D VAL* 5.0 2.7 - - + -
488D TRP* 2.9 19.6 + - + +
489D LYS* 2.7 14.5 + - - +
491D CYS* 1.3 77.0 - - - +
493D GLU* 1.3 60.5 + - - -
494D GLU 3.5 1.1 - - - -
495D GLN* 3.1 19.4 + - + +
497D LEU* 3.4 21.5 - - + +
499D PHE* 3.7 33.7 - - + -
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Residues in contact with GLU 493 (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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489D LYS* 2.7 57.3 + - - +
490D LYS* 3.9 17.0 - - - +
491D CYS 3.5 1.0 - - - -
492D LEU* 1.3 69.2 - - - +
494D GLU* 1.3 57.7 + - - +
495D GLN 3.1 4.9 - - - -
497D LEU 5.3 1.3 - - - -
498D LYS* 2.9 32.8 + - - +
499D PHE* 3.9 15.2 + - - +
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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