Contacts of the strand formed by residues 430 - 434 (chain U) in PDB entry 6QX2
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 GLU 430 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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428U GLU 4.8 5.1 - - - +
429U CYS* 1.3 74.3 - - - +
431U ILE* 1.3 54.5 + - - +
432U PHE* 4.0 10.0 - - + -
451U THR* 2.9 15.9 + - - +
452U GLN* 3.0 27.3 + - + +
453U ALA* 2.8 31.4 + - - +
500U TYR* 3.8 6.3 - - - -
502U LYS* 3.1 33.5 - - + +
504U VAL* 4.6 3.8 - - + -
598U PRO* 4.7 3.9 - - - +
601U ARG* 2.6 46.1 + - - -
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Residues in contact with ILE 431 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418U LEU* 4.6 4.5 - - + -
430U GLU* 1.3 73.2 - - - +
432U PHE* 1.3 66.8 + - - +
433U LEU* 4.1 2.6 + - + -
453U ALA* 3.5 15.5 - - + +
455U LEU* 4.1 20.0 - - + +
484U ALA* 3.9 22.0 - - + -
485U PHE* 3.8 12.6 - - + -
500U TYR* 3.8 42.3 - - + +
502U LYS 2.9 6.1 + - - +
503U ILE* 3.7 31.1 - - + +
504U VAL* 2.8 33.1 + - - +
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Residues in contact with PHE 432 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430U GLU* 4.0 18.6 - - + -
431U ILE* 1.3 74.5 - - - +
433U LEU* 1.3 58.5 + - - +
434U VAL* 4.0 1.8 + - + -
443U THR* 4.6 1.1 - - + -
452U GLN* 3.6 42.0 - - + -
453U ALA 2.9 19.7 + - - +
454U ILE* 3.4 13.0 - - + +
455U LEU 2.9 31.1 + - - +
504U VAL* 3.4 35.2 - - + +
506U MET* 3.8 34.1 - - + -
540U ALA* 5.3 0.2 - - + -
595U THR 4.6 4.3 - - - -
596U MET* 4.0 29.4 - - + -
601U ARG* 4.1 8.3 - - - -
603U LEU* 5.4 1.3 - - + -
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Residues in contact with LEU 433 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431U ILE* 4.5 8.5 - - + +
432U PHE* 1.3 72.3 - - - +
434U VAL* 1.3 59.4 + - - +
455U LEU* 3.5 38.8 - - + +
457U LEU* 4.5 13.7 - - + -
481U MET* 4.4 15.9 - - + -
485U PHE* 4.3 9.4 - - + -
503U ILE* 3.7 15.3 - - + -
504U VAL 2.8 14.6 + - - +
505U ILE* 4.1 13.7 - - + +
506U MET* 2.9 30.5 + - - +
507U THR* 5.3 1.6 - - - +
520U LEU* 4.6 8.5 - - + +
524U PHE* 3.7 32.3 - - + -
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Residues in contact with VAL 434 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432U PHE 4.5 5.2 - - - +
433U LEU* 1.3 78.0 - - - +
435U GLU* 1.3 57.3 + - - +
436U GLY 4.1 0.2 - - - +
439U ALA* 4.0 11.9 - - + -
440U GLY* 3.9 20.0 - - - +
443U THR* 4.0 13.0 - - + +
454U ILE* 4.0 11.7 - - + -
455U LEU 3.4 2.6 + - - +
456U PRO* 3.6 24.9 - - + -
457U LEU* 2.9 35.1 + - - +
506U MET* 3.6 41.1 - - + +
507U THR* 6.0 1.8 - - - -
583U LEU* 4.7 0.2 - - + -
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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