Contacts of the strand formed by residues 434 - 444 (chain Z) in PDB entry 5WTI
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 TRP 434 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18Z LYS* 3.6 42.6 - - + -
19Z GLY* 4.6 0.4 - - - -
22Z LYS* 3.4 39.8 - - + +
200Z GLU* 3.6 33.1 + - + -
201Z ILE* 3.1 22.9 - - + -
202Z LYS* 2.6 42.2 + - - +
426Z ILE* 4.0 6.3 - - + -
427Z TYR 3.6 7.4 - - - -
428Z PRO* 3.6 40.6 - - + -
429Z THR* 4.2 0.4 - - - -
432Z GLY 4.4 6.8 + - - -
433Z GLY* 1.3 90.0 + - - -
435Z GLU* 1.3 55.0 + - - +
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Residues in contact with GLU 435 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201Z ILE* 4.4 2.2 - - - -
202Z LYS* 3.6 28.3 - - + +
426Z ILE* 3.3 2.8 - - - -
427Z TYR* 2.7 40.9 + - + +
428Z PRO 5.7 0.4 - - - +
429Z THR* 3.6 24.8 - - + +
434Z TRP* 1.3 72.8 - - - +
436Z GLU* 1.3 68.0 + - - +
437Z LYS* 3.2 11.1 + - + +
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Residues in contact with GLU 436 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201Z ILE* 4.1 2.4 - - - +
202Z LYS 2.9 14.2 + - - +
203Z TRP* 3.3 34.1 - - + -
204Z MET* 2.6 69.2 + - + +
213Z ARG* 3.4 21.9 + - - +
424Z ARG* 3.2 31.9 + - + -
425Z LEU 4.2 2.9 - - - +
426Z ILE* 4.3 10.8 - - + +
435Z GLU* 1.3 72.1 - - - +
437Z LYS* 1.3 59.5 + - - +
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Residues in contact with LYS 437 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204Z MET* 3.9 5.2 - - + -
424Z ARG* 3.3 4.9 - - - +
425Z LEU 2.8 41.9 + - - +
427Z TYR* 3.5 54.7 - - + -
435Z GLU* 3.2 11.6 + - + +
436Z GLU* 1.3 74.7 - - - +
438Z GLY* 1.3 68.9 + - - +
439Z LYS 5.7 0.9 - - - -
440Z VAL* 3.7 17.6 - - + +
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Residues in contact with GLY 438 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204Z MET* 3.4 20.6 - - - +
423Z ASP 3.3 9.2 - - - -
424Z ARG* 4.3 4.3 - - - -
437Z LYS* 1.3 85.3 - - - +
439Z LYS* 1.3 74.1 + - - +
440Z VAL 3.4 2.8 + - - -
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Residues in contact with LYS 439 (chain Z).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5H G 4.7 15.6 + - - -
421Z GLN* 3.5 35.7 + - + +
422Z LEU 3.1 9.9 - - - -
423Z ASP* 2.7 21.0 + - - +
437Z LYS* 5.7 1.4 - - - -
438Z GLY* 1.3 74.5 - - - +
440Z VAL* 1.3 60.8 + - - +
441Z ASP* 3.7 6.9 + - - +
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Residues in contact with VAL 440 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16Z VAL* 5.3 0.2 - - + -
420Z VAL 3.7 0.7 - - - +
421Z GLN* 3.5 0.2 - - - -
422Z LEU* 2.8 39.8 + - + +
425Z LEU* 3.9 32.8 - - + +
427Z TYR* 3.9 28.7 - - + -
437Z LYS* 3.7 50.9 - - + +
438Z GLY 4.1 0.2 - - - -
439Z LYS* 1.3 72.3 - - - +
441Z ASP* 1.3 71.6 + - - +
442Z ILE* 4.7 4.9 - - + -
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Residues in contact with ASP 441 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16Z VAL* 4.2 10.0 - - - +
405Z LEU* 4.3 7.0 - - - +
419Z THR* 3.9 25.5 - - + +
420Z VAL 3.4 2.2 - - - -
421Z GLN* 3.2 38.3 + - - +
439Z LYS 3.7 3.8 + - - +
440Z VAL* 1.3 77.4 - - - +
442Z ILE* 1.3 63.3 + - - +
443Z VAL* 5.5 2.1 - - + +
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Residues in contact with ILE 442 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10Z ILE* 3.8 29.6 - - + -
16Z VAL* 3.7 32.5 - - + -
20Z LEU* 4.7 4.7 - - + -
419Z THR* 3.3 4.9 - - - +
420Z VAL* 2.7 50.1 + - + +
422Z LEU* 4.0 33.2 - - + -
425Z LEU* 5.2 0.4 - - + -
440Z VAL* 4.5 6.3 - - + +
441Z ASP* 1.3 79.0 - - - +
443Z VAL* 1.3 63.5 + - - +
444Z LEU* 4.2 10.5 - - + -
510Z PHE* 4.2 18.8 - - + -
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Residues in contact with VAL 443 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10Z ILE* 3.5 9.3 - - - +
11Z GLU* 2.8 59.8 + - + +
417Z LYS* 3.8 36.1 - - + -
418Z LEU 3.5 6.5 - - - +
419Z THR* 4.2 13.9 - - + +
441Z ASP* 5.5 1.6 - - + +
442Z ILE* 1.3 81.0 - - - +
444Z LEU* 1.3 64.8 + - - +
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Residues in contact with LEU 444 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8Z LEU* 4.1 27.0 - - + +
9Z LYS 3.7 2.5 - - - +
10Z ILE* 4.0 11.7 - - + -
404Z ILE* 5.8 0.7 - - + -
416Z LYS 4.5 0.2 - - - +
417Z LYS* 3.5 5.5 - - - +
418Z LEU* 2.7 49.0 + - + +
420Z VAL* 3.6 22.2 - - + -
442Z ILE* 4.2 10.5 - - + -
443Z VAL* 1.3 81.5 - - - +
445Z LEU* 1.3 64.4 - - - +
446Z PRO* 4.5 0.3 - - - +
510Z PHE* 3.7 32.5 - - + -
512Z MET* 3.9 26.9 - - + -
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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