Contacts of the strand formed by residues 433 - 439 (chain A) in PDB entry 5H65
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 LYS 433 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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405A ALA* 4.8 3.4 + - - +
407A LYS 5.0 2.6 + - - +
408A THR* 4.5 23.6 - - + +
409A PRO* 3.9 25.6 - - + +
423A ILE* 4.3 17.3 - - + -
424A TRP 3.4 11.2 - - - +
425A THR* 4.7 18.2 - - + -
431A GLY 3.7 9.8 + - - +
432A ARG* 1.3 82.2 - - - +
434A VAL* 1.3 63.4 + - - +
456A GLU 3.9 6.1 - - - +
457A GLY* 4.2 8.3 - - - -
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Residues in contact with VAL 434 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423A ILE* 3.3 6.0 - - - +
424A TRP* 2.8 43.0 + - + +
426A THR* 4.8 1.6 - - + -
432A ARG* 3.2 41.3 - - + +
433A LYS* 1.3 73.3 - - - +
435A ALA* 1.3 65.8 + - - +
436A VAL* 4.2 2.9 - - + -
455A ILE* 4.0 23.1 - - + -
456A GLU 3.4 9.9 - - - +
457A GLY 3.8 4.5 - - - +
458A GLY* 4.8 0.7 - - - -
462A GLU* 4.6 1.8 - - - +
279B LEU* 4.2 20.4 - - + -
281B LEU* 4.5 10.3 - - + -
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Residues in contact with ALA 435 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409A PRO* 4.0 6.1 - - + -
422A LYS 3.4 5.2 - - - +
423A ILE* 3.2 24.0 - - + -
433A LYS 4.0 1.4 + - - -
434A VAL* 1.3 73.1 - - - +
436A VAL* 1.3 60.1 + - - +
437A HIS* 3.8 10.0 - - + +
454A LEU 4.4 0.2 - - - -
455A ILE* 3.3 6.9 - - - +
456A GLU* 2.9 61.6 + - + +
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Residues in contact with VAL 436 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421A SER* 3.5 1.2 - - - -
422A LYS 2.9 32.3 + - - -
424A TRP* 3.4 28.7 - - + -
434A VAL* 4.2 10.5 - - + -
435A ALA* 1.3 75.8 - - - +
437A HIS* 1.3 64.1 + - - +
438A PHE* 3.7 27.7 - - + -
453A LEU* 4.0 32.1 - - + -
454A LEU 3.5 3.8 - - - +
455A ILE* 4.2 14.1 - - + -
466A LEU* 4.9 4.7 - - + -
275B ALA* 4.6 5.4 - - + -
279B LEU* 4.7 6.3 - - + -
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Residues in contact with HIS 437 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413A LEU* 4.5 1.3 - - + -
414A GLN* 4.0 14.1 - - + -
419A TYR* 3.5 24.5 - + + -
420A ASP 3.2 4.5 - - - -
421A SER* 2.9 32.0 + - - -
435A ALA* 3.8 13.2 - - + +
436A VAL* 1.3 73.4 - - - +
438A PHE* 1.3 62.3 - - - +
439A VAL 3.7 1.3 + - - -
453A LEU* 3.3 6.2 - - - -
454A LEU* 2.7 70.0 + - + +
456A GLU* 2.8 29.3 + - + -
476A VAL* 4.3 4.3 - - + -
483A LEU* 3.7 23.7 - - + +
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Residues in contact with PHE 438 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419A TYR* 3.2 3.7 - - - -
420A ASP* 2.7 45.9 + - + +
421A SER 5.2 0.2 - - - -
422A LYS* 4.4 10.8 - - + -
424A TRP* 4.4 1.3 - + - -
436A VAL* 3.7 23.3 - - + -
437A HIS* 1.3 72.3 - - - +
439A VAL* 1.3 63.1 + - - +
440A LYS 3.5 0.2 + - - -
445A LEU* 3.4 26.9 - - + +
451A CYS* 4.3 4.7 - - - -
452A LEU 4.0 3.8 - - - -
453A LEU* 3.3 24.7 - - + -
470A PHE* 4.0 5.2 - + - -
268B GLN* 6.2 0.9 - - + -
271B LEU* 3.5 37.9 - - + -
272B VAL* 3.9 23.6 - - + -
275B ALA* 3.6 25.8 - - + -
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Residues in contact with VAL 439 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418A LEU* 3.6 21.5 - - + +
419A TYR* 4.0 3.8 - - + -
438A PHE* 1.3 72.3 - - - +
440A LYS* 1.3 73.3 + - - +
445A LEU* 3.8 3.0 - - - +
446A PRO* 3.5 19.8 - - - +
451A CYS* 4.0 5.3 - - - -
452A LEU* 3.0 44.9 + - + +
454A LEU* 4.0 27.6 - - + -
515A LEU* 5.0 4.5 - - + -
521A LYS* 4.0 5.4 - - + +
524A TRP* 3.6 28.0 - - + -
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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