Contacts of the strand formed by residues 518 - 527 (chain A) in PDB entry 5LZ6
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 518 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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395A ILE 3.6 1.2 - - - +
396A THR* 3.6 2.5 - - - -
397A VAL* 2.8 41.6 + - + +
422A THR* 4.8 4.7 - - + -
423A ASP 5.4 2.9 - - - +
425A TYR* 3.5 25.8 - - + +
426A ASP 2.7 29.5 + - - +
427A ILE* 4.1 22.0 - - + +
510A ASN* 2.7 40.5 + - + +
512A TYR* 3.5 5.3 + - - -
516A ARG* 3.7 18.8 - - - -
517A SER* 1.3 77.3 - - - +
519A SER* 1.3 61.8 + - - +
520A VAL* 3.6 4.3 + - + +
601A BGC 2.8 26.3 + - - -
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Residues in contact with SER 519 (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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394A VAL* 4.2 10.4 - - - +
395A ILE 3.5 4.4 + - - -
396A THR* 4.7 7.5 + - - +
422A THR* 3.3 27.2 - - - +
423A ASP* 3.5 24.0 + - - +
517A SER 4.2 1.4 + - - -
518A LYS* 1.3 71.2 - - - +
520A VAL* 1.3 60.0 + - - +
521A TYR* 3.7 23.1 + - - -
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Residues in contact with VAL 520 (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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393A SER 3.7 0.5 - - - +
394A VAL* 3.3 5.8 - - - +
395A ILE* 2.6 49.3 + - + +
397A VAL* 4.0 8.5 - - + -
420A PHE* 5.0 1.3 - - + -
421A ALA 3.6 4.7 - - - +
422A THR* 4.0 10.8 - - + -
427A ILE* 3.9 26.7 - - + -
508A PHE* 3.8 38.8 - - + -
518A LYS 3.9 10.1 - - - +
519A SER* 1.3 76.7 + - - +
521A TYR* 1.3 72.5 + - - +
522A TYR* 4.4 6.0 - - + -
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Residues in contact with TYR 521 (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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383A PHE* 4.0 16.3 - - + -
384A LYS* 3.7 28.8 - - + +
387A ILE* 3.9 18.4 - - + -
388A GLN* 3.6 35.7 + - + -
393A SER 3.6 3.6 - - - -
394A VAL* 3.7 26.9 - - + -
420A PHE* 3.2 5.2 - - - +
421A ALA 3.0 40.6 + - - +
423A ASP* 2.5 38.9 + - - -
519A SER* 3.7 18.7 + - - -
520A VAL* 1.3 71.5 - - - +
522A TYR* 1.3 63.6 + - - +
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Residues in contact with TYR 522 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A PHE* 4.6 1.8 - - - -
387A ILE* 4.2 4.1 - - - +
392A ASP 3.7 10.6 + - - -
393A SER* 3.1 50.7 + - - +
395A ILE* 3.3 35.9 - - + -
405A VAL* 3.9 19.0 - - + +
419A GLU 3.3 13.5 - - - +
420A PHE* 4.1 7.9 - - + +
506A LEU* 5.5 2.2 - - + -
508A PHE* 4.2 17.9 - + + -
520A VAL* 4.4 4.3 - - + -
521A TYR* 1.3 78.3 - - - +
523A ARG* 1.3 73.6 + - - +
524A VAL* 4.3 16.8 - - + -
8B PHE* 3.6 12.8 - - - -
10B THR* 2.9 35.8 + - + +
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Residues in contact with ARG 523 (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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383A PHE* 5.9 0.8 - - - -
386A LYS* 3.9 25.8 + - - +
387A ILE* 3.3 33.5 - - + +
390A ASP* 6.3 1.4 - - - +
393A SER* 4.5 11.6 + - - -
418A TRP* 3.3 3.6 - - - +
419A GLU* 2.9 41.5 + - + +
522A TYR* 1.3 75.5 - - - +
524A VAL* 1.3 66.3 - - - +
525A TYR* 3.2 45.7 + - + +
13B SER* 5.8 4.3 - - - -
19B GLU* 5.9 0.8 + - - -
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Residues in contact with VAL 524 (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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407A VAL* 3.9 30.3 - - + -
416A LEU* 4.6 3.1 - - + -
417A PHE 3.5 5.2 - - - +
418A TRP* 4.4 4.7 - - + -
506A LEU* 3.8 29.4 - - + -
522A TYR* 4.3 13.8 - - + -
523A ARG* 1.3 79.0 - - - +
525A TYR* 1.3 69.3 + - - +
10B THR* 4.1 24.9 - - + +
11B ALA 4.2 1.6 - - - +
12B PRO* 4.0 15.9 - - + -
13B SER* 3.1 18.9 + - - -
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Residues in contact with TYR 525 (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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416A LEU* 3.3 18.7 - - - +
417A PHE* 2.8 48.6 + + + +
419A GLU* 2.9 28.8 + - + -
498A TYR* 4.0 1.4 + - - -
523A ARG* 3.2 52.8 + - + +
524A VAL* 1.3 78.3 - - - +
526A TYR* 1.3 63.5 + - - +
12B PRO* 3.3 14.2 - - - +
13B SER* 3.0 27.8 - - - +
14B GLU 4.5 2.2 - - - -
15B ILE* 3.6 39.3 - - + -
19B GLU* 4.8 7.9 - - - -
23B ILE* 4.9 2.1 - - + +
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Residues in contact with TYR 526 (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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410A HIS* 3.4 52.1 + + + -
412A GLU* 4.8 4.5 - - + -
413A GLY* 4.1 9.2 - - - -
415A TYR 3.3 8.1 - - - +
417A PHE 5.1 0.4 - - - +
498A TYR* 3.1 26.2 - - + +
525A TYR* 1.3 73.5 - - - +
527A THR* 1.3 68.9 + - - +
528A ARG* 5.2 2.2 - - + -
12B PRO* 3.2 27.4 - - + -
13B SER* 2.9 21.1 + - - -
14B GLU* 3.1 47.8 + - + +
15B ILE* 3.1 24.2 + - - +
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Residues in contact with THR 527 (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 GLY* 3.2 5.7 - - - -
414A SER* 2.8 41.8 + - - -
415A TYR* 3.3 29.6 + - + +
417A PHE* 5.4 5.4 - - + -
526A TYR* 1.3 75.8 - - - +
528A ARG* 1.3 62.4 + - - +
15B ILE* 3.5 32.3 - - + +
16B ASP 6.1 0.2 - - - -
20B VAL* 4.9 9.0 - - + -
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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