Contacts of the strand formed by residues 37 - 42 (chain 3) in PDB entry 5Z58
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 ILE 37 (chain 3).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103 ARG* 4.2 34.1 - - + +
113 ALA* 4.3 12.3 - - + +
333 SER* 3.5 6.6 + - - -
343 ARG* 2.7 60.4 + - + +
353 GLY 5.5 0.2 - - - +
363 LYS* 1.3 100.8 - - + +
383 LEU* 1.3 71.8 + - - +
393 GLU* 4.6 2.0 - - + -
553 THR* 4.1 15.0 - - - +
563 VAL 3.2 15.3 - - - +
573 GLU* 4.4 13.7 - - + +
583 VAL* 5.3 1.1 - - - -
623 ILE* 5.1 1.7 - - - +
10993 GLU* 5.2 0.2 - - - +
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Residues in contact with LEU 38 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313 VAL* 3.6 26.2 - - + -
323 VAL 4.0 4.0 - - - +
333 SER* 5.1 2.2 - - - -
363 LYS 4.3 0.8 + - - -
373 ILE* 1.3 74.3 - - - +
393 GLU* 1.3 69.3 + - - +
543 LEU* 5.1 0.3 - - - +
563 VAL* 2.8 38.7 + - + +
583 VAL* 4.1 16.4 - - + +
623 ILE* 6.3 2.7 - - + -
653 LEU* 4.5 15.9 - - + -
783 ILE* 5.3 3.1 - - + -
803 VAL* 5.1 7.2 - - + -
903 LEU* 4.0 11.2 - - + -
993 PHE* 3.7 33.7 - - + -
11553 LEU* 3.8 23.1 - - + -
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Residues in contact with GLU 39 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313 VAL* 3.3 9.2 - - - +
323 VAL* 2.9 54.1 + - + +
343 ARG* 2.6 61.8 + - + +
373 ILE* 4.6 1.8 - - + -
383 LEU* 1.3 79.8 - - - +
403 LEU* 1.3 63.4 + - - +
413 LEU* 4.2 17.8 - - + +
523 THR* 4.5 7.2 + - + +
543 LEU 3.8 11.2 - - - +
553 THR* 4.6 12.3 + - - +
993 PHE* 5.5 0.9 - - - -
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Residues in contact with LEU 40 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223 PHE* 4.7 1.8 - - + -
293 GLU* 3.7 26.0 - - + -
303 ILE 3.6 5.2 - - - +
313 VAL* 3.6 23.8 - - + -
393 GLU* 1.3 76.4 - - - +
413 LEU* 1.3 67.9 + - - +
523 THR* 3.7 3.1 - - - +
533 LEU* 2.9 37.4 + - + -
543 LEU* 2.9 26.2 + - + +
923 TYR* 3.8 51.8 - - + -
993 PHE* 4.3 14.1 - - + -
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Residues in contact with LEU 41 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143 ILE* 5.5 4.0 - - + -
293 GLU* 3.7 5.0 - - - +
303 ILE* 2.9 43.4 + - + +
323 VAL* 4.1 29.6 - - + -
343 ARG* 5.9 1.8 - - - +
393 GLU* 4.2 11.7 - - + +
403 LEU* 1.3 79.0 - - - +
423 ARG* 1.3 60.6 + - - +
433 PRO* 3.8 2.4 - - + +
503 VAL* 3.7 25.6 - - + -
513 HIS 3.2 3.4 - - - +
523 THR* 3.1 37.9 - - + +
533 LEU* 4.8 1.1 - - - -
3483 PHE* 5.0 14.1 - - + -
4013 LEU* 5.1 7.4 - - + -
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Residues in contact with ARG 42 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233 SER* 4.3 11.3 + - - -
253 THR* 4.4 5.5 + - - +
273 GLN* 2.3 47.9 + - + +
283 GLN 5.7 1.8 - - - +
293 GLU* 3.2 29.5 + - + +
413 LEU* 1.3 69.2 - - - +
433 PRO* 1.3 73.6 - - + +
503 VAL* 4.4 0.7 - - - -
513 HIS* 2.4 60.7 + - + +
533 LEU* 3.2 41.6 - - + +
923 TYR* 5.9 2.0 - - - -
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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