Contacts of the strand formed by residues 363 - 367 (chain E) in PDB entry 3PRJ
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 HIS 363 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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328E ASP* 3.6 41.9 + - + +
329E LYS 3.0 15.0 + - - +
330E LYS* 3.3 9.0 - - + -
331E ILE 2.9 26.1 + - - +
361E GLY 3.6 2.6 + - - -
362E ALA* 1.3 69.2 - - - +
364E LEU* 1.3 62.0 + - - +
365E HIS* 3.8 12.2 + - + +
393E ARG 3.7 17.9 + - - -
394E LEU* 3.4 27.0 - - + +
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Residues in contact with LEU 364 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331E ILE* 3.4 17.7 - - + +
333E ILE* 3.9 25.8 - - + -
354E SER* 3.7 41.5 - - - +
357E LEU* 4.1 17.0 - - + -
358E MET* 3.8 17.9 - - + -
362E ALA* 3.3 13.2 + - + +
363E HIS* 1.3 70.6 - - - +
365E HIS* 1.3 64.3 + - - +
366E ILE* 4.0 17.7 - - + -
394E LEU 2.8 13.5 + - - +
395E VAL* 4.7 4.5 - - + -
396E THR 2.9 27.4 + - - +
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Residues in contact with HIS 365 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330E LYS* 3.4 47.4 + - + +
331E ILE 2.9 10.7 + - - +
332E ALA* 3.3 4.5 - - - -
333E ILE 2.9 22.1 + - - +
363E HIS* 3.9 9.7 - - - +
364E LEU* 1.3 78.8 - - - +
366E ILE* 1.3 60.8 + - - +
396E THR* 3.4 37.8 + - + +
398E SER* 3.6 16.0 + - - +
403E GLU 4.7 1.0 + - - -
404E ALA* 3.6 24.7 - - - +
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Residues in contact with ILE 366 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333E ILE* 3.5 26.9 - - + +
336E PHE* 3.7 33.0 - - + -
354E SER* 4.5 4.9 - - - +
364E LEU* 4.3 12.3 - - + -
365E HIS* 1.3 73.5 - - - +
367E TYR* 1.3 65.5 + - - +
376E ILE* 3.9 28.2 - - + +
380E LEU* 3.8 29.8 - - + -
395E VAL* 4.1 11.4 - - + -
396E THR 2.9 13.0 + - - +
397E ILE* 3.6 8.5 - - - +
398E SER* 2.8 26.1 + - - +
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Residues in contact with TYR 367 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333E ILE 2.9 8.9 + - - +
334E LEU* 3.7 13.0 - - + -
335E GLY* 2.8 31.0 + - - -
365E HIS 4.0 0.8 + - - -
366E ILE* 1.3 76.5 - - - +
368E ASP* 1.3 69.5 + - - +
369E PRO* 3.4 29.4 - - + +
397E ILE* 5.7 0.4 - - - -
398E SER* 3.6 24.0 - - - +
399E LYS 3.7 7.6 - - - -
400E ASP* 3.7 18.7 - - - +
401E PRO* 3.6 37.3 - - + +
404E ALA* 4.7 1.3 - - + -
419E MET* 3.7 27.4 - - + +
420E PHE* 4.2 12.6 - + - -
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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