Contacts of the strand formed by residues 453 - 460 (chain B) in PDB entry 4NPJ
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 GLU 453 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419B ARG 3.7 7.3 - - - +
420B VAL* 4.2 8.0 - - - -
421B GLY 4.4 5.0 + - - -
451B GLY 3.8 11.7 - - - +
452B GLN* 1.3 80.2 - - - +
454B LEU* 1.3 59.8 + - - +
455B GLU* 3.6 19.8 + - + +
473B MET* 3.8 38.3 - - + +
474B ILE 3.3 19.4 - - - +
475B ASP* 3.2 31.5 - - - +
476B LEU* 4.1 7.1 - - - +
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Residues in contact with LEU 454 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387B LEU* 4.4 6.5 - - + -
389B ILE* 3.8 8.5 - - + -
418B ILE* 3.7 25.4 - - + -
419B ARG 3.6 4.3 - - - +
420B VAL* 3.6 25.8 - - + -
453B GLU* 1.3 71.1 - - - +
455B GLU* 1.3 59.3 + - - +
456B ILE* 4.3 17.0 - - + -
472B LEU 3.6 1.6 - - - +
473B MET* 3.4 4.3 - - - -
474B ILE* 2.9 52.9 + - + +
476B LEU* 3.9 18.3 - - + +
479B VAL* 6.1 0.2 - - + -
501B LEU* 4.7 0.7 - - + -
503B LEU* 3.9 36.8 - - + -
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Residues in contact with GLU 455 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A ALA* 4.4 9.6 - - - +
377A GLN 4.4 14.9 + - - +
378A LEU* 4.8 4.3 - - - +
417B ILE 3.9 0.5 - - - +
418B ILE* 3.6 0.5 - - - -
419B ARG* 2.7 76.4 + - + +
421B GLY 5.2 3.7 - - - +
453B GLU* 4.0 24.6 - - + +
454B LEU* 1.3 76.3 - - - +
456B ILE* 1.3 64.9 + - - +
472B LEU 3.4 5.2 - - - +
473B MET* 3.9 27.4 - - + +
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Residues in contact with ILE 456 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389B ILE* 5.2 2.2 - - + -
391B PHE* 4.2 13.5 - - + -
417B ILE 3.3 9.0 - - - +
418B ILE* 4.0 24.2 - - + -
419B ARG* 5.0 0.4 - - - -
454B LEU* 4.3 16.4 - - + -
455B GLU* 1.3 80.1 - - - +
457B GLU* 1.3 75.1 + - - +
458B LEU* 4.4 4.0 - - + -
471B SER* 3.2 6.2 - - - -
472B LEU* 2.8 47.5 + - + +
474B ILE* 5.6 0.4 - - + -
491B LEU* 6.1 0.7 - - + -
499B LEU* 4.0 23.1 - - + -
501B LEU* 3.7 35.0 - - + -
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Residues in contact with GLU 457 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A ILE* 3.2 41.1 - - + +
376A ALA* 5.0 0.9 - - - +
585A GLU* 5.4 0.3 - - - +
416B GLY* 3.3 2.8 - - - -
417B ILE* 2.8 32.7 + - + -
419B ARG* 2.8 40.1 + - - +
456B ILE* 1.3 77.6 - - - +
458B LEU* 1.3 65.0 + - - +
459B PHE* 3.4 29.0 - - + -
468B PHE* 3.5 17.6 - - + -
470B GLY 3.6 3.8 - - - -
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Residues in contact with LEU 458 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391B PHE* 3.5 34.5 - - + -
394B ALA* 4.7 1.1 - - + -
397B LEU* 4.1 13.0 - - + -
414B PRO* 5.8 0.4 - - + -
415B TYR 3.3 7.0 - - - +
416B GLY* 3.6 12.1 - - - -
438B TRP* 4.0 11.7 - - + -
456B ILE* 4.4 6.5 - - + -
457B GLU* 1.3 73.5 - - - +
459B PHE* 1.3 69.9 - - - +
468B PHE* 3.7 4.3 - - - -
469B LEU* 2.8 36.3 + - + -
470B GLY 2.9 13.7 + - - +
491B LEU* 3.7 38.1 - - + -
499B LEU* 4.4 13.0 - - + -
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Residues in contact with PHE 459 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414B PRO* 3.2 4.5 - - - +
415B TYR* 2.8 63.9 + + + +
417B ILE* 4.2 12.3 - - + -
419B ARG* 5.4 0.4 - - - -
457B GLU* 3.4 51.4 - - + -
458B LEU* 1.3 76.7 - - - +
460B ASP* 1.3 59.4 + - - +
461B GLU 3.9 0.2 - - - -
466B ASP* 4.2 10.1 - - + -
467B ASP 3.2 17.0 - - - +
468B PHE* 3.9 19.7 - + + -
469B LEU* 3.7 6.5 - - - +
703B ACT 3.3 33.4 - - + -
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Residues in contact with ASP 460 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400B LYS* 3.7 20.3 - - - +
412B SER* 3.5 12.4 + - - +
413B ASP* 2.6 35.8 + - - +
415B TYR* 4.3 0.2 - - - -
459B PHE* 1.3 70.5 - - - +
461B GLU* 1.3 73.5 + - - +
462B ASP* 3.1 26.2 + - - +
466B ASP* 3.3 20.9 - - - +
467B ASP* 2.8 21.7 + - + +
469B LEU* 3.7 18.6 - - + +
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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
------------------------------------------------------------
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