Contacts of the strand formed by residues 414 - 420 (chain A) 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 PRO 414 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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397A LEU* 3.8 23.6 - - + -
412A SER* 3.5 4.7 - - - +
413A ASP* 1.3 88.9 - - - +
415A TYR* 1.3 62.7 + - - +
429A VAL* 3.6 0.3 - - - -
430A ILE* 3.2 36.6 + - + +
433A ASN 3.1 28.5 - - - +
434A LEU* 4.9 0.9 - - + -
436A PRO* 4.0 3.6 - - + -
438A TRP* 3.6 20.8 + - + -
458A LEU* 5.9 1.3 - - + -
459A PHE 3.2 8.3 - - - +
469A LEU* 3.8 17.7 - - + -
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Residues in contact with TYR 415 (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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414A PRO* 1.3 77.0 - - - +
416A GLY* 1.3 69.3 + - - +
417A ILE* 4.1 22.2 - - + -
426A GLN* 4.1 24.0 - - + -
427A SER* 3.5 8.5 - - - +
428A ARG 3.4 15.3 - - - +
429A VAL* 3.8 20.9 - - + -
438A TRP* 3.8 4.9 - - - -
458A LEU* 3.4 9.5 - - - +
459A PHE* 2.8 65.6 + + + +
461A GLU* 3.7 24.9 - - + -
466A ASP* 2.6 26.6 + - - +
581B GLU* 6.5 0.7 - - + -
583B VAL* 4.9 8.6 - - + +
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Residues in contact with GLY 416 (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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391A PHE* 4.0 8.6 - - - -
415A TYR* 1.3 76.4 - - - +
417A ILE* 1.3 68.0 + - - +
418A ILE* 3.9 4.6 - - - +
425A PHE 3.8 0.7 - - - +
426A GLN* 3.6 4.3 - - - -
427A SER* 2.8 36.4 + - - -
456A ILE* 5.5 0.4 - - - -
457A GLU 3.3 7.4 - - - -
458A LEU* 3.6 13.9 - - - +
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Residues in contact with ILE 417 (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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415A TYR* 4.1 8.5 - - + +
416A GLY* 1.3 82.2 - - - +
418A ILE* 1.3 62.3 + - - +
419A ARG* 5.7 0.2 - - - +
424A ILE* 3.9 28.7 - - + -
425A PHE 3.5 3.8 - - - +
426A GLN* 3.7 28.5 - - + -
455A GLU 3.7 1.2 - - - +
456A ILE* 3.4 5.6 - - - +
457A GLU* 2.7 39.6 + - + +
459A PHE* 3.9 28.0 - - + -
801A CL 4.5 7.2 - - + -
583B VAL* 4.0 21.8 - - + -
585B GLU* 4.3 16.2 - - - +
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Residues in contact with ILE 418 (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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389A ILE* 3.9 21.3 - - + -
391A PHE* 4.5 19.7 - - + -
416A GLY* 3.9 14.1 - - - +
417A ILE* 1.3 77.4 - - - +
419A ARG* 1.3 64.2 + - - +
424A ILE* 3.4 7.5 - - - +
425A PHE* 2.9 58.9 + - + +
427A SER 4.7 0.2 - - - +
442A TYR* 3.8 31.6 - - + +
454A LEU* 3.6 25.4 - - + -
455A GLU 3.5 2.2 - - - -
456A ILE* 4.1 16.8 - - + -
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Residues in contact with ARG 419 (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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417A ILE 4.2 0.2 - - - -
418A ILE* 1.3 74.6 - - - +
420A VAL* 1.3 69.6 + - - +
421A GLY 2.9 35.5 + - - +
422A ASN* 3.8 14.1 + - - +
423A GLN 3.4 4.9 - - - +
424A ILE* 3.3 18.8 - - + +
453A GLU 3.9 2.3 - - - +
454A LEU* 3.5 2.8 - - - +
455A GLU* 2.7 60.0 + - + +
801A CL 3.2 14.1 - - + +
378B LEU* 3.1 30.4 - - - +
380B PHE* 4.5 8.9 - - - -
585B GLU* 2.9 50.7 + - - +
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Residues in contact with VAL 420 (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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387A LEU* 4.5 5.6 - - + -
389A ILE* 3.9 9.2 - - + -
418A ILE* 4.3 1.3 + - + -
419A ARG* 1.3 78.4 - - - +
421A GLY* 1.3 66.4 + - - +
422A ASN 3.1 0.7 + - - -
423A GLN* 2.9 33.7 + - + +
425A PHE* 5.1 2.2 - - + -
444A ALA* 3.8 31.0 - - + -
445A LEU 4.1 12.8 - - - +
446A VAL* 4.4 13.5 - - + -
452A GLN* 4.3 10.3 - - - +
453A GLU 4.6 3.8 - - - +
454A LEU* 3.4 23.6 - - + -
476A LEU* 4.5 13.0 - - + -
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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