Contacts of the strand formed by residues 415 - 422 (chain A) in PDB entry 5N4D
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 415 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89A LEU* 4.2 10.6 + - + +
95A TRP* 3.5 31.2 - + - -
367A ALA* 5.2 1.6 - - - +
408A ALA 5.6 0.2 - - - -
409A ASN* 4.1 11.0 + - + +
410A ARG 4.7 1.6 + - - +
413A GLN* 3.3 47.7 + - + +
414A THR* 1.3 83.0 + - - +
416A PHE* 1.3 72.1 + - - +
417A PHE* 3.5 32.0 - + - -
431A ARG* 4.7 9.4 - - + +
432A TYR 3.0 18.2 - - - +
433A ASP* 4.3 7.4 - - + +
434A PHE* 4.5 2.7 - - - -
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Residues in contact with PHE 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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367A ALA* 3.9 4.0 - - + -
373A VAL* 3.5 39.9 - - + -
386A LEU* 4.2 4.9 - - + -
397A LEU* 3.7 24.0 - - + -
407A ILE* 4.6 3.1 - - + -
408A ALA 3.8 4.5 - - - +
409A ASN* 3.4 24.0 - - + +
415A HIS* 1.3 79.1 - - - +
417A PHE* 1.3 78.8 + - - +
418A LEU* 4.2 12.8 - - + -
431A ARG* 3.5 4.3 - - - +
432A TYR* 2.9 71.5 + + + +
434A PHE* 3.6 24.5 - + - -
442A PHE* 6.0 0.2 - + - -
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Residues in contact with PHE 417 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A ALA* 4.2 11.7 - - + -
87A PRO* 3.3 34.3 - - + -
88A THR* 5.3 0.2 - - - -
95A TRP* 3.6 21.5 - + - -
117A LEU* 4.5 1.8 - - + -
407A ILE* 3.5 8.1 - - - +
408A ALA* 2.8 49.1 + - + +
409A ASN* 5.5 0.9 - - - -
415A HIS* 3.5 27.6 - + - -
416A PHE* 1.3 76.5 - - - +
418A LEU* 1.3 68.0 + - - +
429A ILE* 4.0 15.3 - - + -
430A ALA 3.1 16.4 - - - +
431A ARG* 3.8 31.6 - - + -
445A LEU* 3.8 17.5 - - + -
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Residues in contact with LEU 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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373A VAL* 4.5 0.2 - - + -
375A ILE* 4.6 0.7 - - + -
384A ILE* 3.8 48.7 - - + -
397A LEU* 4.4 8.5 - - + -
398A ALA* 5.0 0.9 - - + -
405A ALA* 5.7 0.2 - - + -
406A SER 3.3 10.8 - - - +
407A ILE* 4.0 14.4 - - + -
416A PHE* 4.2 15.0 - - + -
417A PHE* 1.3 80.7 - - - +
419A THR* 1.3 64.6 + - - +
420A LEU* 4.0 17.2 - - + +
428A THR 3.6 1.2 - - - +
429A ILE* 3.3 6.2 - - - +
430A ALA* 2.9 35.9 + - + +
442A PHE* 4.0 27.8 - - + -
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Residues in contact with THR 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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86A ALA* 3.8 22.0 - - + -
404A ALA 3.8 1.0 - - - +
405A ALA* 3.4 4.7 - - - -
406A SER* 2.9 37.8 + - - +
408A ALA* 4.8 2.7 - - + -
418A LEU* 1.3 75.8 - - - +
420A LEU* 1.3 58.8 + - - +
428A THR 3.6 3.8 - - - -
429A ILE* 4.5 6.3 - - + -
18C LEU* 4.0 28.9 - - - +
19C ALA* 4.7 3.5 - - - +
22C ASN* 3.2 41.0 + - - +
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Residues in contact with LEU 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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384A ILE* 4.0 9.4 - - + -
398A ALA* 4.5 15.0 - - + -
401A PHE* 3.6 34.1 - - + -
404A ALA 3.6 2.2 - - - -
405A ALA* 3.6 27.8 - - + -
418A LEU* 4.0 17.5 - - + +
419A THR* 1.3 75.7 - - - +
421A SER* 1.3 63.4 + - - +
425A THR* 3.9 2.4 - - - +
427A GLY* 3.5 2.1 - - - -
428A THR* 2.8 63.8 + - + +
430A ALA* 4.7 13.2 - - + -
442A PHE* 5.4 0.4 - - + -
444A ILE* 5.6 1.6 - - + -
18C LEU* 4.1 2.1 - - - +
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Residues in contact with SER 421 (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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401A PHE* 3.3 8.0 - - - -
404A ALA* 2.8 40.3 + - - +
420A LEU* 1.3 76.3 - - - +
422A GLY* 1.3 60.2 + - - +
425A THR* 3.4 18.8 - - - -
426A PRO 4.3 3.6 - - - -
505A PRO 4.9 1.6 + - - -
506A PHE* 4.6 2.4 - - - -
802A GOL 2.7 28.2 + - - -
18C LEU* 3.8 18.0 - - - +
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Residues in contact with GLY 422 (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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402A VAL 4.5 3.6 - - - -
403A GLY* 4.3 5.8 - - - -
421A SER* 1.3 77.6 + - - +
423A PHE* 1.3 66.6 + - - -
424A ASN* 3.1 4.1 + - - -
425A THR* 3.0 18.2 + - - -
505A PRO* 4.1 15.0 - - - -
506A PHE 3.5 9.9 - - - -
507A PHE* 3.3 17.7 - - - +
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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