Contacts of the strand formed by residues 415 - 421 (chain A) in PDB entry 6R4F
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 ASP 415 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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366A CYS* 4.5 0.5 - - - -
367A ARG* 6.0 0.2 - - - +
368A ARG* 2.7 59.4 + - - +
370A ILE* 3.8 13.9 - - + +
411A VAL* 3.5 4.9 - - + +
412A PHE* 2.8 35.6 + - - +
413A ARG 4.0 1.0 - - - +
414A ASP* 1.3 82.3 - - - +
416A VAL* 1.3 61.2 + - - +
417A CYS* 4.0 9.4 - - - -
441A ALA* 3.6 2.5 - - + +
442A LEU* 3.0 26.5 + - - +
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Residues in contact with VAL 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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363A ILE* 4.1 28.5 - - + +
366A CYS* 3.3 38.1 - - + -
368A ARG 2.9 11.4 + - - +
369A LEU* 3.4 11.0 - - + -
370A ILE 2.9 24.9 + - - +
415A ASP* 1.3 71.0 - - - +
417A CYS* 1.3 62.8 - - - +
418A PHE* 3.5 28.6 + - + -
442A LEU* 3.3 14.4 - - + +
444A VAL* 4.1 13.7 - - + -
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Residues in contact with CYS 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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370A ILE* 3.2 30.7 - - + +
372A ILE* 4.7 1.1 - - + -
411A VAL* 4.3 1.3 - - - -
415A ASP* 4.2 3.6 - - - -
416A VAL* 1.3 76.3 - - - +
418A PHE* 1.3 56.8 + - - +
419A PHE* 3.4 26.6 - - + -
436A CYS* 3.8 22.0 - - + -
441A ALA* 3.8 21.8 - - - -
442A LEU 2.7 12.1 + - - +
443A THR* 3.3 2.9 - - + -
444A VAL* 2.8 31.7 + - - +
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Residues in contact with PHE 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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356A LEU* 5.1 1.6 - - + -
363A ILE* 5.2 1.1 - - + -
369A LEU* 3.9 16.4 - - + -
370A ILE 2.7 9.0 + - - +
371A LEU* 3.5 27.8 - - + -
372A ILE* 2.9 26.5 + - - +
416A VAL* 3.5 30.5 - - + -
417A CYS* 1.3 77.7 - - - +
419A PHE* 1.3 64.9 + - - +
420A LEU* 4.1 9.0 - - + -
444A VAL* 3.3 33.4 - - + -
446A ILE* 4.0 19.3 - - + -
485A LEU* 4.5 9.0 - - + -
488A PHE* 3.4 47.3 - + + -
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Residues in contact with PHE 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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372A ILE* 3.4 34.1 - - + -
417A CYS* 3.4 35.4 - - + -
418A PHE* 1.3 75.0 - - - +
420A LEU* 1.3 61.0 - - - +
421A SER 3.8 0.5 + - - -
429A THR* 3.8 22.9 - - + +
432A GLY 3.7 1.8 - - - -
433A LEU* 3.4 53.8 - - + -
436A CYS* 3.8 11.0 - - + -
443A THR* 3.8 6.3 - - + -
444A VAL 2.9 18.7 + - - +
445A GLY* 3.8 1.6 - - - -
446A ILE 2.9 27.1 + - - +
454A ILE* 4.0 22.4 - - + +
458A THR* 4.2 2.7 - - + -
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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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371A LEU* 4.5 11.7 - - + -
372A ILE 3.2 6.7 + - - +
373A ALA* 3.3 23.4 - - + +
374A CYS 4.7 0.2 + - - -
377A SER* 3.3 41.1 - - - +
378A TYR* 5.2 0.4 - - - -
380A ALA* 4.6 2.2 - - + -
381A GLY* 3.9 22.2 - - - +
398A VAL* 6.3 0.2 - - + -
418A PHE* 4.3 12.6 - - + +
419A PHE* 1.3 72.5 - - - +
421A SER* 1.3 63.8 + - - +
429A THR* 4.1 4.1 + - - +
446A ILE* 3.5 36.3 - - + +
481A GLN* 4.2 9.4 - - + +
485A LEU* 4.1 24.2 - - + -
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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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377A SER* 3.9 4.0 - - - -
419A PHE 3.8 2.0 + - - -
420A LEU* 1.3 76.2 - - - +
422A GLN* 1.3 64.5 + - - +
423A SER* 3.6 7.3 + - - -
424A GLY* 2.7 31.2 + - - -
425A GLU 3.7 1.0 + - - -
426A THR* 3.9 9.3 + - - -
429A THR* 4.3 4.7 - - - -
446A ILE 3.0 9.7 + - - -
447A THR* 3.2 23.1 - - - -
454A ILE* 3.6 27.0 - - - +
481A GLN* 3.7 3.5 - - - +
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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