Contacts of the strand formed by residues 410 - 418 (chain A) in PDB entry 4WII
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 SER 410 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378A LEU* 5.0 1.2 - - - +
379A SER 4.4 3.6 + - - -
380A PRO* 4.0 27.7 - - - +
382A VAL 5.1 0.2 - - - -
402A VAL* 3.4 15.3 - - - +
403A ILE 3.8 5.2 - - - -
404A VAL* 4.0 8.2 - - - +
405A ASP* 5.3 1.0 - - - +
408A GLY 4.1 0.4 + - - -
409A ARG* 1.3 76.8 + - - +
411A THR* 1.3 59.2 + - - +
412A GLY* 3.0 19.9 + - - -
459B LEU* 3.9 24.2 - - - +
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Residues in contact with THR 411 (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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403A ILE* 2.6 35.0 + - + +
404A VAL 3.9 10.1 - - - -
405A ASP* 3.9 7.2 - - + +
409A ARG 4.4 0.2 - - - +
410A SER* 1.3 71.7 - - - +
412A GLY* 1.3 58.7 + - - +
413A LYS* 3.2 30.4 + - - +
451B GLU* 5.5 2.0 - - - +
453B LEU* 3.7 33.0 - - + -
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Residues in contact with GLY 412 (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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376A ARG* 3.3 2.6 - - - -
377A ASN* 3.1 13.7 + - - -
378A LEU* 3.0 48.2 + - - +
380A PRO* 6.1 0.2 - - - -
410A SER* 3.0 13.9 + - - -
411A THR* 1.3 76.7 - - - +
413A LYS* 1.3 58.9 + - - +
443A ARG* 5.8 1.1 - - - -
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Residues in contact with LYS 413 (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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374A SER* 5.6 4.9 - - - +
375A VAL 3.3 6.1 - - - +
376A ARG* 3.8 27.0 - - + +
378A LEU* 3.7 4.7 - - - -
402A VAL* 3.7 6.8 - - - +
403A ILE* 2.8 43.3 + - + +
411A THR* 3.2 20.8 + - - +
412A GLY* 1.3 84.5 - - - +
414A GLY* 1.3 53.6 + - - +
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Residues in contact with GLY 414 (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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374A SER* 3.6 5.2 + - - -
375A VAL* 2.8 39.4 + - - +
378A LEU* 3.8 3.2 - - - +
387A LEU* 4.5 0.2 - - - -
401A VAL 3.0 13.0 - - - -
402A VAL* 4.0 2.9 - - - -
403A ILE* 3.9 7.7 - - - +
413A LYS* 1.3 77.2 - - - +
415A ILE* 1.3 68.2 + - - +
450A LEU* 5.4 0.2 - - - +
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Residues in contact with ILE 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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372A ALA* 4.5 1.1 - - + -
373A LEU 3.3 9.6 - - - +
375A VAL* 4.1 0.6 - - - +
387A LEU* 4.1 0.3 - - - +
399A ARG* 4.2 5.3 - - - +
400A ALA* 3.3 2.6 - - - -
401A VAL* 2.7 45.8 + - + +
403A ILE* 4.0 20.6 - - + -
414A GLY* 1.3 78.4 - - - +
416A VAL* 1.3 69.3 + - - +
417A GLU* 3.9 31.0 - - + +
450A LEU* 4.0 36.6 - - + -
455B ASP* 4.2 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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371A ALA 4.0 1.4 - - - +
372A ALA* 3.4 1.0 - - - -
373A LEU* 2.8 41.3 + - + +
375A VAL* 4.1 15.9 - - + +
387A LEU* 3.9 25.4 - - + -
391A PHE* 3.8 24.5 - - + -
397A ILE* 3.7 20.4 - - + -
399A ARG 3.7 6.3 - - - +
400A ALA* 4.2 4.5 - - + -
415A ILE* 1.3 77.9 - - - +
417A GLU* 1.3 62.7 + - - +
418A PHE* 3.5 28.9 + - + -
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Residues in contact with GLU 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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296A ARG* 3.4 14.7 - - - +
369A HIS* 3.3 34.4 - - + +
371A ALA 3.8 4.3 - - - -
372A ALA* 3.9 12.7 - - + +
397A ILE* 3.6 3.5 - - - +
398A GLU* 2.9 28.0 + - - +
399A ARG* 2.8 68.7 + - - +
415A ILE* 3.9 12.3 - - + +
416A VAL* 1.3 74.6 - - - +
418A PHE* 1.3 61.1 + - - +
450A LEU* 5.4 2.1 - - - +
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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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295A GLN* 3.4 2.8 + - - -
369A HIS* 3.3 21.0 - - - -
371A ALA* 3.0 14.8 + - - +
373A LEU* 3.7 10.5 - - + -
391A PHE* 3.4 21.1 - + + -
394A PHE* 4.0 10.1 - - + -
395A GLY 4.0 5.4 - - - -
396A PRO 3.6 12.8 - - - +
397A ILE* 2.9 33.0 - - + -
398A GLU* 3.7 4.3 - - - +
416A VAL* 3.5 21.5 - - + -
417A GLU* 1.3 73.5 - - - +
419A ALA* 1.3 64.0 + - - +
420A SER 3.5 18.8 + - - +
423A ALA* 3.7 12.3 - - + -
424A ALA* 3.7 18.6 - - + +
427A ALA* 3.7 31.6 - - + -
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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