Contacts of the strand formed by residues 412 - 418 (chain A) in PDB entry 3IW4
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 ARG 412 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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352A LYS* 5.9 1.2 - - - +
369A ILE* 4.3 9.3 - - + +
370A LEU 2.9 14.4 - - - +
371A LYS* 3.6 30.4 - - - +
372A LYS* 3.7 2.4 - - - +
408A GLN* 3.3 4.2 - - - +
409A THR* 2.8 40.1 + - + +
411A ASP* 1.3 109.9 + - - +
413A LEU* 1.3 63.1 + - - +
414A TYR* 3.3 24.9 - - + +
637A LEU* 3.5 28.0 - - - +
638A TPO 2.8 51.4 + - - -
639A PRO 5.5 1.2 + - - -
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Residues in contact with LEU 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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368A LYS 3.4 0.7 - - - +
369A ILE* 3.3 5.7 - - - +
370A LEU* 2.7 59.3 + - + +
372A LYS* 3.9 13.9 - - + -
375A VAL* 4.5 4.5 - - + -
384A THR* 3.7 29.6 - - + -
407A PHE 4.0 3.4 - - - -
408A GLN* 3.8 22.2 - - + -
412A ARG* 1.3 73.3 - - - +
414A TYR* 1.3 63.6 + - - +
415A PHE* 4.5 4.6 - - + -
653A PHE* 3.8 34.1 - - + -
656A PHE* 3.8 24.0 - - + -
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Residues in contact with TYR 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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336A LEU* 3.3 31.6 - - + +
341A PHE* 5.2 0.4 - + - -
367A ILE* 4.0 13.7 - - + -
368A LYS 3.2 4.3 - - - +
369A ILE* 3.5 41.5 - - + -
406A CYS* 3.4 8.5 - - - +
407A PHE* 3.0 75.1 + + + +
409A THR* 3.4 28.6 - - + +
412A ARG* 3.3 30.2 - - + -
413A LEU* 1.3 75.4 - - - +
415A PHE* 1.3 63.8 + - - +
416A VAL* 4.0 1.0 + - + -
637A LEU* 3.6 9.8 - - + +
656A PHE* 4.1 0.5 - - - -
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Residues in contact with PHE 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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366A ALA 3.6 1.2 - - - +
367A ILE* 3.1 6.1 - - - -
368A LYS* 2.8 64.2 + - + -
370A LEU* 4.1 22.7 - - + -
384A THR* 4.2 17.5 - - + -
387A GLU* 4.4 12.1 - - + -
388A LYS* 4.0 28.9 - - + -
391A LEU* 3.7 23.1 - - + -
403A LEU* 4.8 0.9 - - + -
405A SER 4.0 2.9 - - - -
406A CYS* 4.1 10.3 - - - -
413A LEU* 4.5 4.9 - - + -
414A TYR* 1.3 74.8 - - - +
416A VAL* 1.3 62.3 + - - +
417A MET* 3.7 12.6 + - - +
656A PHE* 3.5 27.1 - + - -
901A LW4 5.5 0.7 - - + -
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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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334A VAL* 5.0 1.3 - - + -
339A PHE* 3.9 18.8 - - + -
365A TYR* 3.7 30.1 - - + -
366A ALA 3.8 0.4 - - - -
367A ILE* 3.9 20.0 - - + +
403A LEU* 3.4 5.5 - - - +
404A HIS* 2.6 46.3 + - + -
405A SER* 2.8 27.0 + - - +
407A PHE* 3.9 28.3 - - + -
414A TYR 4.6 0.4 - - - +
415A PHE* 1.3 76.3 - - - +
417A MET* 1.3 57.6 + - - +
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Residues in contact with MET 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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365A TYR* 3.2 14.2 - - - +
366A ALA 2.5 40.6 + - - +
368A LYS 4.9 1.1 - - - +
391A LEU* 4.0 22.4 - - + -
401A THR* 3.9 14.1 - - - +
402A GLN 3.2 26.5 - - - +
403A LEU* 3.8 14.1 - - - -
404A HIS 4.7 0.4 - - - -
415A PHE* 3.9 17.9 - - + +
416A VAL* 1.3 83.6 - - - +
418A GLU* 1.3 74.3 + - - +
901A LW4 3.6 47.1 - - + +
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Residues in contact with GLU 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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364A LEU 5.2 0.2 - - - -
365A TYR* 4.6 1.8 - - - -
401A THR* 3.5 3.0 - - - -
402A GLN* 2.8 64.9 + - + +
417A MET* 1.3 70.4 - - - +
419A TYR* 1.3 62.2 + - - +
420A VAL* 3.7 10.7 - - + +
478A LYS* 2.6 41.8 + - - +
663A PHE* 3.7 22.0 - - + -
901A LW4 2.9 21.8 + - - -
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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