Contacts of the strand formed by residues 351 - 358 (chain C) 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 GLY 351 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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347C LYS* 3.4 2.5 - - - -
348C GLY 2.8 20.8 + - - -
349C SER 2.8 6.2 + - - -
350C PHE* 1.3 99.8 - - - +
352C LYS* 1.3 58.3 + - - -
368C LYS* 4.7 0.2 - - - -
370C LEU* 4.0 20.2 - - - -
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Residues in contact with LYS 352 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344C VAL* 4.7 8.1 - - + -
346C GLY 3.9 3.4 - - - +
347C LYS* 4.0 35.9 - - + +
350C PHE 4.0 0.4 + - - -
351C GLY* 1.3 73.2 - - - -
353C VAL* 1.3 66.3 + - - +
354C MET* 4.5 23.6 - - + +
367C ILE 3.6 1.2 - - - +
368C LYS* 3.2 3.3 - - - +
369C ILE* 2.8 60.7 + - + +
371C LYS* 5.1 8.1 - - - +
412C ARG* 5.2 4.6 - - - +
637C LEU* 5.3 7.7 - - + +
638C TPO 5.0 9.5 + - - -
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Residues in contact with VAL 353 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344C VAL* 3.5 3.1 - - - -
345C LEU* 2.6 48.2 + - + -
346C GLY 2.8 17.8 + - - +
350C PHE* 3.8 27.1 - - + +
352C LYS* 1.3 78.1 - - - +
354C MET* 1.3 53.8 + - - +
366C ALA* 4.1 13.7 - - + -
367C ILE 3.7 5.6 - - - +
368C LYS* 4.3 14.4 - - + -
901C LW4 3.4 45.5 - - + -
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Residues in contact with MET 354 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341C PHE* 3.1 52.7 - - + -
343C MET 3.4 16.6 - - - +
344C VAL* 4.0 20.6 - - - -
345C LEU* 4.0 2.5 - - - -
352C LYS* 4.0 14.5 + - + -
353C VAL* 1.3 74.7 - - - +
355C LEU* 1.3 70.9 + - - +
356C ALA 3.6 0.7 + - - -
366C ALA* 3.4 4.2 - - - -
367C ILE* 2.8 43.5 + - + +
369C ILE* 4.3 14.1 - - + -
635C PRO* 3.7 20.6 - - + +
636C VAL 5.5 0.4 - - - +
637C LEU* 4.5 7.2 - - + -
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Residues in contact with LEU 355 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341C PHE 3.7 0.5 - - - -
342C LEU* 2.7 55.3 + - + +
343C MET* 2.5 34.7 + - + +
345C LEU* 3.3 25.5 - - + +
354C MET* 1.3 74.2 - - - +
356C ALA* 1.3 58.3 + - - +
364C LEU* 4.2 11.0 - - + -
365C TYR 3.3 17.3 - - - +
419C TYR* 3.8 44.9 - - + +
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Residues in contact with ALA 356 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339C PHE* 3.9 12.8 - - + -
340C ASN 3.3 11.9 - - - +
341C PHE* 4.0 12.6 - - + -
342C LEU* 4.1 3.4 - - - +
354C MET 3.6 1.0 + - - +
355C LEU* 1.3 76.0 - - - +
357C ASP* 1.3 60.5 + - - +
364C LEU* 3.4 5.9 - - - +
365C TYR 2.7 35.4 + - - +
367C ILE* 3.5 31.4 - - + -
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Residues in contact with ASP 357 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339C PHE* 3.2 6.4 - - - -
340C ASN* 2.8 57.0 + - - +
342C LEU* 3.7 29.2 - - + +
356C ALA* 1.3 74.9 - - - +
358C ARG* 1.3 74.3 + - - +
359C LYS* 3.4 2.8 + - - -
361C THR 3.8 9.4 - - - +
362C GLU* 4.7 1.7 - - - -
363C GLU 3.9 7.0 - - - +
364C LEU* 3.9 12.0 - - + +
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Residues in contact with ARG 358 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332C ASP* 3.1 39.1 + - - -
333C ARG 5.4 1.6 + - - -
334C VAL* 4.2 21.1 - - - +
338C ASP* 3.9 11.1 - - + +
339C PHE* 4.2 13.2 - - + -
357C ASP* 1.3 74.0 + - - +
359C LYS* 1.3 76.8 + - - +
361C THR* 2.9 47.8 + - + +
363C GLU* 2.8 21.9 + - - +
365C TYR* 3.3 40.1 + - + -
404C HIS* 4.4 4.4 - - - -
665C HIS* 4.5 4.8 - - - -
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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