Contacts of the strand formed by residues 357 - 365 (chain C) in PDB entry 3SAJ
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 357 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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226C LYS* 4.0 0.6 - - - +
352C GLU 3.0 6.3 - - - +
353C MET* 3.1 5.0 - - - +
354C LYS* 2.6 45.4 + - - -
355C HIS* 3.0 5.3 + - - -
356C ASP* 1.3 73.9 - - - +
358C ILE* 1.3 66.5 + - - +
359C ARG* 5.0 3.6 - - - -
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Residues in contact with ILE 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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217C PHE* 5.8 1.6 - - + -
218C MET* 4.7 15.7 - - + -
222C LEU* 4.8 13.2 - - + -
226C LYS* 4.1 27.5 - - + +
351C ILE* 3.8 20.4 - - + -
352C GLU 3.4 3.1 - - - +
353C MET* 2.5 45.8 - - + -
356C ASP 4.2 0.8 + - - -
357C GLY* 1.3 79.3 - - - +
359C ARG* 1.3 62.4 + - - +
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Residues in contact with ARG 359 (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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351C ILE* 3.2 6.4 - - - -
352C GLU* 2.6 46.6 + - + +
357C GLY* 5.0 2.9 - - - -
358C ILE* 1.3 78.4 - - - +
360C LYS* 1.3 77.8 + - - +
361C ILE* 3.4 1.9 + - + +
373C ALA 5.9 5.3 + - - -
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Residues in contact with LYS 360 (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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236C GLN* 3.8 23.6 - - - +
239C ASN* 3.3 28.9 + - - +
349C HIS* 4.2 25.4 - - + -
350C VAL 3.2 6.5 - - - +
351C ILE* 3.2 20.8 - - + +
359C ARG* 1.3 91.0 + - + +
361C ILE* 1.3 61.6 + - - +
362C GLY* 4.5 6.5 - - - +
373C ALA* 4.5 8.2 - - + +
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Residues in contact with ILE 361 (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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121C HIS* 4.0 22.4 - - + +
122C TYR* 3.5 11.4 - - + +
233C THR* 4.2 11.2 - - + -
350C VAL* 2.7 15.1 + - + +
351C ILE 4.2 3.4 - - - -
352C GLU* 2.6 66.9 - - + +
359C ARG* 4.0 2.7 - - + +
360C LYS* 1.3 75.2 - - - +
362C GLY* 1.3 57.0 + - - +
370C PHE* 4.0 12.8 - - + -
372C PRO* 3.7 3.6 - - + +
373C ALA* 2.9 25.6 + - - +
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Residues in contact with GLY 362 (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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349C HIS* 3.8 6.2 - - - +
350C VAL* 3.2 23.0 + - - +
360C LYS* 3.4 7.3 - - - +
361C ILE* 1.3 81.8 - - - +
363C TYR* 1.3 67.6 + - - +
370C PHE* 4.1 3.8 - - - -
371C VAL 3.3 13.5 - - - -
373C ALA* 4.0 11.8 - - - +
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Residues in contact with TYR 363 (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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347C THR* 3.7 16.8 - - + -
348C LEU 3.1 13.5 - - - +
349C HIS* 3.7 16.2 - + + -
350C VAL* 4.1 3.4 - - - -
362C GLY* 1.3 78.4 - - - +
364C TRP* 1.3 66.5 + - - +
365C ASN* 4.0 19.3 - - - -
368C ASP* 4.6 6.0 + - + -
369C LYS 3.8 0.6 - - - +
370C PHE* 3.2 11.5 - - - -
371C VAL* 2.8 60.7 + - + +
372C PRO 5.7 1.1 - - - -
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Residues in contact with TRP 364 (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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110C GLU 5.2 0.9 - - - -
113C GLU* 3.7 34.5 - - + -
114C ALA* 3.5 31.0 - - + +
117C SER* 3.0 32.8 + - - -
118C ILE* 5.1 1.1 - - + -
235C PHE* 5.2 1.1 - - + -
346C TYR* 4.0 27.6 - + - -
347C THR* 3.4 7.3 - - - +
348C LEU* 2.8 48.3 + - + +
350C VAL* 5.0 6.3 - - + -
363C TYR* 1.3 77.5 - - - +
365C ASN* 1.3 104.4 + - - +
366C GLU* 3.7 20.2 - - + -
369C LYS* 3.2 32.7 - - + +
370C PHE* 3.8 5.8 - - + -
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Residues in contact with ASN 365 (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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346C TYR 3.9 15.3 - - - +
347C THR* 4.3 7.4 + - - +
363C TYR* 4.0 15.2 - - - -
364C TRP* 1.3 96.1 - - - +
366C GLU* 1.3 57.8 + - - +
367C ASP* 2.8 17.2 + - - +
368C ASP* 2.5 57.4 + - - +
369C LYS* 3.0 30.0 + - - -
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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