Contacts of the strand formed by residues 348 - 354 (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 LEU 348 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109C PRO* 4.8 2.0 - - + -
110C GLU 4.0 17.0 - - - +
111C LEU* 4.0 18.4 - - + -
114C ALA* 3.7 28.3 - - + -
215C LEU* 5.2 4.3 - - + -
235C PHE* 3.9 22.0 - - + -
236C GLN 4.2 5.2 - - - +
237C LEU* 4.3 19.1 - - + -
346C TYR* 3.8 24.7 - - + -
347C THR* 1.3 77.0 - - - +
349C HIS* 1.3 65.4 + - - +
350C VAL* 3.9 0.3 + - - +
363C TYR* 3.1 5.4 - - - +
364C TRP* 2.8 46.6 + - + +
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Residues in contact with HIS 349 (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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235C PHE* 3.4 6.8 - - - +
236C GLN* 2.9 53.4 + - + +
237C LEU 5.3 6.2 + - - -
239C ASN* 5.3 11.2 - - + +
242C ASP* 6.1 1.1 - - - -
347C THR* 3.5 35.3 + - + +
348C LEU* 1.3 74.0 - - - +
350C VAL* 1.3 62.9 + - - +
351C ILE* 4.1 0.8 - - + +
360C LYS* 4.2 33.5 - - + -
362C GLY 3.8 5.4 - - - +
363C TYR* 3.7 12.1 - + + -
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Residues in contact with VAL 350 (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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118C ILE* 3.8 38.4 - - + -
233C THR* 3.7 25.4 - - + -
234C GLY 3.6 7.6 - - - +
235C PHE* 4.6 11.2 - - + +
348C LEU 4.5 1.1 - - - +
349C HIS* 1.3 75.0 - - - +
351C ILE* 1.3 58.9 + - - +
360C LYS* 3.2 7.1 - - - +
361C ILE* 2.7 36.7 + - + -
362C GLY 3.2 10.1 + - - +
363C TYR* 4.1 12.3 - - - -
364C TRP* 4.7 1.3 - - + +
370C PHE* 3.8 23.1 - - + -
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Residues in contact with ILE 351 (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* 3.7 22.6 - - + -
218C MET* 4.9 6.3 - - + -
233C THR* 3.2 8.1 - - - +
234C GLY 3.0 32.3 + - - +
235C PHE 4.8 1.1 - - - -
236C GLN* 3.9 33.0 - - + +
349C HIS 4.1 3.4 - - - +
350C VAL* 1.3 76.4 - - - +
352C GLU* 1.3 64.6 + - - +
358C ILE* 3.8 28.9 - - + -
359C ARG 3.2 8.5 - - - +
360C LYS* 3.2 44.0 - - + +
361C ILE* 4.2 1.8 - - - -
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Residues in contact with GLU 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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122C TYR* 2.6 22.2 + - - +
209C HIS* 6.1 0.2 - - - -
217C PHE* 5.4 0.7 - - - -
231C ASN* 6.4 0.4 - - - -
232C VAL 3.7 2.5 - - - +
233C THR* 4.2 5.2 - - - +
351C ILE* 1.3 75.0 - - - +
353C MET* 1.3 63.4 + - - +
354C LYS* 2.4 50.6 + - + +
357C GLY 3.0 5.7 - - - +
358C ILE* 3.4 2.0 - - - -
359C ARG* 2.6 41.1 + - + +
361C ILE* 2.6 49.7 - - + +
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Residues in contact with MET 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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217C PHE* 4.4 9.6 - - + -
220C ILE* 6.0 0.2 - - - -
222C LEU* 3.6 37.5 - - + +
225C PHE* 3.6 17.9 - - - -
226C LYS* 3.5 29.6 - - + -
230C ALA 2.7 31.4 - - - +
231C ASN* 3.3 12.1 - - - -
232C VAL* 2.8 31.1 + - + +
352C GLU* 1.3 73.7 - - - +
354C LYS* 1.3 61.0 + - - +
355C HIS 4.9 0.9 - - - +
357C GLY 3.1 4.3 - - - +
358C ILE* 2.5 44.6 - - + -
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Residues in contact with LYS 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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122C TYR* 5.7 1.9 - - - -
209C HIS* 6.0 4.5 - - - -
230C ALA 4.3 2.0 - - - -
231C ASN* 4.2 17.7 - - + +
352C GLU* 2.4 47.1 + - + +
353C MET* 1.3 79.0 - - - +
355C HIS* 1.3 94.1 + - + +
357C GLY* 2.6 37.3 + - - -
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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