Contacts of the strand formed by residues 311 - 316 (chain C) in PDB entry 4J2X
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 LYS 311 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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270C TYR* 4.3 6.2 + - - -
292C LYS* 4.7 1.4 - - - +
293C VAL* 3.5 33.1 + - + +
295C LYS* 5.6 5.4 + - - +
309C LEU 3.7 2.6 + - - +
310C HIS* 1.3 72.5 - - - +
312C CYS* 1.3 60.3 + - - +
353C SER* 3.4 25.4 - - - +
354C TRP 3.5 5.2 - - - +
355C THR* 3.6 23.1 - - + +
8F G 4.1 26.2 + - - -
9F G 2.8 27.9 + - - -
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Residues in contact with CYS 312 (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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270C TYR* 3.9 17.3 - - + +
290C ILE* 4.2 10.5 - - + -
291C ARG 3.3 14.1 - - - +
293C VAL* 3.6 6.5 - - - +
306C VAL* 4.8 0.7 - - - -
311C LYS* 1.3 77.3 - - - +
313C ALA* 1.3 60.5 + - - +
314C PHE* 4.2 20.4 - - - -
353C SER* 3.6 4.0 - - - -
354C TRP* 2.8 45.6 + - - +
356C ILE* 4.0 31.4 - - - -
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Residues in contact with ALA 313 (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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289C ILE 3.5 0.3 - - - +
290C ILE* 3.3 5.4 - - - +
291C ARG* 2.8 37.9 + - + +
293C VAL* 3.4 19.7 - - + -
298C ALA* 4.8 2.0 - - + -
312C CYS* 1.3 74.8 - - - +
314C PHE* 1.3 66.9 + - - +
315C TYR 3.9 0.4 - - - -
323C TYR* 3.9 21.1 - - + -
348C ILE* 4.1 4.3 - - + -
352C ALA 3.6 16.2 - - - +
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Residues in contact with PHE 314 (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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215C LEU* 3.7 42.2 - - + -
274C VAL* 4.5 7.9 - - + -
276C LEU* 4.1 13.0 - - + -
288C LEU* 4.0 32.1 - - + +
289C ILE 3.7 2.2 - - - -
290C ILE* 3.6 38.8 - - + -
312C CYS* 4.2 9.4 - - - -
313C ALA* 1.3 78.8 - - - +
315C TYR* 1.3 61.5 + - - +
316C LEU 3.5 0.7 + - - -
323C TYR* 3.5 4.5 - - - -
324C LEU* 3.0 47.6 + - + +
352C ALA 4.7 2.2 + - - -
354C TRP* 3.9 25.9 - + + -
356C ILE* 4.8 3.4 - - + -
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Residues in contact with TYR 315 (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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288C LEU* 3.3 2.6 - - - -
289C ILE* 2.7 55.7 + - + +
291C ARG* 3.3 46.0 - - - +
314C PHE* 1.3 71.4 - - - +
316C LEU* 1.3 62.5 + - - +
317C LYS* 3.0 21.7 + - - -
318C ASP* 3.5 5.8 + - - -
319C THR* 2.5 47.4 + - - -
321C ARG* 3.8 14.6 - - - -
322C MET 3.3 24.7 - - - -
323C TYR* 3.5 16.1 - + + -
346C GLU* 5.6 0.2 - - - -
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Residues in contact with LEU 316 (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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286C PRO* 4.2 20.9 - - + -
287C ARG 3.8 6.1 - - - +
288C LEU* 3.8 20.2 - - + -
315C TYR* 1.3 70.9 - - - +
317C LYS* 1.3 69.5 + - - +
319C THR* 2.7 39.4 + - + -
322C MET 2.9 19.5 + - - +
323C TYR 3.7 4.3 - - - -
324C LEU* 3.4 33.2 - - + +
333C GLN* 3.7 27.1 - - + +
193D PRO* 4.1 23.1 - - + -
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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