Contacts of the strand formed by residues 304 - 310 (chain C) in PDB entry 2JG7
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 THR 304 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272C ASN 3.6 6.7 - - - +
274C ILE* 3.3 36.3 - - + +
289C ALA* 6.1 0.4 - - + -
292C ALA* 3.3 13.8 + - - +
293C SER* 3.8 19.1 + - - +
303C THR* 1.3 84.3 - - - +
305C ARG* 1.3 60.7 + - - +
306C ARG 3.5 24.5 - - - +
307C LEU* 4.7 2.2 - - + +
403C ILE 4.6 3.8 - - - +
404C LEU* 3.9 20.0 - - + +
458C THR* 2.8 19.4 + - - +
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Residues in contact with ARG 305 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270C GLY 4.5 3.6 + - - +
271C ASN* 3.4 25.4 - - - +
272C ASN* 2.8 18.4 + - - +
298C GLY 2.7 31.2 + - - -
300C ARG 3.1 22.4 + - - -
301C CYS* 5.0 0.6 + - - +
303C THR* 3.4 23.2 + - - +
304C THR* 1.3 75.5 - - - +
306C ARG* 1.3 61.9 + - - +
397C THR 6.0 0.7 - - - +
398C GLU* 4.3 13.3 + - + +
399C THR 3.5 19.5 + - - +
400C PHE* 3.2 23.4 - - - -
401C VAL 3.2 20.2 + - - +
403C ILE 4.5 9.1 + - - -
404C LEU* 3.9 5.0 - - - -
405C TYR* 3.0 43.4 + - + -
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Residues in contact with ARG 306 (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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271C ASN* 3.0 49.2 + - - +
272C ASN 3.0 2.6 + - - -
273C ALA* 3.1 23.1 - - + +
274C ILE 2.8 26.0 + - - +
304C THR* 3.5 5.3 - - - +
305C ARG* 1.3 81.2 - - + +
307C LEU* 1.3 60.4 + - - +
308C MET* 3.5 19.3 - - + +
390C HIS 5.5 2.2 + - - -
395C VAL* 3.8 29.6 - - + +
396C HIS* 5.6 0.2 - - - -
405C TYR* 3.5 5.8 - - + +
407C LEU* 4.8 8.1 - - + +
418C TRP* 2.7 25.3 + - - +
419C ASN* 3.0 27.7 + - - +
421C GLU* 4.9 2.2 + - - +
422C VAL* 3.5 23.9 - - - +
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Residues in contact with LEU 307 (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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274C ILE* 3.5 32.1 - - + +
276C VAL* 4.0 4.7 - - + -
285C VAL* 5.4 0.4 - - + -
289C ALA* 4.6 12.8 - - + -
304C THR* 4.8 2.2 - - + -
306C ARG* 1.3 71.7 - - - +
308C MET* 1.3 59.6 + - - +
309C LEU* 3.7 34.8 - - + -
318C VAL* 5.7 0.4 - - + -
321C ILE* 3.5 29.4 - - + -
404C LEU* 3.8 24.8 - - + +
405C TYR 2.9 10.7 + - - +
406C VAL* 3.3 18.2 - - + +
407C LEU* 2.8 24.7 + - - +
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Residues in contact with MET 308 (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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273C ALA* 3.7 18.8 - - + -
274C ILE 2.8 16.5 + - - +
275C ILE* 3.5 18.8 - - + -
276C VAL* 2.8 34.3 + - - +
306C ARG* 3.5 31.4 - - + +
307C LEU* 1.3 76.3 - - - +
309C LEU* 1.3 57.6 + - - +
407C LEU* 3.3 28.0 - - + +
409C PHE* 3.7 15.3 - - + -
415C ALA* 4.0 15.5 - - - +
418C TRP* 3.9 21.8 - - + -
419C ASN* 3.8 14.4 - - + +
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Residues in contact with LEU 309 (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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276C VAL* 3.7 26.0 - - + -
307C LEU* 3.7 25.6 - - + -
308C MET* 1.3 74.8 - - - +
310C HIS* 1.3 65.5 + - - +
313C VAL* 4.8 1.3 - - + -
314C HIS* 3.5 42.2 - - + +
317C VAL* 3.7 30.5 - - + -
318C VAL* 3.6 20.2 - - + -
406C VAL* 3.8 12.1 - - + -
407C LEU 2.8 9.5 + - - -
408C LYS* 3.4 7.3 - - - +
409C PHE* 3.1 21.4 + - - -
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Residues in contact with HIS 310 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276C VAL 3.1 20.3 + - - +
277C PHE* 4.2 3.4 - + - -
278C GLU* 3.7 35.9 + - + +
309C LEU* 1.3 70.8 - - - +
311C GLU* 1.3 79.9 + - + +
312C SER* 2.8 39.4 + - - +
313C VAL* 2.9 10.9 + - + +
314C HIS 2.9 19.2 + - - -
409C PHE* 3.3 24.4 - + + -
410C LYS* 3.0 34.4 + - - +
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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