Contacts of the strand formed by residues 304 - 310 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272D ASN 3.7 6.3 - - - +
273D ALA 4.6 0.2 - - - -
274D ILE* 3.3 29.4 - - + +
289D ALA* 6.1 0.7 - - + -
292D ALA* 3.2 22.0 + - - +
293D SER* 3.8 18.7 + - - +
303D THR* 1.3 84.3 - - - +
305D ARG* 1.3 61.4 + - - +
306D ARG 3.4 24.5 - - - +
307D LEU* 4.6 2.2 - - + +
403D ILE 4.6 3.6 - - - +
404D LEU* 3.8 19.6 - - + +
458D THR* 2.9 19.3 + - - +
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Residues in contact with ARG 305 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270D GLY 4.5 3.8 + - - +
271D ASN* 3.4 25.4 - - - +
272D ASN* 2.9 19.3 + - - +
298D GLY 2.7 31.2 + - - -
300D ARG 3.1 22.2 + - - -
301D CYS* 5.0 0.6 + - - +
303D THR* 3.4 23.7 + - - +
304D THR* 1.3 75.9 + - - +
306D ARG* 1.3 60.9 + - + +
398D GLU* 4.4 13.6 + - + +
399D THR 3.5 19.5 + - - +
400D PHE* 3.2 23.0 - - - -
401D VAL 3.1 21.2 + - - +
402D PRO* 5.2 0.2 - - - +
403D ILE 4.4 9.4 + - - -
404D LEU* 3.8 5.0 - - - +
405D TYR* 3.0 42.4 + - + -
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Residues in contact with ARG 306 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271D ASN* 3.0 48.4 + - - +
272D ASN 3.0 2.2 + - - +
273D ALA* 3.1 23.9 - - + +
274D ILE 2.8 25.8 + - - +
304D THR* 3.4 5.6 - - - +
305D ARG* 1.3 81.2 - - + +
307D LEU* 1.3 60.7 + - - +
308D MET* 3.5 17.7 - - + +
390D HIS 5.5 1.6 + - - -
395D VAL* 3.9 29.6 - - + +
396D HIS* 5.6 0.4 - - - -
405D TYR* 3.4 6.7 - - + +
407D LEU* 4.9 7.2 - - + +
418D TRP* 2.7 26.7 + - - +
419D ASN* 3.0 28.9 + - - +
421D GLU* 4.9 2.2 + - - +
422D VAL* 3.5 22.8 - - - +
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Residues in contact with LEU 307 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274D ILE* 3.5 32.5 - - + +
276D VAL* 4.0 6.1 - - + -
285D VAL* 5.3 0.2 - - + -
289D ALA* 4.5 13.0 - - + -
304D THR* 4.8 1.6 - - + -
306D ARG* 1.3 72.9 - - - +
308D MET* 1.3 60.4 + - - +
309D LEU* 3.7 33.0 - - + -
318D VAL* 5.7 0.4 - - + -
321D ILE* 3.5 30.3 - - + -
404D LEU* 3.9 27.7 - - + +
405D TYR 2.9 10.7 + - - +
406D VAL* 3.3 15.1 - - + +
407D LEU* 2.8 25.1 + - - +
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Residues in contact with MET 308 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273D ALA* 3.7 19.3 - - + -
274D ILE 2.7 16.4 + - - +
275D ILE* 3.9 18.2 - - + -
276D VAL* 2.7 33.6 + - - +
306D ARG* 3.5 31.4 - - + +
307D LEU* 1.3 75.8 - - - +
309D LEU* 1.3 59.3 + - - +
407D LEU* 3.3 26.2 - - + +
409D PHE* 3.7 15.7 - - + -
415D ALA* 4.0 15.3 - - - +
418D TRP* 3.9 21.8 - - + -
419D ASN* 3.7 15.5 - - - +
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Residues in contact with LEU 309 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276D VAL* 3.8 25.6 - - + -
307D LEU* 3.7 27.4 - - + -
308D MET* 1.3 73.6 - - - +
310D HIS* 1.3 63.3 + - - +
313D VAL* 4.8 1.3 - - + -
314D HIS* 3.5 42.2 - - + +
317D VAL* 3.7 29.6 - - + -
318D VAL* 3.5 21.1 - - + -
406D VAL* 3.8 11.7 - - + -
407D LEU 2.7 8.5 + - - -
408D LYS* 3.4 7.1 - - - +
409D PHE* 3.0 23.9 + - - -
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Residues in contact with HIS 310 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276D VAL 3.1 19.1 + - - +
277D PHE* 4.3 3.8 - + - -
278D GLU* 3.7 37.0 + - + +
309D LEU* 1.3 71.9 - - - +
311D GLU* 1.3 77.6 + - + +
312D SER* 2.8 39.6 + - - +
313D VAL* 2.9 10.0 + - + +
314D HIS* 2.9 19.5 + - - -
409D PHE* 3.3 25.3 - + + -
410D LYS* 3.0 37.0 + - + +
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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