Contacts of the strand formed by residues 314 - 321 (chain A) in PDB entry 4JU5
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 ALA 314 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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259A LEU* 3.8 1.3 - - - +
260A PHE* 2.8 35.1 + - - +
307A LEU* 3.8 26.9 - - + -
311A GLU 3.6 14.8 - - - +
312A CYS* 3.9 2.6 - - - +
313A PRO* 1.3 76.5 - - - +
315A VAL* 1.3 67.4 + - - +
316A ARG* 4.8 5.6 - - - +
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Residues in contact with VAL 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257A ILE* 3.5 37.2 - - + -
258A LEU 3.3 5.4 - - - +
259A LEU* 3.7 22.4 - - + -
275A PHE* 5.3 2.7 - - + -
314A ALA* 1.3 82.1 - - - +
316A ARG* 1.3 87.3 + - - +
317A LEU* 4.9 3.1 - - + +
339B ILE* 4.0 24.5 - - + -
342B PHE* 5.7 4.3 - - + -
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Residues in contact with ARG 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256A HIS 3.9 0.5 - - - +
257A ILE* 3.4 2.3 - - - +
258A LEU* 2.7 41.4 + - + +
260A PHE* 3.4 23.6 - - + -
305A PHE* 3.7 40.0 + - + +
307A LEU* 3.7 31.1 - - - +
314A ALA* 4.8 2.8 - - - +
315A VAL* 1.3 95.0 + - - +
317A LEU* 1.3 65.0 + - - +
320B LEU* 5.7 0.9 - - + -
321B GLU 4.2 22.2 + - - -
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Residues in contact with LEU 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255A THR* 4.8 6.5 - - + -
256A HIS 3.3 8.5 - - - +
257A ILE* 3.7 37.2 - - + -
286A ILE* 4.3 18.4 - - + -
315A VAL* 5.3 2.0 - - + -
316A ARG* 1.3 76.2 - - - +
318A ILE* 1.3 62.1 + - - +
320B LEU* 4.0 5.9 - - - +
321B GLU* 3.2 54.2 + - + +
342B PHE* 3.4 37.0 - - + +
343B CYS* 4.1 6.3 - - - -
346B PHE* 3.6 13.7 - - + -
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Residues in contact with ILE 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254A LYS 3.7 1.2 - - - +
255A THR* 3.5 2.4 - - - +
256A HIS* 2.7 58.1 + - + +
258A LEU* 3.7 23.8 - - + -
305A PHE* 4.2 21.8 - - + -
317A LEU* 1.3 76.5 - - - +
319A THR* 1.3 72.3 + - - +
320A LEU* 4.7 6.1 - - + +
304B PHE* 4.5 6.3 - - + -
305B PHE* 4.3 13.5 - - + -
318B ILE* 3.7 33.4 - - + -
319B THR 3.4 10.3 - - - +
320B LEU* 4.2 8.7 - - + -
321B GLU* 4.6 0.7 - - - -
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Residues in contact with THR 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254A LYS* 3.5 5.6 - - + +
255A THR* 3.6 28.5 + - - +
318A ILE* 1.3 76.0 - - - +
320A LEU* 1.3 69.0 + - - +
321A GLU* 3.4 22.4 + - + +
318B ILE* 3.3 7.3 - - - +
319B THR* 2.8 48.5 + - - -
321B GLU* 3.3 15.4 + - - -
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Residues in contact with LEU 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249A PHE* 4.3 22.9 - - + +
254A LYS* 2.8 47.2 + - + +
256A HIS* 3.5 38.1 - - + +
318A ILE* 5.0 7.2 - - + -
319A THR* 1.3 73.5 - - - +
321A GLU* 1.3 66.1 + - - +
304B PHE* 6.0 2.0 - - + +
305B PHE* 3.7 37.5 - - + -
316B ARG* 5.3 7.2 - - - -
317B LEU 4.1 2.0 - - - -
318B ILE* 4.2 7.6 - - + -
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Residues in contact with GLU 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254A LYS* 5.6 0.2 - - - -
319A THR* 3.4 22.0 - - + +
320A LEU* 1.3 78.9 - - - +
322A GLU* 1.3 74.4 + - - +
255B THR* 5.1 5.2 + - - +
316B ARG* 5.0 1.4 - - - -
317B LEU* 2.9 38.7 + - + +
318B ILE 4.2 3.1 - - - -
319B THR* 2.8 32.9 + - - -
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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