Contacts of the helix formed by residues 311 - 321 (chain A) in PDB entry 5MJU
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 ILE 311 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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306A VAL* 3.4 15.7 + - + +
307A ILE* 3.2 42.6 - - + +
309A GLY 3.5 0.6 - - - -
310A LEU* 1.4 84.7 - - + +
312A VAL* 1.3 70.0 + - + +
314A PRO* 3.4 12.3 - - - +
315A LEU* 3.6 17.8 - - + +
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Residues in contact with VAL 312 (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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133A ILE* 3.7 28.3 - - + -
137A LEU* 4.4 17.9 - - + -
307A ILE* 2.8 24.8 + - + +
308A HIS* 3.4 20.4 - - - +
311A ILE* 1.3 72.8 - - + +
313A LEU* 1.4 66.6 + - - +
315A LEU* 3.1 17.5 + - - +
316A ILE* 3.2 26.9 + - + +
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Residues in contact with LEU 313 (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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126A TYR* 3.6 23.8 - - - +
130A THR* 3.9 12.6 - - + -
308A HIS* 2.8 42.4 + - + +
309A GLY* 3.5 22.9 - - - +
312A VAL* 1.4 72.1 - - - +
314A PRO* 1.4 63.1 - - + +
316A ILE* 3.0 30.9 + - + +
317A TYR* 3.2 11.1 + - - +
380A ASP* 4.7 0.7 - - - +
462A VAL* 4.3 10.1 - - + -
465A LEU* 4.4 9.9 - - + -
466A GLY* 4.5 18.8 - - - +
469A LEU* 3.9 17.0 - - + +
473A ILE* 5.4 0.9 - - + +
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Residues in contact with PRO 314 (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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309A GLY 3.2 19.7 - - - +
310A LEU* 3.4 21.8 - - - +
311A ILE* 3.4 16.6 - - - +
313A LEU* 1.4 87.0 - - + +
315A LEU* 1.4 54.0 + - - -
317A TYR* 3.3 2.8 + - + +
318A PHE* 3.0 24.3 + - - +
325A PRO* 3.2 39.2 - - + +
326A PHE* 3.7 21.5 - - + -
329A ILE* 4.7 5.4 - - + -
469A LEU* 4.6 4.4 - - + -
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Residues in contact with LEU 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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311A ILE* 3.6 14.1 - - + +
312A VAL* 3.1 12.4 + - - +
314A PRO* 1.4 76.8 - - - +
316A ILE* 1.4 62.8 + - + +
318A PHE* 3.5 7.9 + - + +
319A LEU* 3.0 45.4 + - + +
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Residues in contact with ILE 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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126A TYR* 4.1 14.1 - - + -
130A THR* 4.3 12.1 - - + -
133A ILE* 5.6 7.0 - - + -
308A HIS* 5.2 2.2 - - + -
312A VAL* 3.4 30.7 - - + +
313A LEU* 3.0 32.0 + - + +
315A LEU* 1.4 77.5 - - + +
317A TYR* 1.4 60.6 + - - +
319A LEU* 3.2 16.4 + - + +
320A ILE* 3.2 22.3 + - + +
473A ILE* 4.1 16.2 - - + -
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Residues in contact with TYR 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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313A LEU 3.2 6.6 + - - +
314A PRO 3.3 8.0 + - - +
316A ILE* 1.4 76.1 - - - +
318A PHE* 1.3 50.7 + - - +
320A ILE* 3.3 0.5 + - - -
321A THR* 2.7 73.6 + - + +
323A LYS* 3.5 39.9 + - + +
324A ASN 4.1 2.9 + - - -
325A PRO* 3.6 22.7 - - + -
328A PHE* 3.3 33.0 - + + +
469A LEU* 3.9 39.0 - - + -
472A GLY* 4.1 18.3 - - - -
473A ILE* 3.8 16.3 - - + +
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Residues in contact with PHE 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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314A PRO 3.0 13.9 + - - +
315A LEU* 3.8 10.1 - - + +
316A ILE 3.3 0.2 - - - -
317A TYR* 1.3 74.6 - - - +
319A LEU* 1.3 58.7 - - - +
320A ILE 3.2 0.2 - - - -
322A ARG* 3.3 57.0 + - + +
323A LYS 3.4 29.6 - - - -
324A ASN* 4.2 10.8 - - + -
325A PRO* 3.8 13.2 - - + -
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Residues in contact with LEU 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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315A LEU* 3.0 33.9 + - + +
316A ILE* 3.2 10.7 + - + +
318A PHE* 1.3 76.0 - - - +
320A ILE* 1.4 71.0 + - + +
322A ARG* 4.5 17.9 + - - +
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Residues in contact with ILE 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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316A ILE* 3.2 22.9 + - + +
317A TYR 4.0 2.2 - - - +
318A PHE 3.2 0.2 - - - -
319A LEU* 1.4 95.7 - - + +
321A THR* 1.3 63.1 + - - +
322A ARG* 3.6 6.5 + - - -
473A ILE* 3.8 51.1 - - + +
476A HIS* 3.4 23.3 + - + +
477A LEU* 3.8 24.9 - - + -
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Residues in contact with THR 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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317A TYR* 2.7 67.4 + - + +
320A ILE* 1.3 76.9 - - + +
322A ARG* 1.4 66.7 + - - +
323A LYS* 3.4 32.2 + - + +
472A GLY 4.0 7.9 - - - +
476A HIS* 3.7 39.5 + - + -
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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