Contacts of the helix formed by residues 318 - 325 (chain B) in PDB entry 4M5X
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 GLY 318 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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308B GLU* 3.2 19.7 + - - -
316B VAL 3.3 0.2 + - - -
317B GLU* 1.3 77.3 - - - +
319B THR* 1.3 64.0 + - - +
320B ILE 3.2 3.1 - - - -
321B PRO* 3.3 13.7 - - - +
322B LYS* 2.9 27.2 + - - +
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Residues in contact with THR 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237B GLN* 4.4 14.1 - - + +
238B LEU* 4.5 3.4 - - - -
241B ALA* 3.7 19.4 - - + +
308B GLU* 3.9 1.2 + - - -
311B MET* 4.0 10.3 - - - -
316B VAL* 2.7 34.7 + - - +
317B GLU 3.3 0.6 + - - -
318B GLY* 1.3 77.7 - - - +
320B ILE* 1.3 63.2 + - + +
322B LYS* 3.4 8.2 + - - +
323B LEU* 2.9 49.7 + - + +
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Residues in contact with ILE 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238B LEU* 3.9 17.0 - - + -
304B LEU* 4.1 28.9 - - + +
307B VAL* 3.6 31.9 - - + -
308B GLU* 3.1 28.4 + - + +
311B MET* 3.8 17.0 - - - -
319B THR* 1.3 79.8 - - - +
321B PRO* 1.4 63.6 - - + +
323B LEU 3.1 2.3 + - - -
324B PHE* 2.9 43.4 + - + +
348B TYR* 4.1 17.9 - - + -
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Residues in contact with PRO 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308B GLU* 3.5 17.7 - - + +
318B GLY* 3.3 23.6 - - - +
320B ILE* 1.4 96.0 - - + +
322B LYS* 1.3 61.1 + - - +
325B ARG* 3.0 52.5 + - + +
348B TYR* 3.8 28.5 - - + +
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Residues in contact with LYS 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237B GLN* 2.9 24.5 + - - +
318B GLY 2.9 20.1 + - - +
319B THR* 3.6 8.3 - - - +
321B PRO* 1.3 77.8 - - - +
323B LEU* 1.3 63.8 + - + +
325B ARG* 5.4 0.8 - - - +
400B PRO* 3.2 23.8 - - + +
523B LYS* 6.2 2.8 - - - +
526B GLU* 2.7 35.2 + - - -
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Residues in contact with LEU 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235B THR* 4.4 5.4 - - + -
237B GLN* 3.4 35.4 - - + +
238B LEU* 3.7 36.3 - - + +
319B THR* 2.9 34.0 + - + +
322B LYS* 1.3 82.1 - - + +
324B PHE* 1.3 79.3 + - + +
325B ARG 3.9 0.2 - - - -
399B PRO* 3.6 0.2 - - - +
400B PRO* 3.4 11.3 - - + +
401B VAL* 3.0 37.4 + - + +
527B VAL* 4.1 18.4 - - + -
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Residues in contact with PHE 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232B LEU* 4.6 3.4 - - + -
235B THR* 4.5 7.9 - - + -
238B LEU* 4.2 19.3 - - + -
304B LEU* 4.1 26.9 - - + -
320B ILE* 2.9 37.0 + - + +
323B LEU* 1.3 97.8 - - + +
325B ARG* 1.3 63.7 + - - +
347B TYR* 3.5 0.9 - - - +
348B TYR* 3.4 40.0 - - + +
399B PRO* 3.5 15.5 - - - +
401B VAL* 3.6 31.8 - - + +
403B HIS* 3.6 39.0 - + - -
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Residues in contact with ARG 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321B PRO* 3.0 39.9 + - + +
322B LYS* 5.4 0.6 - - - +
323B LEU 3.9 0.2 - - - -
324B PHE* 1.3 76.7 - - - +
326B GLY* 1.3 69.7 + - - +
327B LYS* 4.6 14.3 - - - +
344B ARG* 4.2 14.7 - - - +
346B ASP* 3.1 29.7 + - + +
347B TYR 3.3 9.0 - - - +
348B TYR* 3.8 28.3 + - + -
397B THR* 4.8 1.4 + - - -
398B LEU 5.1 0.2 - - - -
399B PRO* 3.6 13.8 - - - +
400B PRO* 5.1 1.2 - - - +
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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