Contacts of the helix formed by residues 322 - 328 (chain B) in PDB entry 4NMQ
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 GLN 322 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297B GLU* 5.9 0.3 - - - +
298B GLY* 3.8 13.5 + - - +
299B LEU 3.8 7.4 - - - +
300B GLY* 3.6 18.0 + - - -
319B HIS* 3.3 32.1 + - - +
320B PRO 3.3 9.1 + - - +
321B GLY* 1.3 81.3 - - - +
323B PRO* 1.3 78.1 - - + +
324B ALA 3.3 1.3 - - - -
325B ASP* 3.0 13.8 + - - +
326B ARG* 3.0 12.2 + - - +
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Residues in contact with PRO 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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291B LEU* 2.9 30.5 - - + +
292B LEU 3.6 11.4 - - - +
293B LYS* 4.8 1.6 - - - -
297B GLU* 3.4 33.4 - - + +
298B GLY 3.3 18.2 - - - +
299B LEU* 3.6 9.2 - - + +
322B GLN* 1.3 90.2 - - + -
324B ALA* 1.3 62.5 + - - +
326B ARG* 3.0 34.2 + - + +
327B CYS 3.1 7.6 + - - -
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Residues in contact with ALA 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B LEU* 3.5 13.8 - - + +
299B LEU 2.9 15.4 + - - +
300B GLY 3.9 5.4 - - - +
301B ILE* 3.3 39.7 - - + -
318B ILE* 4.0 15.7 - - + +
323B PRO* 1.3 71.8 - - - +
325B ASP* 1.3 63.2 + - - +
327B CYS* 3.3 20.0 - - - -
328B GLY* 3.7 2.4 + - - -
330B LEU* 4.2 10.3 - - + +
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Residues in contact with ASP 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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318B ILE* 3.6 18.0 - - + +
319B HIS 3.4 17.4 + - - +
320B PRO* 3.4 10.0 - - - +
321B GLY* 2.8 23.1 + - - +
322B GLN 3.0 10.2 + - - +
324B ALA* 1.3 77.9 - - - +
326B ARG* 1.3 64.9 + - - +
328B GLY* 3.1 15.4 + - - -
330B LEU 5.8 0.2 - - - -
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Residues in contact with ARG 326 (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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292B LEU* 4.5 5.3 + - - +
294B GLU* 6.0 0.4 - - - +
297B GLU* 3.1 30.1 + - - -
321B GLY* 3.1 23.3 + - - +
322B GLN* 3.0 10.6 + - - +
323B PRO* 3.0 40.1 + - + +
325B ASP* 1.3 78.6 - - + +
327B CYS* 1.3 61.7 + - - +
328B GLY* 3.2 1.7 + - - -
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Residues in contact with CYS 327 (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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289B VAL* 3.7 21.8 - - + +
290B LEU 3.5 20.0 - - - +
291B LEU* 4.0 12.8 - - + -
323B PRO 3.1 9.4 + - - +
324B ALA 3.3 21.1 - - - -
325B ASP 3.3 0.8 - - - -
326B ARG* 1.3 76.8 - - - +
328B GLY* 1.3 57.2 + - - +
329B GLY* 3.0 19.8 + - - -
330B LEU* 4.1 11.9 - - - -
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Residues in contact with GLY 328 (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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324B ALA 3.7 1.7 + - - -
325B ASP 3.1 13.2 + - - -
326B ARG 3.1 4.9 - - - -
327B CYS* 1.3 78.3 - - - +
329B GLY* 1.3 56.0 + - - +
330B LEU 3.6 3.1 - - - -
331B HIS* 3.6 19.4 + - - -
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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