Contacts of the helix formed by residues 323 - 330 (chain A) in PDB entry 2HW6
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 SER 323 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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240A ARG* 3.6 27.1 - - - +
243A LEU* 4.1 2.2 - - - -
321A ARG 3.7 0.6 + - - -
322A LEU* 1.3 73.4 - - - +
324A ALA* 1.3 60.0 + - - +
325A ALA* 3.6 8.8 + - - +
326A GLN* 2.9 37.3 + - - +
327A VAL* 2.9 30.1 + - - +
342A SO4 3.7 16.8 - - - -
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Residues in contact with ALA 324 (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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155A ALA* 3.6 10.8 - - - +
158A LEU* 3.9 12.3 - - + -
159A ASP* 3.5 34.3 - - - +
162A HIS* 4.5 6.7 + - + +
243A LEU* 3.7 20.2 - - + +
323A SER* 1.3 72.5 - - - +
325A ALA* 1.3 62.6 + - - +
327A VAL* 3.1 6.7 + - - +
328A LEU* 3.0 29.1 + - - +
342A SO4 5.0 1.0 + - - -
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Residues in contact with ALA 325 (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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159A ASP* 3.8 21.7 + - - +
323A SER* 3.3 8.4 + - - +
324A ALA* 1.3 76.7 - - - +
326A GLN* 1.3 63.0 + - + +
328A LEU* 3.3 14.1 + - - +
329A GLN* 3.1 28.2 + - + +
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Residues in contact with GLN 326 (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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240A ARG* 5.3 3.9 + - - +
320A GLN 5.6 0.2 - - - +
321A ARG 4.4 2.3 - - - +
322A LEU* 3.4 29.3 - - + +
323A SER* 2.9 36.7 + - - +
325A ALA* 1.3 77.7 - - + +
327A VAL* 1.3 66.1 + - - +
329A GLN* 3.2 8.9 + - - +
330A HIS* 3.1 21.0 + - - +
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Residues in contact with VAL 327 (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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151A VAL* 3.8 28.9 - - + -
155A ALA* 4.1 13.5 - - + -
243A LEU* 3.9 12.1 - - + -
246A LEU* 4.5 4.0 - - + -
309A LEU* 4.3 9.0 - - + -
313A LEU* 3.8 31.0 - - + -
322A LEU* 4.1 9.9 - - + -
323A SER 2.9 18.2 + - - +
324A ALA 3.1 7.2 + - - +
326A GLN* 1.3 74.9 - - - +
328A LEU* 1.3 62.8 + - - +
330A HIS* 3.1 21.3 + - - +
333A VAL* 3.3 12.9 - - + +
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Residues in contact with LEU 328 (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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152A ARG* 3.5 39.3 - - + +
155A ALA* 3.6 13.9 - - + -
156A ALA* 3.8 13.5 - - + +
159A ASP* 3.9 30.1 - - + +
324A ALA 3.0 19.0 + - - +
325A ALA* 3.5 10.5 - - - +
326A GLN 3.2 0.2 - - - -
327A VAL* 1.3 75.7 - - - +
329A GLN* 1.3 68.9 + - - +
330A HIS 3.5 0.7 + - - -
333A VAL* 3.9 10.3 - - - +
335A GLY* 3.5 23.0 + - - -
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Residues in contact with GLN 329 (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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325A ALA* 3.1 20.0 + - + +
326A GLN* 3.2 9.3 + - - +
328A LEU* 1.3 84.2 + - - +
330A HIS* 1.3 62.6 + - - +
331A PRO* 3.5 4.9 - - - +
335A GLY* 3.2 34.7 - - - +
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Residues in contact with HIS 330 (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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305A GLU* 3.3 26.9 - - + -
308A ASP* 3.0 25.9 + - - -
309A LEU* 3.7 34.3 + - + +
312A LYS* 4.7 6.5 - - + -
322A LEU* 4.7 9.4 - - + -
326A GLN 3.1 10.4 + - - +
327A VAL* 3.1 16.2 + - - +
329A GLN* 1.3 78.0 - - - +
331A PRO* 1.4 66.1 - - + +
332A TRP* 3.0 36.3 + - + +
333A VAL* 3.2 7.3 + - + +
334A GLN* 2.7 30.3 + - - -
335A GLY 3.9 0.6 + - - -
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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