Contacts of the helix formed by residues 321 - 332 (chain A) in PDB entry 3HDN
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 THR 321 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A GLU* 2.7 41.3 + - + +
320A ILE* 1.3 74.7 - - - +
322A ASN* 1.3 54.6 + - - +
323A SER* 3.9 7.6 + - - -
324A ALA* 3.1 13.7 + - - +
325A ARG* 2.8 31.8 + - - +
354A PHE* 4.6 0.9 - - - -
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Residues in contact with ASN 322 (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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320A ILE 5.0 0.5 - - - +
321A THR* 1.3 72.9 - - - +
323A SER* 1.3 52.9 + - - +
325A ARG* 3.4 19.1 - - - +
326A HIS* 2.8 37.2 + - - +
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Residues in contact with SER 323 (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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321A THR* 3.2 7.2 + - - -
322A ASN* 1.3 77.2 - - - +
324A ALA* 1.3 57.3 + - - +
326A HIS* 3.4 1.7 + - - -
327A LEU* 3.0 30.5 + - - +
352A HIS* 3.5 5.5 - - - -
353A VAL* 3.4 31.0 + - - +
354A PHE* 3.7 27.4 - - - -
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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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196A GLU* 3.7 13.0 - - - +
287A LEU* 5.2 1.5 - - + +
291A LEU* 4.4 10.1 - - + -
320A ILE* 3.9 13.5 - - + -
321A THR* 3.1 21.5 + - - +
323A SER* 1.3 74.9 - - - +
325A ARG* 1.3 64.8 + - - +
327A LEU* 3.5 3.0 + - - +
328A LEU* 3.1 30.5 + - - +
354A PHE* 3.6 24.8 - - + -
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Residues in contact with ARG 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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316A LEU* 3.2 51.0 + - + +
317A LYS 3.3 20.4 + - - -
318A PRO* 4.0 9.1 - - - +
320A ILE* 3.7 27.8 - - + +
321A THR 2.8 19.9 + - - +
322A ASN* 3.4 23.1 - - - +
324A ALA* 1.3 73.6 - - - +
326A HIS* 1.3 56.9 + - - +
329A GLU* 3.1 45.5 + - - +
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Residues in contact with HIS 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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322A ASN 2.8 19.8 + - - +
323A SER* 3.9 4.9 - - - +
324A ALA 3.3 0.2 - - - -
325A ARG* 1.3 70.4 - - - +
327A LEU* 1.3 61.6 + - - +
329A GLU* 3.5 18.2 + - + +
330A GLY* 3.1 25.0 + - - -
340A LEU* 6.0 4.3 - - + -
352A HIS* 3.1 29.6 + + + +
353A VAL* 5.2 5.6 - - + +
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Residues in contact with LEU 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A LEU* 3.6 20.9 - - + -
323A SER 3.0 18.1 + - - +
324A ALA 3.8 4.0 - - - +
326A HIS* 1.3 77.0 - - - +
328A LEU* 1.3 53.5 + - - +
330A GLY* 3.1 2.6 + - - -
331A LEU* 2.8 54.9 + - + +
340A LEU* 3.6 27.6 - - + -
349A ILE* 5.3 2.9 - - + -
352A HIS* 3.5 25.2 - - + +
354A PHE* 3.5 31.4 - - + -
355A PHE* 3.6 18.2 - - + -
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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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284A GLY* 3.2 31.0 - - - +
287A LEU* 3.8 17.0 - - + -
288A TYR* 3.8 18.6 - - + +
291A LEU* 4.1 15.3 - - + -
292A TYR* 4.3 7.0 - - + -
314A LEU* 3.7 3.2 - - - +
316A LEU* 3.8 30.7 - - + -
320A ILE* 3.8 17.0 - - + -
324A ALA 3.1 20.7 + - - +
325A ARG 4.0 2.0 - - - +
327A LEU* 1.3 73.8 - - - +
329A GLU* 1.3 60.0 + - - +
331A LEU* 4.4 3.1 - - + +
332A LEU* 2.9 41.0 + - + +
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Residues in contact with GLU 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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314A LEU* 4.2 11.3 - - + +
316A LEU* 3.8 16.6 - - + +
325A ARG* 3.1 35.0 + - - +
326A HIS* 3.6 22.3 - - + +
327A LEU 3.3 0.2 - - - -
328A LEU* 1.3 76.5 - - - +
330A GLY* 1.3 59.7 + - - +
332A LEU 4.2 1.4 - - - -
333A GLN* 3.2 32.1 + - - +
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Residues in contact with GLY 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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326A HIS* 3.1 13.0 + - - -
327A LEU 3.1 7.1 + - - -
329A GLU* 1.3 77.4 - - - +
331A LEU* 1.3 59.9 + - - +
333A GLN* 3.4 15.8 - - - +
338A LYS 5.9 0.2 - - - -
339A ARG* 3.5 1.4 - - - +
340A LEU* 2.9 40.2 + - - -
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Residues in contact with LEU 331 (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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280A TRP* 3.4 35.2 - - + +
281A TRP* 3.6 13.0 - - - -
283A LEU* 4.1 16.6 - - + -
284A GLY* 3.6 30.3 - - - +
287A LEU* 5.2 2.7 - - + -
327A LEU* 2.8 49.1 + - + +
328A LEU* 4.4 1.3 - - - +
330A GLY* 1.3 73.6 - - - +
332A LEU* 1.3 58.6 + - - +
333A GLN 3.3 1.3 - - - -
339A ARG* 3.4 23.4 + - - -
340A LEU* 3.9 14.6 - - + +
349A ILE* 4.0 17.3 - - + -
355A PHE* 5.9 0.2 - - + -
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Residues in contact with LEU 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A TRP* 3.4 59.2 - - + +
284A GLY* 3.9 15.9 - - - +
285A ALA* 3.7 14.6 - - + +
288A TYR* 4.1 12.8 - - + -
296A PRO* 4.1 16.6 - - + -
297A PHE* 5.0 1.9 - - + -
314A LEU* 3.8 41.0 - - + +
328A LEU* 2.9 23.9 + - + +
329A GLU 4.2 4.5 - - - -
331A LEU* 1.3 77.7 - - - +
333A GLN* 1.3 60.7 + - - +
334A LYS* 3.5 5.4 + - - +
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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