Contacts of the helix formed by residues 326 - 332 (chain A) in PDB entry 4HD8
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 PRO 326 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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298A LEU* 3.7 21.3 - - + -
302A PHE* 3.5 28.9 - - + -
325A GLU* 1.4 89.8 - - + +
327A PHE* 1.3 72.4 + - + +
328A ALA 3.2 3.4 - - - -
329A SER* 3.2 15.1 + - - +
330A LEU* 3.4 14.4 - - + +
2F HIS* 3.4 34.3 - - + +
3F LYS 4.3 10.5 - - - +
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Residues in contact with PHE 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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143A MET* 3.9 15.2 - - + +
226A TYR* 5.6 6.1 - - + -
227A THR 5.2 0.9 - - - -
228A GLN* 3.8 31.6 - - + +
247A ALA* 3.7 32.3 - - + -
248A HIS* 3.9 24.9 - + - -
298A LEU* 4.5 12.3 - - + -
302A PHE* 4.2 9.2 - + - -
322A LEU* 3.8 34.6 - - + +
324A VAL* 3.1 19.1 + - + +
325A GLU 4.3 3.1 - - - -
326A PRO* 1.3 90.7 - - + +
328A ALA* 1.3 67.2 + - - +
330A LEU* 3.5 23.1 + - + +
331A THR 3.7 3.8 + - - -
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Residues in contact with ALA 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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322A LEU* 3.3 21.3 - - - +
323A GLU 4.0 10.1 - - - +
324A VAL 3.2 10.0 + - - +
325A GLU* 3.4 19.3 - - - +
327A PHE* 1.3 76.3 - - - +
329A SER* 1.3 60.3 + - - +
331A THR* 2.9 28.8 + - - -
332A GLU* 4.0 1.3 + - - +
350A PRO* 3.5 17.1 - - + +
353A TRP* 4.4 8.7 - - + -
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Residues in contact with SER 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 GLU* 2.8 28.3 + - - -
326A PRO* 3.2 13.0 + - - +
328A ALA* 1.3 79.4 - - - +
330A LEU* 1.4 53.3 + - - +
332A GLU* 2.8 37.8 + - - +
333A ALA* 3.3 6.7 + - - +
2F HIS* 5.7 2.1 - - - -
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Residues in contact with LEU 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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143A MET* 3.8 24.2 - - + -
226A TYR* 5.1 2.0 - - + -
302A PHE* 3.6 32.3 - - + -
305A HIS* 3.5 38.6 - - + +
309A PHE* 3.4 40.3 - - + -
326A PRO* 3.4 13.9 - - + +
327A PHE* 3.5 13.7 + - + +
328A ALA 3.2 0.6 - - - -
329A SER* 1.4 74.1 + - - +
331A THR* 1.3 65.8 + - - +
332A GLU 3.0 1.6 - - - -
333A ALA* 3.0 18.2 + - + +
334A VAL 4.1 0.5 + - - -
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Residues in contact with THR 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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143A MET* 4.7 0.4 - - - -
309A PHE* 4.8 0.2 - - - -
315A LEU* 3.8 16.2 - - + -
317A ILE* 4.4 11.9 - - + -
322A LEU* 3.2 34.8 - - + -
327A PHE 3.7 1.1 + - - +
328A ALA 2.9 18.7 + - - +
330A LEU* 1.3 75.9 - - - +
332A GLU* 1.3 59.2 + - - +
333A ALA 3.3 0.7 + - - -
334A VAL* 3.5 9.7 - - - +
340A ARG* 3.1 35.8 + - - -
350A PRO* 3.5 25.6 - - + +
351A LEU* 4.4 7.6 - - + -
356A ARG* 4.5 0.2 + - - -
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Residues in contact with GLU 332 (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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328A ALA 5.1 1.3 - - - +
329A SER* 2.8 20.4 + - - +
331A THR* 1.3 84.8 + - - +
333A ALA* 1.4 58.4 + - - +
334A VAL 3.5 2.2 - - - +
340A ARG* 3.2 24.6 + - - -
350A PRO* 4.3 8.4 - - - +
354A HIS* 3.0 42.5 + - - +
356A ARG* 2.9 31.8 + - - +
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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