Contacts of the helix formed by residues 324 - 336 (chain A) in PDB entry 4HRE
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 LYS 324 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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320A GLN 4.6 2.9 - - - +
321A GLN 5.4 5.4 - - - +
322A ASP 5.8 0.9 - - - -
323A THR* 1.3 82.3 - - - +
325A GLY* 1.3 68.3 + - - +
327A TYR* 3.8 9.9 - - - +
328A GLN* 3.3 22.5 + - - +
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Residues in contact with GLY 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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324A LYS* 1.3 75.4 - - - +
326A ASP* 1.3 65.5 + - - -
327A TYR 4.3 0.2 - - - -
328A GLN* 3.3 8.2 + - - +
329A LYS* 3.3 31.1 + - - +
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Residues in contact with ASP 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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53A GLU* 2.8 37.2 - - - +
54A VAL* 3.7 34.3 + - - +
57A VAL* 4.3 9.7 - - - +
95A LEU* 3.5 15.8 - - + +
325A GLY* 1.3 69.4 - - - -
327A TYR* 1.3 66.1 + - - +
329A LYS* 3.4 10.1 + - - +
330A ALA* 3.1 23.2 + - - +
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Residues in contact with TYR 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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94A HIS* 3.5 37.2 - + + -
95A LEU* 4.1 19.9 - - + +
98A VAL* 3.6 29.8 - - + -
285A ASP* 3.3 38.3 + - - +
288A LEU* 4.0 4.3 - - - +
289A ILE* 3.3 11.1 - - + +
323A THR* 3.7 25.1 - - + -
324A LYS 3.8 8.7 - - - +
326A ASP* 1.3 77.8 - - - +
328A GLN* 1.3 61.9 + - - +
330A ALA* 3.2 4.9 + - - +
331A LEU* 3.1 42.4 + - + +
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Residues in contact with GLN 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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319A ILE* 4.3 3.6 - - + +
320A GLN* 2.9 30.9 + - - +
323A THR* 2.5 47.9 + - - +
324A LYS* 3.3 19.6 + - - +
325A GLY 3.3 8.1 + - - +
326A ASP 3.3 0.6 - - - -
327A TYR* 1.3 79.2 - - - +
329A LYS* 1.3 89.2 + - - +
331A LEU* 3.0 5.8 + - - +
332A LEU* 2.9 42.9 + - + +
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Residues in contact with LYS 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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57A VAL* 5.2 3.6 - - + -
325A GLY* 3.3 24.5 + - - +
326A ASP* 3.8 10.8 - - - +
327A TYR 3.4 0.2 - - - -
328A GLN* 1.3 101.4 - - + +
330A ALA* 1.3 62.1 + - - +
332A LEU* 3.2 12.4 + - + +
333A TYR* 3.0 42.5 + - + +
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Residues in contact with ALA 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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57A VAL* 4.1 17.1 - - + +
61A THR* 4.2 10.1 - - + +
95A LEU* 4.0 17.9 - - + -
98A VAL* 4.4 15.3 - - + -
99A ILE* 5.1 0.9 - - + -
326A ASP 3.1 12.7 + - - +
327A TYR 3.3 10.1 - - - +
328A GLN 3.1 0.2 - - - -
329A LYS* 1.3 75.9 - - - +
331A LEU* 1.3 63.2 + - + +
332A LEU 3.2 0.2 + - - -
333A TYR* 3.2 7.6 + - - +
334A LEU* 3.1 26.7 + - - +
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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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98A VAL* 4.0 19.3 - - + -
288A LEU* 3.5 32.3 - - + -
289A ILE* 4.5 7.4 - - + -
292A MET* 3.7 26.0 - - + +
319A ILE* 3.5 29.1 - - + +
323A THR* 4.1 8.5 - - + +
327A TYR* 3.1 41.7 + - + +
328A GLN 3.0 2.9 + - - +
330A ALA* 1.3 77.5 - - - +
332A LEU* 1.3 57.6 + - - +
334A LEU* 3.3 7.6 + - + +
335A CYS* 2.8 27.5 + - - +
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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
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316A TYR* 3.4 61.4 - - + +
319A ILE* 3.7 22.7 - - + -
320A GLN* 4.2 13.2 - - + +
328A GLN* 2.9 44.0 + - + +
329A LYS* 3.5 16.6 - - + +
331A LEU* 1.3 74.8 - - - +
333A TYR* 1.3 66.0 + - - +
335A CYS* 3.0 18.2 + - + +
336A GLY* 3.2 6.8 + - - -
337A GLY 4.5 1.9 + - - -
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Residues in contact with TYR 333 (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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26A SER* 4.6 5.4 + - - +
27A VAL* 4.9 2.1 - - - +
57A VAL* 4.3 11.2 - - + -
58A ASN* 3.1 30.3 + - + +
61A THR* 3.1 42.7 - - - +
62A ASN* 3.5 19.7 - - - +
329A LYS* 3.0 40.0 + - + +
330A ALA* 3.2 3.8 + - - +
332A LEU* 1.3 75.1 - - + +
334A LEU* 1.3 64.4 + - - +
335A CYS 3.4 0.3 + - - -
336A GLY* 3.4 12.7 + - - -
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Residues in contact with LEU 334 (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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26A SER* 2.4 30.5 + - - -
27A VAL* 4.0 19.5 - - + -
61A THR* 4.5 11.2 - - + +
68A ARG* 4.2 6.1 - - - +
98A VAL* 4.2 13.5 - - + -
102A LEU* 3.6 46.2 - - + -
292A MET* 3.9 32.4 - - + +
293A VAL* 4.2 6.3 - - + -
296A SER* 4.3 8.1 - - - -
300A MET* 3.9 5.0 - - - +
330A ALA 3.1 15.6 + - - +
331A LEU* 3.6 9.0 - - + +
332A LEU 3.2 0.2 - - - -
333A TYR* 1.3 76.8 - - - +
335A CYS* 1.3 55.2 + - - +
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Residues in contact with CYS 335 (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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26A SER* 3.2 9.5 - - - -
292A MET* 3.5 14.3 - - + +
300A MET* 3.6 1.5 - - - +
304A ARG* 3.1 39.1 + - - -
315A LEU* 4.2 12.6 - - - -
316A TYR* 4.0 26.9 - - + -
319A ILE* 4.0 4.3 - - + -
331A LEU 2.8 14.2 + - - +
332A LEU* 3.0 19.0 + - + +
334A LEU* 1.3 75.0 - - - +
336A GLY* 1.3 54.2 + - - +
337A GLY 3.6 20.0 - - - +
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Residues in contact with GLY 336 (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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26A SER* 3.9 17.7 - - - +
304A ARG* 3.6 10.6 + - - -
332A LEU 3.2 6.9 + - - -
333A TYR* 3.4 12.0 + - - -
335A CYS* 1.3 78.0 - - - +
337A GLY* 1.3 56.4 + - - +
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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