Contacts of the helix formed by residues 320 - 334 (chain A) in PDB entry 1IEQ
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 320 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287A GLU* 5.8 3.6 - - - -
290A ASP* 4.1 19.6 + - - -
297A GLY* 5.6 5.5 - - - -
300A TYR* 4.6 7.0 + - - +
317A VAL* 3.3 18.8 - - + +
319A ASN* 1.3 75.3 - - + +
321A TYR* 1.3 58.9 + - - +
322A GLN* 3.3 3.6 - - - +
323A GLN* 3.4 35.0 + - + +
324A PHE 3.1 20.4 + - - -
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Residues in contact with TYR 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A THR* 4.2 10.1 - - + -
35A ILE* 3.6 27.8 - - + -
39A VAL* 3.8 31.3 + - + -
44A VAL* 3.2 41.8 - - + +
48A ASN* 3.7 23.6 - - + -
50A ILE* 5.0 0.9 - - + -
317A VAL* 4.2 7.6 - - + -
319A ASN 2.8 30.7 + - - -
320A LYS* 1.3 69.6 - - - +
322A GLN* 1.3 85.2 + - + +
324A PHE* 3.7 4.3 - - - -
325A ILE* 2.8 39.6 + - + +
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Residues in contact with GLN 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A ASN* 5.9 0.9 - - - -
320A LYS* 3.3 1.2 - - - +
321A TYR* 1.3 96.9 - - + +
323A GLN* 1.3 56.9 + - - +
325A ILE* 4.1 2.8 - - - +
326A SER* 2.9 38.2 + - - -
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Residues in contact with GLN 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A TYR* 3.3 38.5 - - + +
320A LYS* 3.4 46.5 + - + +
321A TYR 3.3 0.2 - - - -
322A GLN* 1.3 80.1 - - - +
324A PHE* 1.3 63.3 + - - +
326A SER* 3.8 4.1 - - - -
327A ILE* 3.0 40.1 + - + +
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Residues in contact with PHE 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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29A ILE* 4.6 3.6 - - + -
32A MET* 4.1 12.3 - - + -
33A THR* 3.3 35.2 - - + -
289A ILE* 4.5 2.7 - - + -
300A TYR* 3.7 30.0 - + - +
304A VAL* 4.0 28.7 - - + -
308A ILE* 4.8 2.7 - - + -
315A ILE* 3.6 38.4 - - + -
317A VAL* 4.1 11.9 - - + -
320A LYS 3.1 9.2 + - - +
321A TYR 3.7 5.2 - - - +
323A GLN* 1.3 80.8 - - - +
325A ILE* 1.3 66.4 + - - +
327A ILE* 3.9 1.2 - - - +
328A LEU* 3.0 48.1 + - + +
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Residues in contact with ILE 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ALA* 5.8 5.4 - - + +
29A ILE* 3.9 19.2 - - + +
30A GLY* 5.2 1.6 - - - -
33A THR* 3.8 25.8 - - + +
48A ASN* 3.8 45.3 - - + +
50A ILE* 4.5 8.3 - - + -
321A TYR* 2.8 28.1 + - + +
322A GLN* 4.1 2.7 - - - +
324A PHE* 1.3 75.4 - - + +
326A SER* 1.3 58.8 + - - +
328A LEU* 4.0 0.9 - - - +
329A THR* 2.6 42.4 + - - +
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Residues in contact with SER 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A GLN* 2.9 25.3 + - - -
323A GLN* 3.8 5.2 - - - -
325A ILE* 1.3 79.2 - - - +
327A ILE* 1.3 59.6 + - - +
329A THR* 3.3 6.1 + - - -
330A GLY* 3.0 24.8 + - - -
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Residues in contact with ILE 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A TYR* 3.5 30.7 - - + -
301A SER* 3.9 24.2 - - - +
304A VAL* 3.8 16.8 - - + -
323A GLN* 3.0 27.9 + - + +
324A PHE 3.9 2.5 - - - +
326A SER* 1.3 75.7 - - - +
328A LEU* 1.3 66.2 + - - +
330A GLY* 3.2 2.8 + - - +
331A HIS* 3.1 47.2 + - + +
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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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29A ILE* 3.9 31.4 - - + -
32A MET* 4.2 22.7 - - + -
304A VAL* 3.9 16.6 - - + +
308A ILE* 4.3 6.3 - - + -
324A PHE* 3.0 41.2 + - + +
325A ILE 4.1 2.2 - - - +
327A ILE* 1.3 73.9 - - - +
329A THR* 1.3 67.7 + - - +
331A HIS* 3.2 2.5 + - - +
332A VAL* 3.0 28.4 + - + +
337A ILE* 3.5 30.7 - - + -
342A ILE* 4.3 5.8 - - + -
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Residues in contact with THR 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LEU* 4.3 11.2 - - + -
26A ALA* 5.9 1.9 - - - -
29A ILE* 3.4 20.0 - - - +
325A ILE* 2.6 31.7 + - - +
326A SER* 3.4 6.3 - - - -
328A LEU* 1.3 76.0 - - - +
330A GLY* 1.3 64.4 + - - +
332A VAL* 3.1 3.8 + - - +
333A ASN* 2.9 42.7 + - - +
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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 SER 3.0 14.0 + - - -
327A ILE* 3.2 3.6 + - - -
328A LEU 3.2 0.4 - - - -
329A THR* 1.3 79.1 - - - +
331A HIS* 1.3 58.1 + - - +
333A ASN* 3.2 7.9 + - - +
334A GLY* 2.8 27.9 + - - -
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Residues in contact with HIS 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A SER* 3.1 45.8 + - - -
304A VAL* 4.5 3.4 - - - +
305A LYS* 3.7 28.8 + - + +
327A ILE* 3.1 27.0 + - + +
328A LEU 3.6 8.1 - - - +
330A GLY* 1.3 76.0 - - - +
332A VAL* 1.3 60.7 + - - +
334A GLY 3.3 1.0 + - - -
335A GLY 3.0 3.3 + - - -
336A VAL* 2.9 53.1 + - + +
337A ILE* 3.4 20.8 + - + +
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Residues in contact with VAL 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LEU* 4.0 32.1 - - + -
29A ILE* 4.6 2.0 - - + -
328A LEU* 3.0 20.8 + - + +
329A THR 3.7 5.2 - - - +
331A HIS* 1.3 72.6 - - - +
333A ASN* 1.3 67.9 + - - +
335A GLY* 2.9 14.4 + - - -
337A ILE* 3.5 21.5 - - + +
339A MET* 4.2 21.3 - - + +
342A ILE* 3.9 29.2 - - + -
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Residues in contact with ASN 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LEU* 3.6 17.9 - - - +
329A THR* 2.9 37.2 + - - +
330A GLY* 3.6 7.6 - - - +
332A VAL* 1.3 76.5 - - - +
334A GLY* 1.3 59.3 + - - +
335A GLY 3.6 0.3 + - - -
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Residues in contact with GLY 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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330A GLY 2.8 15.5 + - - -
331A HIS* 3.7 1.3 - - - -
332A VAL 3.0 0.4 - - - -
333A ASN* 1.3 79.3 - - - +
335A GLY* 1.3 58.8 - - - +
336A VAL* 3.3 10.6 + - - +
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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