Contacts of the helix formed by residues 320 - 331 (chain A) in PDB entry 3IQS
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 ARG 320 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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289A PHE* 3.6 35.6 + - + +
293A GLN* 5.0 12.3 - - - +
317A ASP* 3.3 5.7 + - - -
319A GLY* 1.3 71.6 - - - -
321A CYS* 1.3 58.8 + - - +
322A GLN 3.3 2.7 - - - -
323A GLU* 3.2 46.7 + - - +
324A GLY* 2.9 24.0 + - - +
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Residues in contact with CYS 321 (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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287A PRO 4.9 3.2 - - - +
288A CYS* 4.0 1.6 - - - -
289A PHE* 3.7 24.4 - - - +
315A TYR* 3.4 34.8 - - - +
316A ASP* 3.7 11.4 - - - +
317A ASP* 3.1 47.2 + - - +
319A GLY 3.5 0.4 - - - -
320A ARG* 1.3 77.0 - - - +
322A GLN* 1.3 59.1 + - - +
324A GLY* 3.0 2.9 + - - -
325A LEU* 2.9 34.3 + - + +
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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
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316A ASP* 3.5 33.5 + - - +
318A GLN* 4.9 9.5 + - - +
319A GLY 4.6 8.3 + - - +
320A ARG 3.3 0.2 - - - -
321A CYS* 1.3 77.4 - - - +
323A GLU* 1.3 62.6 + - - +
325A LEU* 3.4 3.1 + - - -
326A ARG* 3.2 45.0 + - - +
378A ILE* 3.8 42.0 - - + +
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Residues in contact with GLU 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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319A GLY 5.0 1.5 + - - +
320A ARG* 3.2 60.4 + - + +
322A GLN* 1.3 78.4 - - - +
324A GLY* 1.3 57.4 + - - +
326A ARG* 3.3 25.2 + - + +
327A THR* 2.9 38.1 + - - +
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Residues in contact with GLY 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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289A PHE* 4.6 9.9 - - - -
292A ALA* 3.4 29.0 - - - +
293A GLN* 5.5 0.4 - - - -
320A ARG* 2.9 14.6 + - - +
321A CYS 3.0 5.3 + - - -
323A GLU* 1.3 75.9 - - - +
325A LEU* 1.3 55.0 + - - +
327A THR* 3.2 8.8 + - - -
328A LEU* 2.9 24.6 + - - +
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Residues in contact with LEU 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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286A SER* 4.2 22.4 - - - +
287A PRO* 4.1 35.7 - - + +
292A ALA* 5.3 0.9 - - + -
314A ILE* 4.8 8.7 - - + -
315A TYR 5.1 3.1 - - - +
316A ASP* 6.3 0.4 - - + -
321A CYS* 2.9 18.2 + - + +
322A GLN* 3.8 7.2 - - - +
324A GLY* 1.3 75.8 - - - +
326A ARG* 1.3 62.9 + - - +
328A LEU* 3.4 0.8 + - + -
329A ALA* 3.1 21.1 + - - +
335A ILE* 3.2 29.1 - - + +
375A LEU* 4.0 21.8 - - + -
378A ILE* 4.4 17.9 - - + -
379A LEU* 4.0 14.8 - - + +
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Residues in contact with ARG 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 GLN* 3.2 34.4 + - - +
323A GLU* 3.3 33.2 + - + +
325A LEU* 1.3 75.5 - - - +
327A THR* 1.3 57.4 + - - +
329A ALA* 3.5 3.8 + - - +
330A GLU* 2.9 32.8 + - - +
378A ILE* 2.8 39.2 + - - +
379A LEU* 3.6 25.8 - - + +
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Residues in contact with THR 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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292A ALA 5.6 0.7 - - - -
293A GLN* 4.9 12.8 - - + -
296A ALA* 4.1 16.2 - - + -
323A GLU* 2.9 24.3 + - - +
324A GLY* 3.2 12.6 + - - -
326A ARG* 1.3 74.1 - - - +
328A LEU* 1.3 59.2 + - - +
330A GLU* 3.3 10.3 + - + +
331A ALA* 2.9 27.4 + - - +
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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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287A PRO* 4.1 26.2 - - + -
292A ALA* 3.7 19.1 - - + +
295A MET* 4.0 20.0 - - + -
296A ALA* 3.8 27.8 - - - +
299A ILE* 4.2 2.7 - - + -
307A LEU* 4.4 3.6 - - + -
309A ILE* 4.8 8.5 - - + -
324A GLY 2.9 12.7 + - - +
325A LEU* 3.4 0.9 + - + -
327A THR* 1.3 76.7 - - - +
329A ALA* 1.3 62.5 + - - +
331A ALA* 3.2 9.9 + - - +
332A GLY 3.3 0.3 + - - -
333A ALA* 3.1 47.2 + - + +
335A ILE* 3.4 26.2 - - + -
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Residues in contact with ALA 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 LEU 3.1 16.7 + - - +
326A ARG* 3.8 6.5 - - - +
328A LEU* 1.3 72.9 - - - +
330A GLU* 1.3 63.0 + - - +
332A GLY* 2.9 20.1 + - - -
333A ALA 3.6 15.6 - - - +
335A ILE* 3.8 8.2 - - + +
379A LEU* 4.6 15.7 - - + -
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Residues in contact with GLU 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 ARG* 2.9 20.9 + - - +
327A THR* 3.5 11.1 - - + +
329A ALA* 1.3 76.7 - - - +
331A ALA* 1.3 61.3 + - - +
332A GLY* 3.2 1.9 + - - -
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Residues in contact with ALA 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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296A ALA* 3.7 24.9 - - + +
299A ILE* 3.2 27.9 - - + +
300A SER* 3.9 13.3 + - - +
327A THR 2.9 13.8 + - - +
328A LEU 3.4 10.8 - - - +
329A ALA 3.1 0.4 - - - -
330A GLU* 1.3 76.7 - - - +
332A GLY* 1.3 56.3 + - - +
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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