Contacts of the helix formed by residues 326 - 338 (chain A) in PDB entry 4IRI
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 ASP 326 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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311A SER 3.8 8.5 - - - +
312A CYS* 3.0 23.2 + - + +
324A MET* 4.5 0.2 - - - -
325A THR* 1.3 77.9 - - - +
327A PRO* 1.3 67.3 - - - +
328A ASP* 3.0 19.2 + - - +
329A GLU* 3.1 25.5 + - - +
330A VAL* 3.3 14.2 + - - +
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Residues in contact with PRO 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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324A MET* 3.7 22.9 - - + +
325A THR 3.8 3.6 - - - +
326A ASP* 1.3 89.1 - - - +
328A ASP* 1.3 67.0 + - - +
330A VAL* 3.5 4.1 + - + +
331A ALA* 3.2 21.1 + - - +
345A TYR* 3.7 35.8 - - + -
348A LEU* 5.7 0.3 - - - +
369A TYR* 3.6 41.5 - - + +
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Residues in contact with ASP 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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326A ASP* 3.1 8.1 + - - +
327A PRO* 1.3 84.1 - - - +
329A GLU* 1.3 60.3 + - - +
331A ALA* 3.3 7.2 + - - +
332A ARG* 2.9 27.4 + - - +
345A TYR* 4.1 14.9 + - - +
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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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312A CYS* 4.1 13.0 - - + -
326A ASP* 3.1 31.3 + - + +
328A ASP* 1.3 72.8 - - - +
330A VAL* 1.3 67.6 + - - +
332A ARG* 2.6 42.4 + - - +
333A ARG* 3.0 49.2 + - - +
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Residues in contact with VAL 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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299A PHE* 4.4 3.2 - - + -
300A LEU* 3.9 27.8 - - + -
303A LEU* 4.5 9.2 - - + -
312A CYS* 3.6 33.4 - - - +
313A ILE* 4.2 9.0 - - + -
324A MET* 4.2 20.6 - - + -
326A ASP 3.3 13.5 + - - +
327A PRO 3.7 8.1 - - - +
329A GLU* 1.3 78.2 - - - +
331A ALA* 1.3 62.2 + - - +
333A ARG* 3.2 6.1 + - - +
334A TRP* 3.0 21.8 + - - +
348A LEU* 4.1 13.9 - - + -
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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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327A PRO 3.2 9.1 + - - +
328A ASP* 3.6 8.7 - - - +
329A GLU 3.2 0.6 - - - -
330A VAL* 1.3 77.3 - - - +
332A ARG* 1.3 67.8 + - - +
334A TRP* 4.5 0.9 - - - -
335A GLY* 3.0 17.8 + - - -
343A MET* 3.5 11.5 - - + +
344A ASN* 3.5 39.3 - - - +
345A TYR* 3.6 6.5 - - - +
348A LEU* 4.0 15.2 - - + +
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Residues in contact with ARG 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 ASP 2.9 14.6 + - - +
329A GLU* 2.6 51.2 + - - +
331A ALA* 1.3 76.6 - - - +
333A ARG* 1.3 68.2 + - - +
335A GLY* 3.5 1.9 + - - -
336A GLU* 3.0 54.1 + - - +
343A MET* 5.0 5.8 - - - +
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Residues in contact with ARG 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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299A PHE* 4.0 13.4 - - + -
303A LEU* 3.7 25.9 - - - +
308A SER 5.8 0.4 + - - -
309A ASN* 2.7 30.8 + - - +
311A SER* 4.9 7.9 + - - -
312A CYS* 4.3 16.6 - - - +
329A GLU* 3.0 36.7 + - - +
330A VAL* 3.5 9.6 - - - +
332A ARG* 1.3 93.1 - - - +
334A TRP* 1.3 59.3 + - - +
336A GLU* 3.2 13.6 + - - +
337A ARG* 3.0 27.5 + - - +
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Residues in contact with TRP 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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294A ILE* 3.5 41.1 - - + -
296A LEU* 3.5 39.3 - - + +
299A PHE* 3.6 40.8 - + + -
330A VAL 3.0 16.4 + - - +
331A ALA 3.4 2.7 + - - +
333A ARG* 1.3 72.9 - - - +
335A GLY* 1.3 65.1 + - - +
337A ARG* 3.3 4.4 + - + +
338A LYS* 3.1 54.9 + - + +
343A MET* 3.9 18.2 - - + -
348A LEU* 3.8 23.8 - - + +
16C C 4.0 8.5 - - - -
17C T 2.9 28.8 + - - -
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Residues in contact with GLY 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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331A ALA 3.0 9.7 + - - -
332A ARG* 3.7 4.7 - - - -
334A TRP* 1.3 79.6 - - - +
336A GLU* 1.3 59.8 + - - +
338A LYS* 3.3 0.4 + - - -
339A SER* 3.0 4.7 + - - -
340A LYS* 2.9 50.6 + - - -
341A PRO* 5.0 3.3 - - - +
343A MET* 3.5 14.7 - - - +
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Residues in contact with GLU 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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332A ARG* 3.0 39.7 + - - +
333A ARG* 3.3 14.6 - - - +
335A GLY* 1.3 74.6 - - - +
337A ARG* 1.3 65.3 + - - +
339A SER* 3.3 15.3 + - - +
341A PRO* 6.3 0.2 - - - -
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Residues in contact with ARG 337 (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 GLY* 4.9 5.7 - - - -
294A ILE* 3.8 40.0 - - + +
299A PHE* 4.0 19.7 - - + -
302A GLU* 2.7 41.5 + - - -
333A ARG 3.0 16.5 + - - +
334A TRP* 3.5 12.8 - - + +
336A GLU* 1.3 80.2 - - - +
338A LYS* 1.3 58.8 + - - +
339A SER* 3.8 1.2 + - - -
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Residues in contact with LYS 338 (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 GLY* 3.6 49.6 + - - +
294A ILE* 4.1 11.5 + - + +
334A TRP* 3.1 53.8 + - + +
335A GLY 4.1 1.8 - - - +
337A ARG* 1.3 78.5 - - - +
339A SER* 1.3 67.9 + - - +
340A LYS* 3.1 20.3 + - + +
16C C 3.2 15.2 + - - -
17C T 3.1 36.5 + - - +
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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