Contacts of the helix formed by residues 311 - 325 (chain A) in PDB entry 2AC3
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 CYS 311 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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303A CYS* 3.3 15.5 - - + -
304A GLY 3.7 5.8 + - - +
305A TRP* 3.8 20.8 - - - +
310A ALA* 1.3 75.3 - - - +
312A PRO* 1.3 70.8 - - - +
313A ALA* 3.5 10.3 - - - -
314A CYS* 3.2 16.9 - - + +
315A GLN* 3.3 22.3 + - - +
531A ZN 2.3 36.3 - - - -
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Residues in contact with PRO 312 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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310A ALA 4.1 5.2 - - - +
311A CYS* 1.3 86.2 - - - +
313A ALA* 1.3 62.1 + - + +
315A GLN* 3.4 5.3 + - + +
316A ASN* 3.0 29.0 + - - +
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Residues in contact with ALA 313 (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 CYS* 3.5 23.1 - - + -
311A CYS* 3.4 7.4 - - - -
312A PRO* 1.3 79.9 - - + +
314A CYS* 1.3 64.2 + - - +
316A ASN* 3.3 11.7 + - - +
317A MET* 3.0 26.0 + - - +
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Residues in contact with CYS 314 (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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297A GLY* 3.2 30.0 - - - +
298A ARG* 4.1 1.8 - - - -
299A CYS* 3.5 19.5 - - - +
303A CYS* 3.8 8.7 - - - -
305A TRP* 4.0 16.2 - - + +
311A CYS* 3.2 14.6 - - + +
313A ALA* 1.3 79.1 - - - +
315A GLN* 1.3 58.0 + - - +
317A MET* 3.2 1.7 + - - +
318A LEU* 2.9 22.7 + - - +
531A ZN 2.5 31.8 - - - -
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Residues in contact with GLN 315 (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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311A CYS 3.3 14.2 + - - +
312A PRO* 3.4 5.4 + - + +
313A ALA 3.3 0.2 - - - -
314A CYS* 1.3 76.8 - - - +
316A ASN* 1.3 60.3 + - - +
318A LEU* 3.5 19.2 - - + +
319A PHE* 3.0 63.3 + - + -
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Residues in contact with ASN 316 (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 PRO 3.0 13.5 + - - +
313A ALA* 3.4 13.9 - - - +
315A GLN* 1.3 76.3 - - - +
317A MET* 1.3 66.0 + - - +
319A PHE* 3.4 11.9 + - - +
320A GLU* 3.0 37.8 + - - +
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Residues in contact with MET 317 (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 VAL 4.6 0.8 - - - +
297A GLY* 3.8 2.2 - - - -
298A ARG* 3.7 38.6 - - + +
299A CYS* 4.2 8.3 - - - +
313A ALA 3.0 17.1 + - - +
314A CYS 3.5 7.6 - - - +
316A ASN* 1.3 82.0 - - - +
318A LEU* 1.3 61.0 + - - +
320A GLU* 3.3 22.0 + - + +
321A SER* 2.8 30.8 + - - -
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Residues in contact with LEU 318 (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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295A PHE* 3.5 35.7 - - + +
296A VAL* 4.0 2.7 - - - +
297A GLY* 3.3 14.5 - - - +
314A CYS 2.9 13.5 + - - +
315A GLN* 3.5 25.1 - - + +
316A ASN 3.3 0.2 - - - -
317A MET* 1.3 77.0 - - - +
319A PHE* 1.3 64.3 + - + +
321A SER* 3.1 4.3 + - - -
322A ILE* 2.8 54.6 + - + +
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Residues in contact with PHE 319 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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315A GLN* 3.0 53.7 + - + +
316A ASN* 3.6 9.9 - - - +
317A MET 3.3 0.2 - - - -
318A LEU* 1.3 82.1 - - + +
320A GLU* 1.3 57.0 + - - +
322A ILE* 3.5 17.0 + - + +
323A GLN* 3.0 41.2 + - + +
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Residues in contact with GLU 320 (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 ASN* 3.0 31.4 + - - +
317A MET* 3.5 24.5 - - + +
319A PHE* 1.3 74.8 - - - +
321A SER* 1.3 60.2 + - - +
323A GLN* 3.4 8.7 + - + +
324A GLU* 2.9 34.3 + - + +
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Residues in contact with SER 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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295A PHE* 3.5 29.8 - - - +
296A VAL 4.1 15.5 + - - -
317A MET 2.8 20.2 + - - -
318A LEU* 3.4 4.7 - - - -
320A GLU* 1.3 70.3 - - - +
322A ILE* 1.3 67.5 + - - +
324A GLU* 3.4 10.3 + - - +
325A GLY 2.9 18.5 + - - -
326A LYS 4.1 8.0 + - - -
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Residues in contact with ILE 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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279A TRP* 4.0 30.3 - - + +
295A PHE* 3.9 28.3 - - + -
318A LEU* 2.8 42.2 + - + +
319A PHE* 3.7 18.2 - - + +
321A SER* 1.3 74.9 - - - +
323A GLN* 1.3 62.5 + - + +
325A GLY* 3.0 20.4 + - - -
351A ARG* 4.6 2.8 - - - +
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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
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319A PHE* 3.0 25.4 + - + +
320A GLU* 3.9 6.8 - - - +
321A SER 3.3 0.2 - - - -
322A ILE* 1.3 79.5 - - + +
324A GLU* 1.3 61.4 + - - +
351A ARG* 3.2 24.2 + - - +
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Residues in contact with GLU 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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320A GLU* 2.9 21.9 + - + +
321A SER* 3.7 9.1 - - - +
323A GLN* 1.3 75.9 - - - +
325A GLY* 1.3 61.7 + - - +
326A LYS* 3.3 40.2 + - + +
351A ARG* 3.4 23.6 + - - +
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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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279A TRP* 4.6 2.6 - - - -
295A PHE* 3.8 10.5 - - - -
321A SER 2.9 9.7 + - - -
322A ILE 3.0 13.6 + - - -
324A GLU* 1.3 77.0 - - - +
326A LYS* 1.3 62.5 + - - +
327A TYR* 3.4 19.4 - - - -
349A LEU 5.0 2.8 - - - +
351A ARG* 4.1 15.5 - - - -
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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