Contacts of the helix formed by residues 296 - 315 (chain A) in PDB entry 3DAN
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 GLY 296 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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292A ILE 3.8 1.4 + - - -
293A GLY 3.5 10.1 + - - -
294A LEU 3.3 4.2 - - - -
295A ALA* 1.3 79.1 - - - +
297A GLU* 1.3 66.4 + - - -
298A ASN* 3.2 3.8 - - - -
299A LEU* 3.2 9.7 + - - +
300A HIS* 3.1 23.4 + - - -
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Residues in contact with GLU 297 (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 GLY* 1.3 67.9 - - - -
298A ASN* 1.3 59.5 + - - +
300A HIS* 3.4 10.0 - - + +
301A THR* 2.8 45.3 + - + +
449A SER* 3.4 24.6 + - - +
469A LYS* 3.9 23.9 + - - -
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Residues in contact with ASN 298 (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 ALA 5.4 3.1 - - - +
296A GLY* 3.2 1.7 - - - +
297A GLU* 1.3 77.1 - - - +
299A LEU* 1.3 61.4 + - - +
301A THR* 2.8 26.0 + - - -
302A GLN* 3.3 25.6 - - - +
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Residues in contact with LEU 299 (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 ILE* 3.8 31.0 - - + -
295A ALA* 3.4 32.6 + - + +
296A GLY 3.2 9.0 + - - +
298A ASN* 1.3 77.9 - - - +
300A HIS* 1.3 66.6 + - - +
302A GLN* 3.1 10.2 + - - +
303A LEU* 2.9 35.3 + - + +
329A LEU* 3.9 22.9 - - + -
333A VAL* 4.3 3.4 - - + -
392A TYR* 4.6 0.4 - - + -
394A PRO* 3.7 33.7 - - + -
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Residues in contact with HIS 300 (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 ILE* 2.8 44.4 + - + +
293A GLY* 4.1 6.2 + - - -
296A GLY* 3.1 19.3 + - - -
297A GLU* 3.1 13.6 + - + +
299A LEU* 1.3 78.3 - - + +
301A THR* 1.3 57.6 + - + +
303A LEU* 3.4 1.4 + - - +
304A ALA* 2.9 31.4 + - - +
444A PHE* 3.8 22.4 - + + -
448A ASP 3.5 16.6 - - - +
449A SER* 2.8 33.0 - - - +
450A PHE* 3.7 24.4 + + - -
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Residues in contact with THR 301 (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 GLU* 2.8 32.6 + - + +
298A ASN* 2.8 25.7 + - - -
300A HIS* 1.3 73.8 - - + +
302A GLN* 1.3 65.2 + - - +
304A ALA* 3.9 5.3 - - - +
305A GLU* 3.1 25.3 + - - +
448A ASP 5.0 4.3 - - - +
449A SER* 6.3 0.4 - - - -
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Residues in contact with GLN 302 (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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298A ASN* 3.3 29.6 + - - +
299A LEU* 3.1 15.8 + - - +
301A THR* 1.3 81.3 + - - +
303A LEU* 1.3 64.7 + - - +
305A GLU* 3.6 5.6 + - - +
306A GLU* 3.0 24.8 + - - +
329A LEU* 3.7 22.4 - - + +
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Residues in contact with LEU 303 (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 ILE* 4.4 5.4 - - + -
299A LEU* 2.9 42.8 + - + +
300A HIS 3.8 3.8 - - - +
302A GLN* 1.3 74.6 - - - +
304A ALA* 1.3 60.4 + - - +
306A GLU* 3.3 2.7 + - - +
307A ILE* 2.8 39.9 + - + +
329A LEU* 3.7 25.4 - - + -
330A THR* 3.7 29.8 - - - +
333A VAL* 4.1 10.8 - - + -
440A VAL* 4.3 8.1 - - + -
444A PHE* 3.6 35.9 - - + -
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Residues in contact with ALA 304 (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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300A HIS 2.9 18.5 + - - +
301A THR* 3.9 6.1 - - - +
303A LEU* 1.3 75.5 - - - +
305A GLU* 1.3 63.2 + - - +
307A ILE* 4.7 0.7 - - - -
308A ARG* 3.0 62.6 + - - +
444A PHE* 4.1 18.7 - - + -
447A TYR 4.7 0.9 - - - +
448A ASP* 4.8 5.8 - - + +
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Residues in contact with GLU 305 (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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301A THR 3.1 16.9 + - - +
302A GLN* 3.8 6.1 - - - +
304A ALA* 1.3 78.4 - - - +
306A GLU* 1.3 63.3 + - - +
308A ARG* 4.4 1.7 - - - +
309A GLY* 2.9 32.7 + - - -
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Residues in contact with GLU 306 (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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302A GLN 3.0 18.4 + - - +
303A LEU* 3.3 4.1 + - - +
305A GLU* 1.3 84.3 + - - +
307A ILE* 1.3 58.0 + - - +
309A GLY 3.9 0.2 - - - -
310A ALA* 3.0 30.0 + - - +
326A GLN 4.4 4.5 - - - +
327A MET* 3.3 22.1 - - + -
328A PRO* 3.1 14.4 - - + +
329A LEU* 2.7 33.0 + - + +
330A THR* 2.8 38.5 + - - -
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Residues in contact with ILE 307 (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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303A LEU* 2.8 28.5 + - + +
304A ALA* 4.0 2.9 - - - +
306A GLU* 1.3 70.0 - - - +
308A ARG* 1.3 68.5 + - + +
310A ALA 3.4 0.2 + - - -
311A ILE* 3.1 37.8 + - + +
327A MET* 3.8 15.8 - - + +
330A THR* 3.3 26.7 - - - +
440A VAL* 4.0 17.7 - - + +
441A ILE* 3.9 39.0 - - + +
444A PHE* 3.8 26.5 - - + -
445A ARG* 4.1 4.3 - - + -
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Residues in contact with ARG 308 (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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304A ALA* 3.0 27.4 + - - +
305A GLU* 4.4 2.5 - - - +
307A ILE* 1.3 77.1 - - + +
309A GLY* 1.3 62.4 + - - +
311A ILE* 3.5 8.3 + - + +
312A LYS* 3.1 26.3 + - - +
444A PHE 2.8 29.9 + - - +
445A ARG* 4.3 12.9 + - + +
447A TYR 3.0 14.6 + - - -
448A ASP* 2.7 31.5 + - - +
471A ALA* 3.3 24.9 + - - +
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Residues in contact with GLY 309 (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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305A GLU* 2.9 24.7 + - - -
306A GLU* 4.0 0.4 - - - -
308A ARG* 1.3 78.0 - - - +
310A ALA* 1.3 56.6 + - - +
312A LYS* 3.4 16.1 + - - -
313A SER* 2.9 35.1 + - - -
314A TYR* 5.9 0.2 - - - -
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Residues in contact with ALA 310 (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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306A GLU 3.0 19.4 + - - +
309A GLY* 1.3 73.1 - - - +
311A ILE* 1.3 61.5 + - - +
314A TYR* 2.8 43.8 + - + +
315A GLY 3.2 4.5 + - - -
323A ALA* 3.7 15.8 - - - +
326A GLN 4.0 10.3 - - - +
327A MET* 3.7 27.1 - - + -
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Residues in contact with ILE 311 (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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307A ILE* 3.1 26.5 + - + +
308A ARG* 3.8 7.6 - - - +
310A ALA* 1.3 76.0 - - - +
312A LYS* 1.3 57.8 + - - +
315A GLY* 3.0 17.8 + - - +
316A ASP 3.0 0.3 + - - -
317A GLY* 2.9 46.7 + - - +
318A ASN 3.6 14.6 - - - +
319A VAL* 3.9 14.1 - - + -
323A ALA* 4.4 2.7 - - + -
327A MET* 3.9 12.1 - - + -
441A ILE* 4.3 1.8 - - + -
445A ARG* 3.4 46.2 - - + +
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Residues in contact with LYS 312 (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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308A ARG 3.1 12.2 + - - +
309A GLY* 3.8 15.9 + - - -
311A ILE* 1.3 83.6 - - - +
313A SER* 1.3 82.2 + - - +
316A ASP* 3.6 15.2 + - - +
317A GLY* 4.0 8.8 + - - +
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Residues in contact with SER 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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309A GLY 2.9 13.2 + - - -
312A LYS* 1.3 100.4 + - - +
314A TYR* 1.3 81.1 + - - +
316A ASP* 4.4 2.8 + - - +
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Residues in contact with TYR 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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310A ALA* 2.8 30.2 + - + +
313A SER* 1.3 87.3 - - - +
315A GLY* 1.3 59.4 + - - +
316A ASP* 3.4 1.2 - - - +
320A THR* 4.2 4.9 + - - -
322A GLU* 4.4 10.5 - - + +
323A ALA* 3.9 15.5 - - - -
326A GLN* 3.6 45.6 + - + -
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Residues in contact with GLY 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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310A ALA 3.2 4.6 + - - -
311A ILE 3.0 11.4 + - - -
314A TYR* 1.3 76.6 - - - +
316A ASP* 1.3 73.2 + - - +
317A GLY 3.1 2.7 - - - -
318A ASN* 3.1 33.3 + - - +
320A THR* 3.9 18.6 - - - +
323A ALA* 4.0 2.9 - - - +
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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