Contacts of the helix formed by residues 311 - 332 (chain A) in PDB entry 1B43
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 GLU 311 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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300A LEU* 4.9 1.8 - - + -
304A CYS* 3.6 28.3 - - + +
305A ASP* 4.4 12.6 - - - +
309A PHE 3.3 3.2 + - - +
310A SER* 1.3 69.5 + - - +
312A GLU* 1.3 61.7 + - - +
314A VAL* 4.1 0.2 - - - +
315A LYS* 2.9 59.5 + - - +
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Residues in contact with GLU 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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310A SER* 3.3 7.4 + - - +
311A GLU* 1.3 79.9 - - - +
313A ARG* 1.3 54.8 + - - +
315A LYS* 3.2 7.6 + - - +
316A ASN* 2.8 37.5 + - + +
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Residues in contact with ARG 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A TYR* 3.0 36.9 + - + +
310A SER* 3.1 23.4 + - - +
312A GLU* 1.3 82.7 - - - +
314A VAL* 1.3 58.0 + - - +
316A ASN* 3.3 13.5 + - - +
317A GLY* 2.9 24.3 + - - -
320A ARG* 5.1 1.5 + - - +
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Residues in contact with VAL 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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61A PHE* 3.7 23.0 - - + -
62A TYR* 3.5 15.5 - - - +
299A ILE* 4.0 17.5 - - + +
300A LEU* 3.9 18.2 - - + -
303A LEU* 4.2 5.6 - - + -
304A CYS* 3.8 11.4 - - - -
309A PHE* 3.5 28.7 - - + -
310A SER 2.8 25.9 + - - +
311A GLU 4.1 0.2 - - - +
313A ARG* 1.3 71.9 - - - +
315A LYS* 1.3 57.8 + - - +
317A GLY* 3.0 2.9 + - - -
318A LEU* 2.9 29.3 + - + +
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Residues in contact with LYS 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A LEU* 3.9 30.2 - - + +
311A GLU* 2.9 56.7 + - - +
312A GLU* 3.5 6.1 - - - +
314A VAL* 1.3 75.0 - - - +
316A ASN* 1.3 63.1 + - - +
318A LEU* 3.2 20.5 + - + +
319A GLU* 3.3 19.7 + - - +
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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 GLU* 2.8 18.6 + - + +
313A ARG* 3.6 13.9 - - - +
314A VAL 3.2 0.2 - - - -
315A LYS* 1.3 76.1 - - - +
317A GLY* 1.3 61.1 + - - +
319A GLU* 3.4 9.9 + - - +
320A ARG* 3.2 48.3 + - - +
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Residues in contact with GLY 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A PHE* 4.2 5.6 - - - -
62A TYR* 5.1 0.4 - - - -
65A ILE* 3.4 19.3 - - - +
313A ARG 2.9 13.5 + - - -
314A VAL 3.0 5.3 + - - -
316A ASN* 1.3 78.4 - - - +
318A LEU* 1.3 55.5 + - - +
320A ARG* 3.3 21.8 + - - +
321A LEU* 2.8 29.8 + - - +
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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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61A PHE* 4.2 8.7 - - + -
294A PRO* 4.4 6.7 - - + -
296A GLU* 3.9 47.8 - - + +
299A ILE* 3.3 37.7 - - + -
300A LEU* 4.3 15.7 - - + -
314A VAL* 2.9 22.7 + - + +
315A LYS* 3.2 13.4 + - + +
317A GLY* 1.3 77.2 - - - +
319A GLU* 1.3 57.4 - - - +
321A LEU* 3.4 11.9 + - + +
322A LYS* 3.0 35.1 + - - +
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Residues in contact with GLU 319 (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 GLU* 3.9 11.3 - - - +
315A LYS 3.3 14.6 + - - +
316A ASN* 3.8 12.1 - - - +
317A GLY 3.3 0.2 - - - -
318A LEU* 1.3 74.9 - - - +
320A ARG* 1.3 61.5 + - + +
322A LYS* 3.5 29.8 + - - +
323A LYS* 3.0 28.1 + - - +
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Residues in contact with ARG 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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62A TYR* 4.7 16.2 + - - +
65A ILE* 3.4 22.2 - - + +
66A ASN* 3.1 17.4 - - - +
69A GLU* 2.9 45.6 + - + +
313A ARG* 5.1 1.2 + - - +
316A ASN* 3.2 37.4 + - - +
317A GLY* 3.5 26.6 - - - +
319A GLU* 1.3 74.5 - - + +
321A LEU* 1.3 60.0 + - - +
323A LYS* 3.4 10.0 + - + +
324A ALA* 2.9 30.0 + - - +
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Residues in contact with LEU 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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61A PHE* 5.0 0.7 - - + -
65A ILE* 4.2 18.8 - - + +
68A MET* 3.9 26.9 - - + -
141A MET* 3.8 32.5 - - + +
143A ILE* 4.7 3.8 - - + -
294A PRO* 3.8 27.6 - - + -
317A GLY 2.8 17.3 + - - +
318A LEU* 3.5 15.9 - - + +
319A GLU 3.2 0.2 - - - -
320A ARG* 1.3 77.7 - - - +
322A LYS* 1.3 56.1 + - - +
324A ALA* 3.1 5.5 + - - +
325A ILE* 2.9 52.8 + - + +
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Residues in contact with LYS 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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293A ASP* 4.9 6.3 - - - +
294A PRO* 4.1 23.1 - - + -
296A GLU* 3.4 31.6 + - - +
318A LEU 3.0 19.3 + - - +
319A GLU* 3.5 38.2 + - - +
321A LEU* 1.3 76.1 - - - +
323A LYS* 1.3 62.3 + - - +
325A ILE* 3.2 8.9 + - - +
326A LYS* 3.1 24.9 + - - +
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Residues in contact with LYS 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 GLU 3.0 18.6 + - - +
320A ARG* 3.7 10.5 - - + +
322A LYS* 1.3 76.6 - - - +
324A ALA* 1.3 61.1 + - - +
326A LYS* 3.5 5.8 + - - +
327A SER* 2.8 34.6 + - - +
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Residues in contact with ALA 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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65A ILE 5.3 0.2 - - - +
68A MET* 3.7 47.8 - - + +
69A GLU* 4.3 6.7 - - + +
320A ARG 2.9 18.6 + - - +
321A LEU* 3.1 5.8 + - - +
323A LYS* 1.3 77.6 - - - +
325A ILE* 1.3 62.0 + - - +
327A SER* 3.7 5.6 - - - -
328A GLY* 3.2 19.4 + - - -
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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
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68A MET* 3.9 19.1 - - + -
141A MET 4.3 2.7 - - - +
143A ILE* 5.8 0.9 - - + -
291A TRP* 3.9 27.1 - - + +
292A ARG 3.3 22.9 - - - +
293A ASP* 4.0 13.7 - - - +
294A PRO* 3.9 18.6 - - + -
321A LEU* 2.9 35.4 + - + +
322A LYS* 3.2 6.9 + - - +
324A ALA* 1.3 74.1 - - - +
326A LYS* 1.3 65.8 + - - +
327A SER 3.5 0.3 + - - -
328A GLY* 3.5 7.7 + - - -
329A LYS* 3.2 30.6 + - - +
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Residues in contact with LYS 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 LYS 3.1 15.3 + - - +
323A LYS* 3.9 6.7 - - - +
325A ILE* 1.3 77.5 - - - +
327A SER* 1.3 63.9 + - - +
329A LYS* 3.2 28.0 + - + +
330A GLN* 4.1 2.3 + - - +
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Residues in contact with SER 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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19A TYR* 4.6 16.3 + - - -
323A LYS* 2.8 28.7 + - - +
324A ALA* 3.7 6.9 - - - -
325A ILE 3.3 0.2 - - - -
326A LYS* 1.3 75.5 - - - +
328A GLY* 1.3 58.3 + - - +
329A LYS 3.0 9.9 + - - -
330A GLN* 3.5 15.6 + - - +
331A SER* 4.6 1.6 + - - -
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Residues in contact with GLY 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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19A TYR* 6.0 2.0 - - - -
73A LYS* 3.4 27.8 - - - -
324A ALA 3.2 12.6 + - - -
325A ILE 3.5 4.4 + - - -
326A LYS 3.4 0.4 - - - -
327A SER* 1.3 77.8 - - - +
329A LYS* 1.3 56.5 + - - +
330A GLN 3.6 0.4 - - - -
331A SER* 2.8 23.9 + - - -
332A THR* 3.9 5.4 - - - +
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Residues in contact with LYS 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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291A TRP 4.6 9.1 + - - -
293A ASP* 4.2 18.6 + - - -
325A ILE* 3.2 32.7 - - - +
326A LYS* 3.2 19.4 - - + +
327A SER 3.0 1.0 - - - -
328A GLY* 1.3 77.3 - - - +
330A GLN* 1.3 64.5 + - - +
331A SER 3.2 2.0 - - - -
332A THR* 2.8 29.2 + - + +
333A LEU* 4.0 2.1 + - - +
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Residues in contact with GLN 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 LYS 4.1 2.2 + - - +
327A SER 3.5 10.0 + - - +
329A LYS* 1.3 76.5 - - - +
331A SER* 1.3 58.3 + - - +
332A THR 3.0 0.2 - - - -
333A LEU* 2.9 47.7 + - + +
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Residues in contact with SER 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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20A GLY* 5.9 3.6 - - - -
73A LYS* 3.2 20.8 + - - -
327A SER 4.6 1.4 + - - -
328A GLY* 2.8 27.1 + - - -
330A GLN* 1.3 77.5 - - - +
332A THR* 1.3 58.7 + - - +
333A LEU 3.2 5.2 + - - +
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Residues in contact with THR 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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73A LYS* 4.8 7.0 - - - -
328A GLY 3.9 15.9 - - - +
329A LYS* 2.8 21.6 + - + +
330A GLN 3.0 1.8 - - - -
331A SER* 1.3 81.2 - - - +
333A LEU* 1.3 61.0 + - - +
334A GLU* 3.6 3.5 + - - +
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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
------------------------------------------------------------
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