Contacts of the helix formed by residues 297 - 314 (chain A) in PDB entry 6E8Z
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 LEU 297 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A VAL* 4.9 3.8 - - + -
269A ARG* 4.0 10.3 - - + +
270A ASN* 3.5 51.6 - - + +
273A VAL* 3.7 36.1 - - + -
274A ALA* 4.9 2.7 - - + +
284A ILE* 4.5 7.9 - - + -
288A GLU* 2.8 23.8 + - + +
295A GLN 3.6 3.0 + - - -
296A LYS* 1.3 74.1 - - - +
298A GLN* 1.3 63.7 + - - +
299A GLY 3.6 0.2 - - - -
300A PRO* 3.8 27.5 - - + +
301A GLU* 4.0 16.3 - - - +
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Residues in contact with GLN 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A HIS* 6.0 5.9 - - - +
120A LYS 4.3 9.8 + - - +
121A GLY* 4.1 19.5 - - - -
205A ASN* 3.5 25.6 + - - +
270A ASN* 3.7 7.9 + - - +
296A LYS 4.2 7.6 - - - +
297A LEU* 1.3 75.3 - - - +
299A GLY* 1.3 66.8 + - - +
301A GLU* 3.3 9.2 + - - +
302A THR* 3.2 28.3 + - - +
401A NAD 5.9 0.6 + - - -
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Residues in contact with GLY 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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205A ASN* 3.8 27.0 - - - +
206A VAL* 3.5 12.3 - - - +
209A VAL* 4.2 3.4 - - - -
270A ASN* 2.9 17.3 + - - -
298A GLN* 1.3 77.1 - - - +
300A PRO* 1.3 67.5 - - - +
302A THR* 3.4 1.6 + - - -
303A ALA* 3.1 19.3 + - - +
325A VAL* 5.1 0.7 - - - -
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Residues in contact with PRO 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A VAL* 4.1 10.7 - - + -
270A ASN* 3.9 3.4 - - - +
284A ILE* 4.9 11.4 - - + -
288A GLU* 5.7 0.2 - - - +
297A LEU* 3.8 33.4 - - + +
298A GLN 3.7 2.7 - - - -
299A GLY* 1.3 89.1 - - - +
301A GLU* 1.3 62.1 + - + +
303A ALA* 3.1 10.8 + - + +
304A ARG 3.1 17.2 + - - -
325A VAL* 4.9 1.3 - - + -
329A CYS* 4.0 28.9 - - + -
330A TYR* 3.2 24.2 - - + +
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Residues in contact with GLU 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A LYS* 4.5 16.3 - - + +
297A LEU 4.0 13.3 - - - +
298A GLN* 3.3 8.4 + - - +
300A PRO* 1.3 73.0 - - + +
302A THR* 1.3 67.6 + - - +
304A ARG* 3.0 28.4 + - - +
305A GLU* 3.0 25.2 + - + +
330A TYR* 3.5 15.5 - - - +
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Residues in contact with THR 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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129A LEU* 4.2 20.0 - - + +
202A ALA* 4.0 28.1 + - + +
203A LEU* 4.6 4.0 - - + -
205A ASN* 5.9 0.2 - - - +
206A VAL* 3.9 16.6 - - + -
298A GLN* 3.2 14.6 + - - +
299A GLY* 3.7 7.9 - - - -
301A GLU* 1.3 77.5 - - - +
303A ALA* 1.3 58.6 + - - +
305A GLU* 3.0 9.3 + - - +
306A LEU* 2.8 41.5 + - + +
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Residues in contact with ALA 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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206A VAL* 3.9 6.4 - - + +
299A GLY 3.1 13.1 + - - +
300A PRO 3.1 11.6 + - - +
302A THR* 1.3 75.9 - - - +
304A ARG* 1.3 62.4 + - - +
306A LEU* 3.2 16.2 + - - +
307A TYR* 3.0 22.2 + - - +
322A PHE 4.1 6.1 - - - +
323A MET* 3.9 4.0 - - - +
325A VAL* 4.1 12.1 - - + -
326A TYR* 3.9 29.3 - - + +
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Residues in contact with ARG 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 PRO 3.1 9.7 + - - +
301A GLU* 3.0 35.1 + - - +
303A ALA* 1.3 74.6 - - - +
305A GLU* 1.3 72.4 + - - +
307A TYR* 3.2 13.5 + - + +
308A SER* 3.3 15.1 + - - +
326A TYR* 3.5 29.1 - - + +
330A TYR* 3.4 39.5 + - + -
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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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129A LEU* 4.2 32.1 + - + +
301A GLU* 3.0 17.1 + - + +
302A THR* 3.0 8.5 + - - +
304A ARG* 1.3 86.0 + - - +
306A LEU* 1.3 63.7 + - - +
308A SER* 3.2 13.1 + - - -
309A ILE* 3.1 28.5 + - + +
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Residues in contact with LEU 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A LEU* 3.6 14.8 - - + -
203A LEU* 4.0 10.8 - - + -
206A VAL* 4.2 8.7 - - + -
238A PHE* 3.4 40.8 - - + -
302A THR* 2.8 33.4 + - + +
303A ALA* 3.4 15.7 - - - +
305A GLU* 1.3 72.3 - - - +
307A TYR* 1.3 58.2 + - - +
309A ILE* 3.4 4.0 + - - +
310A LEU* 2.8 39.0 + - + +
322A PHE* 3.8 29.4 - - + -
323A MET* 3.9 10.5 - - + -
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Residues in contact with TYR 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 ALA 3.0 13.0 + - - +
304A ARG* 3.4 10.1 - - + +
305A GLU 3.2 0.4 - - - -
306A LEU* 1.3 77.8 - - - +
308A SER* 1.3 66.1 + - - +
310A LEU* 3.4 1.4 + - - +
311A GLN* 2.7 60.2 + - + +
316A VAL* 4.1 11.4 - - + -
323A MET* 3.6 29.2 - - + -
326A TYR* 3.4 43.3 - + + -
327A LYS* 3.9 20.3 + - - -
331A GLU* 3.9 11.2 + - - -
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Residues in contact with SER 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A ARG* 3.3 9.9 + - - +
305A GLU* 3.2 17.3 + - - -
307A TYR* 1.3 80.1 - - - +
309A ILE* 1.3 66.7 + - - +
311A GLN* 3.3 14.6 + - - +
312A HIS* 3.2 37.3 + - - -
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Residues in contact with ILE 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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129A LEU* 3.5 50.9 - - + +
238A PHE* 4.2 20.0 - - + -
241A LEU* 5.3 0.2 - - + -
242A PHE* 4.1 16.2 - - + -
305A GLU* 3.1 18.7 + - + +
306A LEU* 3.8 5.8 - - - +
308A SER* 1.3 77.4 - - - +
310A LEU* 1.3 64.3 + - + +
312A HIS* 3.2 21.6 + - + +
313A LYS* 3.3 33.2 + - + +
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Residues in contact with LEU 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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238A PHE* 4.0 23.3 - - + -
241A LEU* 4.6 6.7 - - + -
306A LEU* 2.8 31.3 + - + +
307A TYR 4.0 0.9 - - - +
309A ILE* 1.3 74.8 - - + +
311A GLN* 1.3 61.1 + - - +
313A LYS* 3.2 4.4 + - + +
314A GLY 2.9 23.6 + - - -
315A LEU* 2.9 22.3 + - + +
316A VAL* 3.8 19.2 + - + +
319A PHE* 3.6 48.9 - - + -
322A PHE* 5.1 1.3 - - + -
323A MET* 3.6 28.0 - - + -
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Residues in contact with GLN 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A TYR* 2.7 58.1 + - + +
308A SER* 3.5 13.0 + - - +
310A LEU* 1.3 76.8 - - - +
312A HIS* 1.3 71.2 + - + +
313A LYS 3.0 1.4 + - - -
314A GLY* 3.0 12.6 + - - +
316A VAL* 3.6 17.9 - - + +
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Residues in contact with HIS 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 SER* 3.2 24.6 + - - -
309A ILE* 3.2 13.2 + - - +
311A GLN* 1.3 83.8 + - + +
313A LYS* 1.3 62.8 + - + +
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Residues in contact with LYS 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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241A LEU* 3.8 44.2 + - + -
242A PHE* 5.3 6.5 - - - +
309A ILE* 3.3 26.4 + - + +
310A LEU* 3.2 5.5 + - + +
311A GLN 3.0 0.8 - - - -
312A HIS* 1.3 81.1 - - + +
314A GLY* 1.3 63.2 + - - +
315A LEU* 3.3 24.8 - - + +
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Residues in contact with GLY 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 LEU 2.9 5.1 + - - -
311A GLN* 3.0 10.6 + - - -
312A HIS 3.5 0.2 - - - -
313A LYS* 1.3 79.5 - - - +
315A LEU* 1.3 63.8 + - - +
316A VAL* 3.6 3.1 - - - -
317A ASP* 5.3 2.1 + - - +
318A LYS* 5.9 0.3 - - - +
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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