Contacts of the helix formed by residues 306 - 321 (chain A) in PDB entry 6EKK
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 306 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A LEU* 4.3 18.1 - - + +
164A PRO 3.8 18.6 - - - +
165A SER* 4.0 7.9 - - - +
304A THR 3.2 0.9 + - - +
305A GLY* 1.3 71.4 - - - -
307A GLY* 1.3 58.8 + - - +
308A VAL 3.4 2.5 - - - -
309A ALA 3.3 3.8 + - - -
310A ARG* 2.9 51.3 + - + +
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Residues in contact with GLY 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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302A THR* 3.2 27.7 - - - +
303A THR* 4.0 0.2 - - - -
304A THR 2.8 17.9 + - - -
305A GLY 3.2 1.0 - - - -
306A ASP* 1.3 80.1 + - - +
308A VAL* 1.3 56.5 + - - +
310A ARG* 3.3 7.4 + - - +
311A ALA* 2.9 27.2 + - - +
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Residues in contact with VAL 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A ILE* 4.0 15.9 - - + -
172A LEU* 4.1 24.4 - - + +
176A PHE* 3.8 27.8 - - + -
184A MET* 4.2 16.2 - - + -
217A MET* 4.4 0.4 - - - -
297A LEU* 4.1 17.9 - - + -
302A THR 3.8 0.9 + - - -
303A THR* 3.8 28.9 + - + +
305A GLY 4.9 0.8 + - - -
306A ASP 3.4 0.4 - - - -
307A GLY* 1.3 74.0 - - - +
309A ALA* 1.3 64.2 + - - +
311A ALA* 3.2 11.3 + - - +
312A PHE* 3.2 20.2 + - + -
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Residues in contact with ALA 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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163A LEU* 4.0 15.1 - - + +
164A PRO* 3.7 46.2 - - + +
172A LEU* 4.4 2.3 - - + +
217A MET* 4.2 17.0 - - + -
306A ASP 3.3 5.1 + - - +
308A VAL* 1.3 80.3 - - - +
310A ARG* 1.3 57.8 + - - +
312A PHE* 3.5 2.3 + - - +
313A LEU* 3.0 28.6 + - - +
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Residues in contact with ARG 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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163A LEU* 3.4 19.9 - - + +
306A ASP* 2.9 49.9 + - - +
307A GLY* 3.5 8.1 - - - +
309A ALA* 1.3 75.2 - - - +
311A ALA* 1.3 58.8 + - - +
313A LEU* 3.3 18.3 + - - +
314A LYS* 2.9 52.3 + - - +
384A VAL* 4.4 13.5 + - - +
387A GLU* 5.7 2.0 + - - +
388A GLU* 3.0 28.4 + - - -
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Residues in contact with ALA 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A LEU* 3.6 25.9 - - + +
296A ARG* 3.9 37.4 + - + +
297A LEU* 4.1 10.5 - - + -
302A THR 5.1 0.2 - - - +
307A GLY 2.9 13.3 + - - +
308A VAL* 3.2 9.4 + - - +
310A ARG* 1.3 76.1 - - - +
312A PHE* 1.3 61.9 + - - +
314A LYS* 3.3 4.6 + - - +
315A ALA* 3.1 17.2 + - - +
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Residues in contact with PHE 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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175A TYR* 5.5 1.1 - - - -
184A MET* 3.6 43.7 - - + -
185A LEU* 4.8 0.9 - - + -
188A TYR* 3.7 44.3 + + + -
217A MET* 3.4 48.7 - - + +
293A LEU* 4.0 17.0 - - + -
297A LEU* 3.9 28.0 - - + -
308A VAL* 3.2 21.0 + - + -
309A ALA 4.0 2.5 - - - +
310A ARG 3.4 0.2 - - - -
311A ALA* 1.3 79.3 - - - +
313A LEU* 1.3 57.6 + - - +
315A ALA* 3.2 3.9 + - - +
316A GLN* 2.9 32.8 + - - +
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Residues in contact with LEU 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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163A LEU* 4.0 11.4 - - + -
219A TYR* 3.8 39.0 - - + +
309A ALA 3.0 18.6 + - - +
310A ARG* 3.5 23.3 - - - +
312A PHE* 1.3 77.8 - - - +
314A LYS* 1.3 55.8 + - - +
316A GLN* 3.3 5.9 + - - +
317A ALA* 2.9 27.5 + - - +
384A VAL* 3.8 35.7 - - + +
385A PHE* 3.9 22.6 - - + +
388A GLU* 4.2 12.8 - - + +
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Residues in contact with LYS 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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296A ARG* 3.5 47.7 - - - +
310A ARG* 2.9 39.1 + - - +
311A ALA 3.7 5.2 - - - +
313A LEU* 1.3 76.0 - - - +
315A ALA* 1.3 57.7 + - - +
317A ALA* 3.4 2.5 + - - +
318A ALA* 3.0 27.5 + - - +
388A GLU* 2.6 48.5 + - - +
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Residues in contact with ALA 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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188A TYR* 3.5 17.5 - - + +
289A VAL* 3.9 21.9 - - + +
293A LEU* 4.0 25.1 - - + -
296A ARG* 5.5 0.8 - - - +
311A ALA 3.1 12.7 + - - +
312A PHE 3.2 7.2 + - - +
314A LYS* 1.3 74.3 - - - +
316A GLN* 1.3 60.1 + - - +
318A ALA* 3.2 2.5 + - - +
319A PHE* 2.8 33.8 + - - -
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Residues in contact with GLN 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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188A TYR* 2.6 33.7 + - - +
192A LEU* 3.8 7.2 - - - +
217A MET 3.9 8.5 - - - +
218A LEU* 2.8 29.6 + - - +
219A TYR 3.6 20.4 - - - +
220A PRO* 4.4 0.4 - - + -
221A MET* 3.9 12.1 - - - +
312A PHE 2.9 20.3 + - - +
313A LEU 3.6 4.7 - - - +
315A ALA* 1.3 74.6 - - - +
317A ALA* 1.3 58.1 + - - +
319A PHE* 4.1 0.6 - - - -
320A PHE* 2.9 63.1 + - + +
363A LEU* 5.4 0.2 - - - +
385A PHE* 3.6 10.3 - - + -
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Residues in contact with ALA 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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313A LEU 2.9 17.6 + - - +
314A LYS 3.6 5.6 - - - +
315A ALA 3.2 0.2 - - - -
316A GLN* 1.3 78.5 - - - +
318A ALA* 1.3 57.7 + - - +
321A GLY* 2.8 28.2 + - - -
385A PHE* 3.5 17.9 - - + -
388A GLU* 3.9 30.1 - - + +
389A ILE* 4.4 11.9 - - + +
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Residues in contact with ALA 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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289A VAL* 3.9 25.4 - - + +
314A LYS 3.0 17.0 + - - +
315A ALA* 3.2 5.1 + - - +
317A ALA* 1.3 78.1 - - - +
319A PHE* 1.3 62.4 + - - +
321A GLY 4.6 0.9 + - - -
322A SER 5.7 0.3 + - - -
351A MET* 4.1 12.1 - - - +
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Residues in contact with PHE 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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188A TYR* 3.3 35.2 - + - -
192A LEU* 3.7 19.7 - - + -
285A LEU* 4.3 12.1 - - + -
286A PRO* 3.7 23.6 - - + -
289A VAL* 3.5 39.5 - - + -
290A ILE* 4.2 14.6 - - + -
315A ALA 2.8 15.0 + - - +
316A GLN* 4.1 1.6 - - - -
318A ALA* 1.3 78.1 - - - +
320A PHE* 1.3 69.0 + - + +
322A SER* 5.1 1.4 + - - -
351A MET* 3.6 22.1 - - - +
354A PHE* 3.5 38.4 - + + -
355A LEU* 4.1 7.6 - - - +
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Residues in contact with PHE 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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192A LEU* 4.0 15.0 - - + -
221A MET* 3.4 29.6 - - + -
316A GLN* 2.9 47.3 + - - +
319A PHE* 1.3 88.8 - - + +
321A GLY* 1.3 65.5 + - - +
322A SER* 3.2 4.0 - - - -
323A TYR* 3.1 27.9 + - + +
342A PHE* 4.4 5.5 - + - -
354A PHE* 3.6 17.0 - + - -
358A ALA* 3.8 21.3 - - + -
361A LEU* 4.7 4.3 - - + -
363A LEU* 4.6 4.7 - - + -
364A PHE* 3.5 40.6 - + + -
367A PHE* 5.5 0.2 - - + -
385A PHE* 4.2 5.6 - - + -
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Residues in contact with GLY 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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316A GLN 4.1 0.2 + - - -
317A ALA* 2.8 22.0 + - - +
318A ALA 4.5 0.6 + - - -
319A PHE 3.7 1.0 - - - -
320A PHE* 1.3 78.8 - - - +
322A SER* 1.3 55.7 + - - +
323A TYR* 3.0 6.1 + - - -
324A ARG* 3.6 14.0 + - - +
325A ASN* 5.6 0.2 - - - -
385A PHE* 4.7 0.2 - - - -
389A ILE* 3.7 38.6 - - - +
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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