Contacts of the helix formed by residues 296 - 310 (chain D) in PDB entry 1C7G
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68D ASP 3.8 10.3 - - - -
69D GLU* 2.6 21.7 + - - +
76D ASN* 2.9 40.4 - - - +
294D LEU 3.7 1.4 + - - -
295D ALA* 1.3 71.9 - - - +
297D ARG* 1.3 59.2 + - - +
299D MET* 3.2 21.6 + - - +
300D GLU 3.3 0.5 + - - -
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Residues in contact with ARG 297 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B MET* 3.6 15.4 - - - +
61B TRP* 4.5 6.7 - - - -
64B MET* 3.4 28.5 - - - +
261B VAL* 6.0 0.8 - - - +
262B ASN* 2.9 40.6 + - - +
263B ILE* 4.3 8.1 - - - +
297B ARG* 5.0 0.6 - - - +
298B ASP* 2.8 28.9 + - - -
63D GLY 4.3 2.1 - - - +
64D MET* 3.5 46.6 - - - +
67D GLY* 3.7 12.0 - - - -
69D GLU* 3.1 15.5 + - - +
295D ALA* 3.9 12.6 - - + +
296D GLY* 1.3 75.0 - - - +
298D ASP* 1.3 66.8 + - - +
300D GLU* 3.3 8.6 + - - +
301D ALA* 3.0 26.0 + - - +
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Residues in contact with ASP 298 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263B ILE* 5.1 1.9 - - - +
297B ARG* 2.7 32.2 + - - -
298B ASP* 4.1 11.8 - - - +
64D MET* 4.0 6.4 - - - +
261D VAL* 5.0 1.7 - - - +
263D ILE* 3.8 23.2 - - + +
294D LEU* 4.3 17.7 - - + +
295D ALA* 3.1 28.1 + - - +
297D ARG* 1.3 80.5 + - - +
299D MET* 1.3 60.5 + - - +
300D GLU 3.1 1.8 - - - -
301D ALA* 3.9 5.5 - - - +
302D MET* 3.0 28.6 + - - +
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Residues in contact with MET 299 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74D SER* 4.6 6.3 - - - +
76D ASN* 3.8 14.1 - - + +
77D PHE* 3.9 35.0 - - + +
80D LEU* 3.9 18.2 - - + +
95D PRO* 4.5 4.7 - - - -
290D SER 3.7 5.8 - - - +
291D TYR* 3.6 41.3 - - + +
294D LEU* 3.9 28.3 - - + +
295D ALA 3.4 3.8 + - - +
296D GLY* 3.2 22.5 + - - +
298D ASP* 1.3 79.3 - - - +
300D GLU* 1.3 58.1 + - - +
302D MET* 3.5 6.1 + - - +
303D ALA* 3.0 27.7 + - - +
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Residues in contact with GLU 300 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63D GLY* 3.6 31.9 - - - +
66D ILE* 4.3 9.5 - - + +
76D ASN* 2.6 36.4 + - - +
79D HIS* 2.6 41.1 + - - +
296D GLY 3.3 2.9 + - - +
297D ARG 3.3 10.5 + - - +
299D MET* 1.3 79.3 - - - +
301D ALA* 1.3 64.1 + - - +
303D ALA* 3.2 5.7 + - - +
304D ILE* 3.1 42.3 + - + +
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Residues in contact with ALA 301 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297B ARG* 5.7 0.4 - - - +
56D MET* 4.2 13.0 - - - -
60D GLN* 3.0 19.3 + - - +
63D GLY 5.3 0.2 - - - -
64D MET* 4.1 22.0 - - + -
261D VAL* 3.7 13.2 - - + -
297D ARG 3.0 16.7 + - - +
298D ASP* 3.9 7.0 - - - +
300D GLU* 1.3 77.5 - - - +
302D MET* 1.3 58.0 + - - +
304D ILE* 3.5 8.3 + - - +
305D GLY 2.8 23.9 + - - -
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Residues in contact with MET 302 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80D LEU* 3.8 32.0 - - + +
255D GLY* 4.0 15.5 - - - -
259D CYS* 4.0 17.9 - - + +
261D VAL* 3.7 15.7 - - + +
263D ILE 5.4 0.4 - - - +
264D GLY* 3.9 9.4 - - - -
265D GLY 3.8 37.2 - - - +
266D PHE* 4.0 13.7 - - + -
294D LEU* 3.8 15.9 - - + -
298D ASP 3.0 16.7 + - - +
299D MET* 3.8 3.1 - - - +
300D GLU 3.2 0.2 - - - -
301D ALA* 1.3 75.8 - - - +
303D ALA* 1.3 64.8 + - - +
305D GLY 4.4 0.2 - - - +
306D LEU* 3.1 24.5 + - + +
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Residues in contact with ALA 303 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79D HIS* 3.9 16.4 - - + +
80D LEU* 3.7 31.8 - - - +
83D THR* 3.6 23.1 + - - +
299D MET 3.0 17.9 + - - +
300D GLU* 3.2 6.0 + - - +
302D MET* 1.3 77.8 - - - +
304D ILE* 1.3 64.9 + - + +
306D LEU 3.7 0.2 + - - -
307D ARG* 3.5 16.3 + - - +
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Residues in contact with ILE 304 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59D LYS* 3.8 26.7 - - + +
60D GLN* 3.8 24.2 - - + +
63D GLY* 4.1 7.6 - - - -
300D GLU* 3.1 42.9 + - + +
301D ALA* 3.8 3.6 - - - +
303D ALA* 1.3 77.0 - - + +
305D GLY* 1.3 64.3 + - - +
307D ARG* 3.2 9.8 + - + +
308D GLU* 3.1 32.9 + - + +
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Residues in contact with GLY 305 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60D GLN* 3.5 18.8 - - - +
259D CYS 3.2 22.0 - - - -
260D LEU* 3.6 8.5 - - - +
301D ALA 2.8 12.0 + - - -
302D MET 3.9 0.2 - - - -
304D ILE* 1.3 75.8 - - - +
306D LEU* 1.3 65.0 + - - +
308D GLU* 3.0 8.1 + - - +
309D ALA* 2.9 20.6 + - - +
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Residues in contact with LEU 306 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80D LEU* 5.4 2.0 - - + -
83D THR* 4.1 11.4 - - + -
84D VAL* 3.9 30.7 - - + -
87D LEU* 3.8 13.2 - - + -
88D PHE* 4.0 32.3 - - + -
219D VAL* 5.2 2.7 - - + -
253D MET* 4.4 3.1 - - + -
258D ASP 4.9 3.6 - - - +
259D CYS* 3.7 29.7 + - - +
266D PHE* 4.6 3.1 - - + -
302D MET* 3.1 18.3 + - + +
303D ALA 3.8 5.4 - - - +
305D GLY* 1.3 74.1 - - - +
307D ARG* 1.3 61.8 + - - +
309D ALA* 3.4 14.8 + - - +
310D MET* 3.5 25.4 - - + +
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Residues in contact with ARG 307 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82D LYS* 4.6 5.7 - - - +
83D THR* 3.2 41.3 + - - +
86D GLU* 3.1 40.8 + - - -
87D LEU* 4.2 19.2 - - + +
238D LYS* 5.5 3.2 - - - +
303D ALA 3.5 7.0 + - - +
304D ILE* 3.2 11.8 + - + +
305D GLY 3.1 0.6 - - - -
306D LEU* 1.3 78.8 - - - +
308D GLU* 1.3 63.8 + - + +
310D MET* 3.1 21.6 + - + +
311D GLN* 4.2 1.6 + - - +
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Residues in contact with GLU 308 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C THR* 4.1 12.6 - - + +
57D SER* 2.4 29.1 + - - -
59D LYS* 4.0 6.9 - - - +
60D GLN* 3.5 7.9 - - - +
260D LEU* 4.0 7.7 - - + +
304D ILE* 3.1 28.2 + - + +
305D GLY 3.0 9.4 + - - +
307D ARG* 1.3 76.9 - - + +
309D ALA* 1.3 61.9 - - - +
310D MET 3.2 1.2 + - - -
311D GLN* 3.2 22.0 + - - +
314D TYR* 3.8 8.0 - - - +
410D ARG* 2.8 36.9 + - - +
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Residues in contact with ALA 309 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219D VAL* 3.4 31.9 - - + +
237D ILE* 4.6 0.3 - - - +
258D ASP 3.4 25.8 - - - +
260D LEU* 3.9 3.8 - - + +
305D GLY 2.9 10.0 + - - +
306D LEU* 3.5 12.1 - - - +
307D ARG 3.2 0.4 - - - -
308D GLU* 1.3 77.4 - - - +
310D MET* 1.3 60.3 + - + +
311D GLN 3.2 4.1 + - - +
314D TYR* 3.6 29.5 - - + -
315D ILE* 4.2 2.1 - - - +
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Residues in contact with MET 310 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87D LEU* 4.1 25.8 - - + -
88D PHE* 5.3 1.1 - - + -
219D VAL* 3.6 31.9 - - + -
237D ILE* 3.6 19.8 + - - +
238D LYS* 4.0 37.4 + - + +
241D VAL* 4.2 24.9 - - + -
306D LEU* 3.5 32.1 - - + +
307D ARG* 3.3 12.8 - - + +
308D GLU 3.1 0.8 - - - -
309D ALA* 1.3 76.9 - - - +
311D GLN* 1.3 61.7 + - - +
312D TYR 3.2 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
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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