Contacts of the helix formed by residues 248 - 260 (chain D) in PDB entry 3COG
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 SER 248 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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248C SER* 3.5 31.9 - - - +
251C ASP* 2.7 30.7 + - - -
246D VAL 4.0 1.2 + - - -
247D PRO* 1.3 74.1 - - - +
249D PRO* 1.3 73.7 - - - +
250D ILE* 3.2 14.9 + - - +
251D ASP* 3.2 13.8 + - - +
252D CYS* 3.0 19.9 + - - -
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Residues in contact with PRO 249 (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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219C ASP 5.9 2.0 - - - +
220C VAL* 6.6 0.4 - - - -
221C VAL* 6.2 3.6 - - + +
251C ASP* 4.8 3.8 - - - +
41D ILE* 3.8 3.0 - - + +
42D SER 3.3 30.3 - - - +
43D LEU* 4.3 17.0 - - + +
61D SER* 4.4 10.5 - - - +
65D ASN* 4.0 23.6 - - - +
67D THR* 3.3 18.4 - - - +
247D PRO 4.0 3.4 - - - +
248D SER* 1.3 88.7 - - - +
250D ILE* 1.3 57.2 + - - +
252D CYS* 3.3 10.2 + - + -
253D TYR* 3.0 22.3 + - - +
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Residues in contact with ILE 250 (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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41B ILE* 5.6 3.6 - - + -
250C ILE* 3.5 47.8 - - + -
251C ASP* 4.2 8.3 - - - +
254C LEU* 4.2 11.2 - - + -
41D ILE* 3.8 24.5 - - + -
43D LEU* 3.3 30.7 - - + -
248D SER* 3.1 6.1 + - - +
249D PRO* 1.3 77.6 - - - +
251D ASP* 1.3 58.4 + - - +
253D TYR* 3.2 3.9 + - + +
254D LEU* 3.0 38.6 + - + +
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Residues in contact with ASP 251 (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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248C SER* 2.8 32.9 + - - -
250C ILE* 4.2 3.6 - - - +
220D VAL* 3.8 14.3 - - + +
221D VAL 4.0 4.2 - - - +
222D MET* 3.7 10.6 - - + +
247D PRO* 5.0 0.7 - - + +
248D SER* 3.2 14.6 + - - +
250D ILE* 1.3 72.7 - - - +
252D CYS* 1.3 60.3 + - - +
254D LEU* 3.3 8.7 + - - +
255D CYS* 2.9 31.5 + - - +
605D GOL 2.3 45.8 + - - -
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Residues in contact with CYS 252 (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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67D THR* 4.1 7.4 - - + +
68D ARG* 3.7 34.8 - - - -
71D LEU* 3.8 23.4 - - + +
222D MET* 3.9 0.7 - - - -
247D PRO* 3.5 29.4 - - - -
248D SER 3.0 18.9 + - - -
249D PRO* 3.3 12.1 - - + +
251D ASP* 1.3 75.2 - - - +
253D TYR* 1.3 59.0 + - - +
255D CYS* 3.5 1.4 + - - +
256D ASN* 2.9 31.2 + - - +
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Residues in contact with TYR 253 (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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217A HIS 4.6 0.7 + - - -
219A ASP* 2.4 45.5 + - - +
254A LEU* 5.2 2.5 - - + -
43B LEU* 3.8 18.4 - - + +
38D VAL* 3.4 29.4 - - + +
39D PRO* 3.6 16.2 - - + -
41D ILE* 3.7 30.3 - - + -
67D THR* 3.7 13.1 - - + +
249D PRO 3.0 12.7 + - - +
250D ILE* 3.2 10.1 + - + +
252D CYS* 1.3 77.4 - - - +
254D LEU* 1.3 68.7 + - + +
256D ASN* 3.2 7.2 + - + +
257D ARG* 2.8 40.9 + - + +
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Residues in contact with LEU 254 (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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253A TYR* 5.1 2.5 - - + -
254A LEU* 3.9 28.3 - - + -
257A ARG* 3.3 30.2 + - - +
43C LEU* 3.9 17.3 - - + -
250C ILE* 6.0 0.4 - - + -
215D ASN* 3.2 7.7 - - - +
219D ASP* 4.6 3.4 - - - +
220D VAL* 3.6 18.8 - - + -
250D ILE* 3.0 29.3 + - + +
251D ASP* 3.3 5.1 + - - +
253D TYR* 1.3 84.7 - - + +
255D CYS* 1.3 57.4 + - - +
257D ARG* 3.3 4.2 + - - -
258D GLY 2.9 22.7 + - - -
605D GOL 3.8 21.8 - - - +
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Residues in contact with CYS 255 (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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71D LEU* 4.2 12.6 - - + -
210D ALA* 4.1 16.8 - - - -
214D MET 4.4 3.2 - - - +
215D ASN* 3.2 28.7 + - + +
220D VAL* 4.6 2.2 - - + +
222D MET* 3.8 27.1 - - + -
224D LEU* 4.6 6.5 - - - -
251D ASP 2.9 17.9 + - - +
252D CYS 3.8 3.8 - - - +
254D LEU* 1.3 73.0 - - - +
256D ASN* 1.3 61.7 + - - +
258D GLY* 3.2 1.7 + - - -
259D LEU* 2.9 31.4 + - - +
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Residues in contact with ASN 256 (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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22D ALA 4.8 1.6 + - - -
27D GLN* 3.0 34.4 + - - +
39D PRO* 5.5 0.3 - - - +
67D THR* 5.0 1.2 - - + +
70D CYS* 3.8 2.8 - - - +
71D LEU* 3.3 36.6 + - + +
74D ALA* 4.2 11.5 - - - +
252D CYS 2.9 19.4 + - - +
253D TYR* 3.6 8.1 - - + +
255D CYS* 1.3 76.2 - - - +
257D ARG* 1.3 61.4 + - - +
259D LEU* 3.3 15.0 + - - +
260D LYS* 3.3 27.3 - - - +
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Residues in contact with ARG 257 (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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215A ASN* 2.9 29.1 + - - +
217A HIS* 3.5 39.1 + - + +
219A ASP* 2.8 35.6 + - - +
254A LEU* 3.2 36.8 + - - +
257A ARG* 3.5 32.6 - - - +
258A GLY* 3.6 12.9 - - - +
344A PHE* 5.0 3.1 - - + -
217D HIS* 5.9 0.4 + - - -
253D TYR* 2.8 26.7 + - + +
254D LEU* 3.4 9.9 - - - +
256D ASN* 1.3 74.5 - - - +
258D GLY* 1.3 64.6 + - - +
260D LYS* 3.2 26.1 + - - +
261D THR 4.2 0.5 + - - -
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Residues in contact with GLY 258 (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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217A HIS* 5.8 0.2 - - - -
257A ARG* 3.8 1.7 - - - +
214D MET 4.0 0.9 - - - -
215D ASN 3.5 19.5 - - - -
217D HIS* 3.8 15.0 - - - -
254D LEU 2.9 13.6 + - - -
255D CYS 3.2 2.9 + - - -
257D ARG* 1.3 75.8 - - - +
259D LEU* 1.3 60.9 + - - +
261D THR* 3.1 14.7 + - - -
265D ARG* 2.9 22.5 + - - -
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Residues in contact with LEU 259 (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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22D ALA* 3.8 17.2 - - - +
71D LEU* 3.7 18.2 - - + -
74D ALA* 4.7 6.3 - - + -
75D VAL* 3.5 31.4 - - + -
78D LEU* 4.0 21.1 - - + -
214D MET* 3.1 48.7 - - + +
255D CYS* 2.9 12.3 + - - +
256D ASN* 3.4 17.9 - - - +
257D ARG 3.2 0.2 - - - -
258D GLY* 1.3 76.8 - - - +
260D LYS* 1.3 56.7 + - - +
261D THR 3.1 0.2 - - - -
262D LEU* 3.0 30.6 + - + +
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Residues in contact with LYS 260 (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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217A HIS* 5.0 0.7 - - + -
344A PHE* 3.6 57.8 - - + +
380A LEU* 4.6 1.4 - - - +
22D ALA* 3.9 8.7 - - - +
23D ILE* 3.7 41.9 + - + +
27D GLN* 2.9 33.0 + - - +
37D VAL 5.6 0.6 + - - -
38D VAL* 5.0 6.7 - - - +
39D PRO* 4.7 5.3 - - - +
256D ASN* 3.3 28.9 + - - +
257D ARG* 3.5 12.6 - - - +
258D GLY 3.1 1.4 - - - -
259D LEU* 1.3 76.6 - - - +
261D THR* 1.3 60.7 + - - +
262D LEU 3.5 0.2 - - - -
263D HIS* 3.3 19.8 - - - -
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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