Contacts of the helix formed by residues 272 - 285 (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 GLU 272 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91D LYS* 2.6 23.3 + - - -
92D HIS* 2.5 33.6 + - + +
270D ASN 3.4 7.9 + - - +
271D ASP* 1.3 72.0 + - - +
273D GLU* 1.3 69.9 + - - +
275D PHE* 3.1 8.9 + - + +
276D SER* 2.9 32.1 + - - +
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Residues in contact with GLU 273 (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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445B GLN* 5.3 0.9 + - - -
271D ASP* 3.3 19.1 - - - +
272D GLU* 1.3 81.1 + - - +
274D MET* 1.3 63.0 + - - +
276D SER* 3.4 5.2 + - - -
277D ALA* 3.1 24.0 + - - +
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Residues in contact with MET 274 (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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106D LEU* 3.6 28.5 - - + -
109D LEU* 4.0 26.0 - - + +
110D ALA* 5.1 5.6 - - + -
210D LYS* 4.8 9.4 - - - +
212D PHE* 3.6 27.6 - - + -
267D LEU* 5.4 0.9 - - + -
269D MET* 3.4 31.7 - - + +
271D ASP* 3.2 29.3 + - + +
272D GLU 3.2 0.2 - - - -
273D GLU* 1.3 76.9 - - - +
275D PHE* 1.3 56.5 + - - +
277D ALA* 3.3 5.8 + - - +
278D ALA* 2.7 36.7 + - - +
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Residues in contact with PHE 275 (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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81D GLU* 6.0 2.2 - - - -
92D HIS* 3.4 54.7 - + + -
93D ILE 4.3 7.9 - - - -
94D VAL* 3.8 26.2 - - + -
269D MET* 3.8 10.5 - - - -
271D ASP 2.8 15.5 + - - +
272D GLU* 3.4 11.2 - - + +
274D MET* 1.3 77.3 - - - +
276D SER* 1.3 58.2 + - - +
278D ALA* 3.1 2.6 + - - +
279D LYS* 2.9 64.9 + - + +
289D PRO* 5.9 1.1 - - + -
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Residues in contact with SER 276 (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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445B GLN* 3.6 32.7 - - - +
272D GLU* 2.9 19.1 + - - +
273D GLU* 3.7 5.7 - - - -
275D PHE* 1.3 75.7 - - - +
277D ALA* 1.3 62.4 + - - +
279D LYS* 3.3 27.6 + - - +
280D GLU* 3.4 9.4 + - - +
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Residues in contact with ALA 277 (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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445B GLN* 4.1 12.7 - - - +
109D LEU* 3.3 27.2 - - + +
273D GLU 3.1 17.3 + - - +
274D MET* 3.8 3.6 - - - +
276D SER* 1.3 74.7 - - - +
278D ALA* 1.3 64.6 + - - +
280D GLU* 3.5 6.9 + - - +
281D LEU* 3.3 18.5 + - - +
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Residues in contact with ALA 278 (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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94D VAL* 4.3 11.5 - - + +
105D LEU* 4.8 3.6 - - + +
109D LEU* 3.6 21.3 - - + +
267D LEU* 4.2 10.3 - - + -
269D MET* 3.8 17.0 - - + -
274D MET 2.7 18.6 + - - +
275D PHE* 3.3 5.8 - - - +
277D ALA* 1.3 78.3 - - - +
279D LYS* 1.3 61.3 + - - +
281D LEU* 3.4 3.4 + - - +
282D VAL* 3.1 26.5 + - - +
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Residues in contact with LYS 279 (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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446B LEU* 4.2 9.3 - - + +
449B PHE* 4.9 10.1 - - + -
450B THR* 4.8 23.6 + - - +
94D VAL* 5.2 2.2 - - + +
275D PHE* 2.9 60.2 + - + +
276D SER* 3.4 20.2 + - - +
277D ALA 3.2 0.2 - - - -
278D ALA* 1.3 77.4 - - - +
280D GLU* 1.3 60.5 + - - +
282D VAL* 3.3 9.8 - - - +
283D VAL* 3.3 21.0 - - - +
289D PRO* 3.4 33.3 - - + +
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Residues in contact with GLU 280 (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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445B GLN* 3.0 45.7 + - + +
446B LEU* 4.1 19.4 + - + +
276D SER 3.4 4.2 + - - +
277D ALA* 3.9 8.9 - - - +
278D ALA 3.3 0.6 - - - -
279D LYS* 1.3 80.6 - - - +
281D LEU* 1.3 63.9 + - + +
283D VAL* 3.8 13.5 - - - +
284D VAL* 4.4 7.8 + - - +
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Residues in contact with LEU 281 (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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128B PHE* 5.7 4.3 - - + -
105D LEU* 4.1 23.3 - - + +
108D GLN* 3.6 43.3 - - + +
109D LEU* 4.4 13.2 - - + -
277D ALA 3.3 12.3 + - - +
278D ALA* 3.4 4.7 + - - +
280D GLU* 1.3 80.0 - - + +
282D VAL* 1.3 64.1 + - - +
283D VAL 3.2 0.7 - - - -
284D VAL* 3.0 27.4 - - + +
285D TYR* 3.4 22.8 - - + -
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Residues in contact with VAL 282 (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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94D VAL* 4.1 20.0 - - + -
95D PRO 4.1 7.6 - - - +
105D LEU* 4.1 15.8 - - + +
278D ALA 3.1 15.1 + - - +
279D LYS* 3.3 17.5 - - - +
281D LEU* 1.3 73.9 - - - +
283D VAL* 1.3 66.5 + - - +
285D TYR 3.0 0.5 + - - -
286D GLU* 2.7 57.9 + - + +
287D GLY 3.0 17.3 + - - +
288D MET 4.8 0.2 - - - +
289D PRO* 3.9 21.1 - - + -
292D GLY* 4.5 2.5 - - - -
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Residues in contact with VAL 283 (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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100B ARG* 2.7 49.4 + - - +
124B THR* 6.1 0.4 - - - +
125B THR* 5.2 3.4 - - + -
446B LEU* 3.6 29.6 - - + -
448B PHE* 6.1 2.9 - - + -
279D LYS 3.3 20.0 - - - +
280D GLU 3.8 10.5 - - - +
282D VAL* 1.3 84.6 - - - +
284D VAL* 1.3 60.9 + - + +
285D TYR 3.4 0.2 + - - -
287D GLY 3.3 9.3 + - - -
288D MET* 4.2 19.1 - - + -
289D PRO* 4.3 4.7 - - + -
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Residues in contact with VAL 284 (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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100B ARG* 3.9 9.4 - - - +
124B THR 6.2 0.4 - - - -
125B THR* 4.6 11.8 - - + -
128B PHE* 3.9 46.7 - - + -
129B HIS* 2.9 28.1 + - + -
280D GLU 4.6 7.2 - - - +
281D LEU* 3.0 27.4 - - + +
283D VAL* 1.3 81.3 - - + +
285D TYR* 1.3 78.4 + - + +
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Residues in contact with TYR 285 (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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97B HIS* 3.3 18.2 - - - -
100B ARG* 4.7 9.2 - - - +
101B GLY* 4.8 3.8 + - - -
104B ASN* 3.9 27.6 - - + -
108B GLN* 5.7 0.2 - - - -
128B PHE* 4.5 6.6 - + - -
129B HIS* 4.0 15.5 - + - -
132B LYS* 3.7 19.2 - - - +
285B TYR* 4.8 10.5 - + - -
286B GLU* 5.0 1.0 - - - +
104D ASN* 3.7 23.3 - - - +
105D LEU* 4.4 4.9 - - + -
108D GLN* 3.6 33.0 + - - -
281D LEU* 3.4 32.5 - - + +
282D VAL 3.0 2.0 + - - +
284D VAL* 1.3 95.2 - - + +
286D GLU* 1.3 73.2 + - + +
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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