Contacts of the helix formed by residues 293 - 304 (chain D) in PDB entry 1RD4
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 293 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145D ASP* 5.2 0.9 - - - +
149D LYS* 3.6 24.9 + - - +
291D THR* 3.1 17.3 - - - +
292D PHE* 1.3 90.4 + - - +
294D LYS* 1.3 69.3 + - - +
295D LEU 3.0 1.4 + - - -
296D LYS* 3.3 43.8 + - - +
297D ASP* 4.3 2.8 + - - -
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Residues in contact with LYS 294 (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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289D LEU* 3.9 22.9 - - + +
290D ASP* 3.4 25.6 - - - +
291D THR* 3.0 38.6 + - - +
293D GLU* 1.3 84.7 - - - +
295D LEU* 1.3 62.9 - - - +
296D LYS 3.1 0.9 - - - -
297D ASP* 3.0 30.1 + - + +
298D LEU* 2.9 20.6 + - - +
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Residues in contact with LEU 295 (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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149D LYS* 3.8 33.0 - - + +
150D ILE* 4.1 9.4 - - + +
153D PHE* 3.4 52.8 - - + -
237D ILE* 5.4 2.9 - - + -
259D ILE* 4.6 4.3 - - + -
261D ILE* 4.2 21.3 - - + -
289D LEU* 3.9 23.4 - - + +
292D PHE* 3.1 19.7 + - + +
293D GLU 3.0 1.2 - - - -
294D LYS* 1.3 78.3 - - - +
296D LYS* 1.3 59.5 + - + +
298D LEU* 3.1 7.6 + - + +
299D PHE* 3.0 22.7 + - - +
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Residues in contact with LYS 296 (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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149D LYS* 5.3 11.7 - - - +
153D PHE* 5.6 0.2 - - - -
292D PHE 5.5 0.7 - - - +
293D GLU* 3.6 34.3 - - - +
294D LYS 3.1 0.4 - - - -
295D LEU* 1.3 76.6 - - + +
297D ASP* 1.3 69.2 + - - +
299D PHE* 3.2 9.5 + - - +
300D THR* 3.0 25.6 + - - -
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Residues in contact with ASP 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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289D LEU* 6.3 0.2 - - + -
293D GLU 5.0 1.3 - - - -
294D LYS* 3.0 39.2 + - + +
296D LYS* 1.3 80.1 - - - +
298D LEU* 1.3 57.8 + - - +
300D THR* 3.3 8.5 + - - -
301D GLU* 3.0 30.1 + - - +
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Residues in contact with LEU 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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153D PHE* 3.6 16.6 - - + -
259D ILE* 3.4 35.9 - - + -
287D LYS* 4.0 19.7 - - + +
289D LEU* 4.2 20.2 - - + +
294D LYS 2.9 12.2 + - - +
295D LEU* 3.4 10.5 - - + +
297D ASP* 1.3 78.7 - - - +
299D PHE* 1.3 52.2 + - - +
301D GLU* 3.1 19.4 + - - +
302D LEU* 2.7 37.8 + - + +
3328D L08 3.4 31.9 - - + +
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Residues in contact with PHE 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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153D PHE* 3.9 11.4 - + + -
156D ASP* 3.4 58.8 - - + +
157D VAL* 3.8 18.8 - - + -
160D LYS* 4.1 10.3 - - + -
295D LEU 3.0 12.2 + - - +
296D LYS* 3.2 11.9 + - - +
298D LEU* 1.3 78.9 - - - +
300D THR* 1.3 62.4 + - - +
302D LEU* 3.5 10.0 - - + +
303D GLN* 3.1 71.1 + - + +
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Residues in contact with THR 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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163C ASN* 4.4 4.4 - - + +
296D LYS 3.0 13.7 + - - -
297D ASP* 3.6 11.4 + - - -
298D LEU 3.2 0.2 - - - -
299D PHE* 1.3 79.5 - - - +
301D GLU* 1.3 62.8 + - - +
303D GLN* 3.6 17.1 + - - +
304D LYS* 3.3 37.7 + - - +
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Residues in contact with GLU 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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287D LYS* 3.7 26.6 + - - -
297D ASP 3.0 18.2 + - - +
298D LEU* 3.5 11.6 - - - +
300D THR* 1.3 77.0 - - - +
302D LEU* 1.3 62.3 + - - +
304D LYS* 3.5 20.9 + - - +
305D LYS* 3.9 11.8 - - - +
3328D L08 3.1 28.1 - - + +
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Residues in contact with LEU 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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308C VAL* 3.3 34.2 - - + +
153D PHE* 4.9 3.6 - - + -
157D VAL* 4.0 21.8 - - + -
161D LEU* 6.5 0.2 - - + -
298D LEU* 2.7 20.7 + - + +
299D PHE* 3.5 14.1 - - + +
301D GLU* 1.3 71.8 - - - +
303D GLN* 1.3 65.1 + - + +
305D LYS* 3.0 19.3 + - + +
306D ILE* 4.1 1.9 + - + +
3328D L08 3.7 66.6 - - + +
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Residues in contact with GLN 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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163C ASN* 3.2 42.3 + - - +
164C THR* 3.5 9.9 - - + -
160D LYS* 3.4 31.5 - - + +
299D PHE* 3.1 57.5 + - + +
300D THR* 3.8 9.6 + - - +
301D GLU 3.4 0.2 - - - -
302D LEU* 1.3 72.0 - - + +
304D LYS* 1.3 57.2 + - - +
305D LYS 2.8 6.1 - - - -
306D ILE* 2.8 47.0 + - + +
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Residues in contact with LYS 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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163C ASN* 3.8 16.5 + - - +
164C THR 3.8 17.5 - - - -
165C SER* 2.6 33.9 + - - +
300D THR* 3.3 35.1 - - - +
301D GLU* 3.5 14.1 - - - +
302D LEU 3.2 0.6 - - - -
303D GLN* 1.3 76.7 - - - +
305D LYS* 1.3 60.9 + - + +
306D ILE 3.4 1.3 - - - -
307D TYR* 3.5 11.8 + - - -
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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