Contacts of the helix formed by residues 297 - 309 (chain A) in PDB entry 3KDO
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 297 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122A ARG* 3.3 34.3 + - - +
123A LEU 3.1 21.4 + - - -
124A GLU* 3.7 16.5 + - - -
289A THR* 4.3 1.1 - - - -
296A ILE* 1.3 76.2 - - - +
298A MET* 1.3 56.7 + - - +
299A PHE* 2.8 31.9 + - - +
300A VAL* 2.9 18.8 + - - +
301A LEU* 3.5 3.6 + - - +
333A PHE* 4.8 3.6 - - - -
351A HIS* 5.4 1.2 + - - -
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Residues in contact with MET 298 (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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122A ARG* 5.1 0.2 - - - +
282A ARG* 3.8 34.1 - - + +
285A HIS* 4.7 5.2 - - + -
289A THR* 4.0 20.8 + - - +
296A ILE 3.7 2.4 + - - -
297A SER* 1.3 72.9 + - - +
299A PHE* 1.3 57.0 + - - +
301A LEU* 3.9 22.2 - - + -
302A ALA* 2.9 32.1 + - + +
305A TYR* 5.6 1.1 - - + -
313A LEU* 4.0 22.2 - - + -
314A HIS 3.1 27.8 - - - +
315A VAL* 4.5 5.8 - - + +
333A PHE* 3.5 33.7 - - + -
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Residues in contact with PHE 299 (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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124A GLU 3.7 6.5 - - - +
125A ASP* 3.4 31.0 - - - -
297A SER* 2.8 16.9 + - - +
298A MET* 1.3 75.4 - - - +
300A VAL* 1.3 66.2 + - - +
302A ALA* 3.3 0.9 + - - -
303A LYS* 3.3 8.2 + - - +
332A GLY* 4.4 12.6 - - - -
333A PHE* 3.5 24.7 - + + -
336A LEU* 3.3 53.6 - - + +
342A TYR* 3.3 24.0 - + - -
351A HIS* 3.0 54.1 - + + +
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Residues in contact with VAL 300 (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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105A LEU* 5.4 1.8 - - + -
123A LEU* 3.7 41.7 - - + +
124A GLU 3.9 10.3 - - - +
125A ASP* 3.9 13.7 - - - +
126A LEU* 4.3 16.8 - - + +
296A ILE* 4.0 13.7 - - + -
297A SER 2.9 9.4 + - - +
299A PHE* 1.3 76.9 - - - +
301A LEU* 1.3 66.0 + - + +
303A LYS* 3.0 9.1 + - - +
304A LEU* 2.9 45.7 + - + +
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Residues in contact with LEU 301 (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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257A VAL* 4.4 5.6 - - + -
261A TRP* 4.2 16.8 - - + -
282A ARG* 5.9 0.2 - - + -
285A HIS* 4.4 8.1 - - + -
288A PHE* 3.8 29.8 - - + -
289A THR* 4.0 12.6 - - + -
296A ILE* 3.7 28.9 - - + -
297A SER 3.5 2.1 + - - +
298A MET* 3.8 21.8 - - - +
299A PHE 3.4 0.2 - - - -
300A VAL* 1.3 82.2 - - + +
302A ALA* 1.3 57.0 + - - +
304A LEU* 4.5 5.4 - - - -
305A TYR* 2.9 66.1 + - + +
313A LEU* 4.9 0.2 - - - -
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Residues in contact with ALA 302 (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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298A MET* 2.9 22.9 + - + +
299A PHE* 3.5 8.5 - - - +
300A VAL 3.1 0.4 + - - -
301A LEU* 1.3 75.7 - - - +
303A LYS* 1.3 60.8 + - - +
305A TYR* 4.1 1.0 - - - +
306A ARG* 3.2 12.1 + - - +
313A LEU* 3.9 15.0 - - + -
315A VAL* 5.7 0.2 - - + -
333A PHE* 4.7 13.5 - - + -
336A LEU* 4.0 11.9 - - + -
337A LEU* 3.2 35.7 - - + +
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Residues in contact with LYS 303 (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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125A ASP* 3.4 18.1 + - - -
126A LEU* 2.6 33.1 + - - +
127A TYR* 4.2 1.4 - - - +
128A PHE* 5.2 4.0 - - - +
133A ILE* 5.5 0.7 - - + -
299A PHE* 3.3 3.4 + - - +
300A VAL* 3.0 9.8 + - - +
302A ALA* 1.3 75.4 - - - +
304A LEU* 1.3 65.1 + - + +
306A ARG* 3.2 6.5 + - - +
307A LEU* 2.9 47.2 + - + +
336A LEU* 4.0 24.1 - - + +
352A LEU 5.3 0.8 + - - -
354A GLN* 3.1 34.5 - - + +
356A PHE* 3.6 32.5 - - + -
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Residues in contact with LEU 304 (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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101A LEU* 4.0 23.7 - - + +
105A LEU* 4.0 22.9 - - + -
126A LEU* 4.8 7.6 - - + -
128A PHE* 4.2 22.7 - - + -
136A PHE* 5.2 1.7 - - + -
261A TRP* 3.8 34.8 - - + -
300A VAL* 2.9 39.7 + - + +
301A LEU 4.0 0.9 - - - +
303A LYS* 1.3 81.8 - - + +
305A TYR* 1.3 58.1 + - - +
307A LEU* 3.4 9.8 + - + +
308A ILE* 3.0 34.8 + - - +
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Residues in contact with TYR 305 (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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256A VAL* 3.5 21.6 + - + -
257A VAL* 3.5 30.3 - - + +
261A TRP* 3.5 30.5 - + - -
264A LEU* 3.3 34.8 - - + -
282A ARG* 5.8 2.0 - - + -
298A MET* 5.6 1.3 - - + -
301A LEU* 2.9 49.4 + - + +
304A LEU* 1.3 75.4 - - - +
306A ARG* 1.3 63.1 + - - +
308A ILE* 3.6 2.4 + - + -
309A GLY 3.2 4.0 + - - -
310A ILE* 2.9 46.5 + - + +
313A LEU* 4.2 29.4 - - + -
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Residues in contact with ARG 306 (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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138A GLY* 3.3 0.2 - - - -
139A PRO* 2.9 29.8 - - + +
302A ALA 3.2 17.0 + - - +
303A LYS* 3.2 6.1 + - - +
305A TYR* 1.3 75.6 - - - +
307A LEU* 1.3 64.3 + - - +
309A GLY 3.2 3.5 + - - -
310A ILE 4.6 7.0 - - - -
336A LEU 3.1 24.9 + - - -
337A LEU* 3.3 28.5 + - + +
338A ARG 4.6 0.2 + - - -
339A GLU 2.8 34.2 + - - -
340A SER* 4.4 2.2 - - - +
356A PHE* 3.3 29.9 - - + +
359A ILE* 3.0 26.2 + - + +
360A LYS 2.6 26.1 + - - +
361A ALA* 3.4 8.1 - - - +
362A ALA* 3.8 13.7 - - + -
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Residues in contact with LEU 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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128A PHE* 3.9 29.8 - - + -
133A ILE* 4.0 21.8 - - + +
136A PHE* 3.1 32.8 - - + +
138A GLY* 2.8 27.8 + - - -
303A LYS* 2.9 34.3 + - + +
304A LEU* 3.6 9.6 - - + +
305A TYR 3.3 0.2 - - - -
306A ARG* 1.3 77.8 - - - +
308A ILE* 1.3 57.7 + - - +
356A PHE* 3.9 18.8 - - + -
359A ILE* 3.7 29.6 - - + -
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Residues in contact with ILE 308 (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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101A LEU* 3.9 10.3 - - + -
136A PHE* 4.2 21.1 - - + -
137A ASP* 5.1 1.9 + - - +
138A GLY 4.3 1.9 + - - -
261A TRP* 3.9 20.2 - - + +
264A LEU* 3.8 30.3 - - + +
265A ARG* 4.4 24.5 - - + +
268A ARG* 3.2 39.5 + - + +
304A LEU 3.0 21.9 + - - +
305A TYR* 3.9 5.8 - - + +
306A ARG 3.3 0.2 - - - -
307A LEU* 1.3 77.3 - - - +
309A GLY* 1.3 57.6 + - - +
310A ILE* 4.5 10.8 - - + -
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Residues in contact with GLY 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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138A GLY 3.2 28.3 - - - -
139A PRO* 3.3 10.6 - - - +
140A ALA 4.4 1.2 + - - -
268A ARG* 4.0 10.9 + - - +
278A ILE* 4.1 9.4 - - - +
305A TYR 3.2 2.2 + - - -
306A ARG 3.2 3.4 + - - -
308A ILE* 1.3 80.5 - - - +
310A ILE* 1.3 67.5 + - - +
311A ASP* 3.2 11.6 + - - +
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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