Contacts of the helix formed by residues 297 - 309 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122C ARG* 3.7 38.0 + - - +
123C LEU 3.0 20.7 + - - -
124C GLU* 3.8 15.3 + - - -
289C THR* 4.3 0.7 - - - -
296C ILE* 1.3 75.6 - - - +
298C MET* 1.3 61.7 + - - +
299C PHE* 2.9 20.0 + - - +
300C VAL* 2.9 25.4 + - - +
301C LEU* 3.5 5.0 + - - +
333C PHE* 4.7 3.6 - - - -
351C HIS* 5.1 1.6 + - - -
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Residues in contact with MET 298 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122C ARG* 5.0 0.2 - - - +
282C ARG* 3.4 38.6 - - + +
285C HIS* 4.3 6.3 - - + -
289C THR* 3.9 18.8 + - - +
296C ILE 3.8 1.8 + - - -
297C SER* 1.3 73.3 + - - +
299C PHE* 1.3 55.9 + - - +
300C VAL 3.2 0.4 - - - -
301C LEU* 3.8 26.5 - - + -
302C ALA* 2.9 31.0 + - + +
305C TYR* 5.3 1.1 - - + -
313C LEU* 4.1 21.8 - - + -
314C HIS 3.4 26.5 - - - +
315C VAL* 4.9 3.1 - - + -
333C PHE* 3.5 31.2 - - + -
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Residues in contact with PHE 299 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124C GLU 3.6 10.3 - - - +
125C ASP* 3.3 35.0 - - - -
297C SER* 2.9 15.6 + - - +
298C MET* 1.3 80.4 - - - +
300C VAL* 1.3 61.9 + - - +
303C LYS* 3.4 7.3 + - - +
332C GLY* 4.1 13.9 - - - -
333C PHE* 3.5 26.7 - + + -
336C LEU* 3.1 55.0 - - + +
342C TYR* 3.7 25.4 - + - -
351C HIS* 3.4 47.8 - + + +
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Residues in contact with VAL 300 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105C LEU* 5.5 2.0 - - + -
123C LEU* 3.6 47.3 - - + +
124C GLU 4.0 13.0 - - - +
125C ASP* 4.1 9.2 - - - +
126C LEU* 4.6 11.9 - - + +
296C ILE* 3.9 15.3 - - + -
297C SER 2.9 10.1 + - - +
299C PHE* 1.3 75.5 - - - +
301C LEU* 1.3 69.1 + - + +
303C LYS* 3.2 7.4 + - - +
304C LEU* 3.0 45.3 + - + +
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Residues in contact with LEU 301 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257C VAL* 4.4 5.8 - - + -
261C TRP* 4.2 17.3 - - + -
285C HIS* 4.3 9.2 - - + -
288C PHE* 3.8 30.1 - - + -
289C THR* 4.0 14.4 - - + -
296C ILE* 4.0 24.7 - - + -
297C SER 3.5 2.0 + - - +
298C MET* 3.4 23.5 + - - +
300C VAL* 1.3 80.7 - - + +
302C ALA* 1.3 64.9 + - - +
304C LEU* 3.3 3.9 + - - -
305C TYR* 2.8 59.0 + - + +
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Residues in contact with ALA 302 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298C MET* 2.9 22.2 + - + +
299C PHE* 3.8 7.0 - - - +
300C VAL 3.2 0.2 - - - -
301C LEU* 1.3 76.0 - - - +
303C LYS* 1.3 62.9 + - - +
305C TYR* 4.0 0.9 - - - +
306C ARG* 3.1 18.0 + - - +
313C LEU* 3.8 14.8 - - + -
315C VAL* 5.4 0.2 - - + -
333C PHE* 4.8 12.3 - - + +
336C LEU* 3.9 11.2 - - + -
337C LEU* 3.3 32.2 - - + +
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Residues in contact with LYS 303 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125C ASP* 3.3 20.5 + - - +
126C LEU* 2.8 32.9 + - + +
127C TYR* 4.0 1.2 - - - +
128C PHE* 5.2 4.3 - - + -
299C PHE* 3.4 9.1 + - - +
300C VAL* 3.2 9.5 + - - +
302C ALA* 1.3 79.7 - - - +
304C LEU* 1.3 66.2 + - + +
306C ARG* 3.2 7.1 + - - +
307C LEU* 2.9 45.0 + - + +
336C LEU* 3.8 27.6 - - + +
337C LEU* 5.4 0.2 - - - -
352C LEU 5.0 1.0 + - - -
354C GLN* 2.9 42.7 - - - +
356C PHE* 4.1 11.4 - - + -
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Residues in contact with LEU 304 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101C LEU* 4.1 19.5 - - + -
105C LEU* 4.0 23.1 - - + -
126C LEU* 4.5 6.5 - - + -
128C PHE* 3.8 30.7 - - + -
136C PHE* 5.2 1.1 - - + -
261C TRP* 3.8 35.4 - - + -
300C VAL* 3.0 38.8 + - + +
301C LEU 4.0 0.7 - - - +
303C LYS* 1.3 81.1 - - + +
305C TYR* 1.3 60.5 + - - +
307C LEU* 3.2 8.2 + - + +
308C ILE* 2.9 34.5 + - - +
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Residues in contact with TYR 305 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256C VAL* 3.7 20.5 + - + -
257C VAL* 3.5 30.3 - - + +
261C TRP* 3.5 32.8 - + - -
264C LEU* 3.3 34.5 - - + -
282C ARG* 5.7 0.7 - - + -
288C PHE* 6.0 0.2 - - - -
298C MET* 5.3 1.8 - - + -
301C LEU* 2.8 53.6 + - + +
304C LEU* 1.3 71.7 - - - +
306C ARG* 1.3 60.1 + - - +
308C ILE* 3.6 2.3 + - + +
309C GLY 3.1 4.5 + - - -
310C ILE* 2.9 45.6 + - + +
313C LEU* 4.0 31.0 - - + -
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Residues in contact with ARG 306 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139C PRO* 3.3 22.3 - - + +
302C ALA 3.1 14.1 + - - +
303C LYS* 3.4 9.0 - - - +
305C TYR* 1.3 75.8 - - - +
307C LEU* 1.3 65.5 + - - +
309C GLY* 3.2 9.2 + - - -
310C ILE 4.6 8.5 - - - -
336C LEU 2.7 32.9 + - - -
337C LEU* 3.2 35.0 + - + +
338C ARG 4.3 1.0 + - - -
339C GLU 2.8 32.9 + - - -
340C SER* 4.2 2.8 - - - +
356C PHE* 3.6 29.6 - - + +
359C ILE* 3.0 30.1 + - + +
360C LYS 3.0 24.6 + - - +
361C ALA* 3.8 4.2 - - - +
362C ALA* 4.4 8.3 - - + -
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Residues in contact with LEU 307 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128C PHE* 3.7 34.3 - - + -
133C ILE* 4.0 17.7 - - + -
136C PHE* 3.2 33.5 - - + +
137C ASP 3.8 0.2 + - - -
138C GLY* 2.9 28.0 + - - -
303C LYS* 2.9 33.3 + - + +
304C LEU* 3.6 9.9 - - + +
306C ARG* 1.3 75.4 - - - +
308C ILE* 1.3 57.6 + - - +
356C PHE* 3.8 28.3 - - + -
359C ILE* 4.0 19.7 - - + -
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Residues in contact with ILE 308 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C LEU* 4.0 9.2 - - + -
136C PHE* 4.1 19.7 - - + -
137C ASP* 4.9 2.1 + - - +
138C GLY 4.1 2.6 + - - +
261C TRP* 3.9 26.2 - - + +
264C LEU* 3.7 35.7 - - + -
265C ARG* 4.2 27.9 + - + +
268C ARG* 3.2 37.4 + - + -
304C LEU 2.9 17.8 + - - +
305C TYR* 3.9 5.4 - - + +
307C LEU* 1.3 76.4 - - - +
309C GLY* 1.3 59.6 + - - +
310C ILE* 4.6 6.1 - - + -
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Residues in contact with GLY 309 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138C GLY 3.3 27.6 - - - -
139C PRO* 3.5 10.6 - - - +
140C ALA 4.5 1.0 + - - -
268C ARG* 3.9 10.4 + - - +
278C ILE* 3.8 15.4 - - - +
305C TYR 3.1 3.6 + - - -
306C ARG 3.2 2.5 + - - -
308C ILE* 1.3 80.5 - - - +
310C ILE* 1.3 66.5 + - - +
311C ASP* 3.4 6.9 + - - +
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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