Contacts of the helix formed by residues 297 - 309 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B ARG* 3.6 33.1 + - - +
123B LEU 2.9 21.8 + - - -
124B GLU* 3.6 16.4 + - - -
289B THR* 4.2 0.2 - - - -
296B ILE* 1.3 78.1 - - - +
298B MET* 1.3 63.7 + - - +
299B PHE* 2.9 21.7 + - - +
300B VAL* 3.0 18.1 + - - +
301B LEU* 3.6 4.3 + - - +
333B PHE* 4.7 2.9 - - - -
351B HIS* 5.0 1.7 + - - -
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Residues in contact with MET 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B ARG* 4.8 0.8 - - - +
282B ARG* 3.3 40.4 - - + +
285B HIS* 4.4 4.9 - - + -
289B THR* 3.9 21.4 + - - +
296B ILE 3.6 1.8 + - - -
297B SER* 1.3 73.2 + - - +
299B PHE* 1.3 61.3 + - - +
301B LEU* 3.3 23.8 + - + -
302B ALA* 3.0 31.6 + - + +
305B TYR* 5.3 0.7 - - + -
313B LEU* 4.1 20.6 - - + -
314B HIS 3.7 23.8 - - - +
315B VAL* 5.0 3.4 - - + -
333B PHE* 3.8 28.9 - - + -
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Residues in contact with PHE 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B GLU 3.8 9.2 - - - +
125B ASP* 3.8 28.7 - - - -
297B SER* 2.9 14.4 + - - +
298B MET* 1.3 80.2 - - - +
300B VAL* 1.3 60.1 + - - +
302B ALA* 3.7 0.4 + - - -
303B LYS* 3.5 10.1 + - - +
332B GLY* 3.7 21.3 - - - -
333B PHE* 3.6 28.9 - + + -
336B LEU* 3.0 51.8 - - + +
342B TYR* 3.6 35.0 - + - -
351B HIS* 3.5 37.7 - + - +
352B LEU 5.5 0.2 - - - -
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Residues in contact with VAL 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B LEU* 5.6 1.1 - - + -
123B LEU* 3.9 31.9 - - + +
124B GLU 3.8 5.6 - - - +
125B ASP* 3.8 35.9 - - - +
126B LEU* 4.0 14.6 - - + +
296B ILE* 4.0 13.2 - - + -
297B SER 3.0 9.3 + - - +
299B PHE* 1.3 77.0 - - - +
301B LEU* 1.3 65.9 + - + +
303B LYS* 3.4 4.7 + - - +
304B LEU* 3.0 44.0 + - + +
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Residues in contact with LEU 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257B VAL* 4.3 4.7 - - + -
261B TRP* 3.7 28.9 - - + -
282B ARG* 5.7 0.2 - - + -
285B HIS* 4.2 9.0 - - + -
288B PHE* 3.9 35.7 - - + -
289B THR* 3.9 12.8 - - + -
296B ILE* 4.5 12.3 - - + -
297B SER 4.1 9.2 - - - +
298B MET* 3.3 21.5 + - + +
300B VAL* 1.3 78.2 - - + +
302B ALA* 1.3 66.8 + - - +
304B LEU* 3.1 4.1 + - - -
305B TYR* 2.8 51.9 + - + +
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Residues in contact with ALA 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B MET* 3.0 23.3 + - + +
299B PHE* 3.8 7.6 - - - +
300B VAL 3.4 0.2 - - - -
301B LEU* 1.3 75.5 - - - +
303B LYS* 1.3 61.2 + - - +
305B TYR* 4.0 0.9 - - - +
306B ARG* 3.0 18.7 + - - +
313B LEU* 3.8 16.4 - - + -
315B VAL* 5.7 0.2 - - + -
333B PHE* 4.6 13.2 - - + -
336B LEU* 4.0 10.1 - - + -
337B LEU* 3.2 31.3 - - + +
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Residues in contact with LYS 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B ASP* 3.4 18.8 + - - +
126B LEU* 2.7 32.3 + - + +
127B TYR* 4.1 1.0 - - - +
128B PHE* 5.4 4.3 - - + -
299B PHE* 3.5 6.2 + - - +
300B VAL* 3.4 8.2 + - - +
301B LEU 3.2 0.4 - - - -
302B ALA* 1.3 78.3 - - - +
304B LEU* 1.3 62.4 + - + +
306B ARG* 3.3 5.6 + - - +
307B LEU* 2.9 51.0 + - + +
336B LEU* 3.7 32.7 - - + +
342B TYR* 6.2 1.1 - - - -
352B LEU* 5.3 1.8 + - - +
354B GLN* 2.7 43.5 - - - +
356B PHE* 4.0 11.8 - - + -
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Residues in contact with LEU 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B LEU* 4.1 17.9 - - + +
105B LEU* 4.0 23.3 - - + -
126B LEU* 4.8 6.3 - - + -
128B PHE* 4.0 29.8 - - + -
136B PHE* 5.4 0.4 - - + -
261B TRP* 3.6 36.6 - - + -
300B VAL* 3.0 39.1 + - + +
301B LEU* 3.7 2.5 - - + +
303B LYS* 1.3 80.4 - - + +
305B TYR* 1.3 57.8 + - - +
307B LEU* 3.1 10.6 + - + +
308B ILE* 2.8 34.5 + - - +
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Residues in contact with TYR 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256B VAL* 3.6 23.4 + - + -
257B VAL* 3.4 30.3 - - + +
260B GLY 6.4 0.2 - - - -
261B TRP* 3.6 31.4 - + - -
264B LEU* 3.4 33.7 - - + -
282B ARG* 5.6 0.9 - - + -
298B MET* 5.3 1.3 - - + -
301B LEU* 2.8 55.8 + - + +
302B ALA 4.1 2.0 - - - +
304B LEU* 1.3 69.8 - - - +
306B ARG* 1.3 64.1 + - - +
308B ILE* 3.4 2.1 + - - +
309B GLY 3.0 5.9 + - - -
310B ILE* 2.9 45.1 + - + +
313B LEU* 4.1 26.5 - - + -
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Residues in contact with ARG 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B GLY* 3.5 0.5 - - - -
139B PRO* 3.3 16.3 - - + +
302B ALA 3.0 19.1 + - - +
303B LYS* 3.5 4.3 - - - +
304B LEU 3.2 0.2 - - - -
305B TYR* 1.3 76.6 - - - +
307B LEU* 1.3 64.2 + - - +
309B GLY 3.0 9.7 + - - -
310B ILE 4.6 8.7 - - - -
336B LEU 2.9 26.2 + - - -
337B LEU* 3.3 35.5 + - + +
339B GLU 2.8 32.9 + - - -
340B SER* 4.5 2.4 - - - +
356B PHE* 3.4 29.3 - - + +
359B ILE* 2.9 30.9 + - + +
360B LYS 3.0 24.3 + - - +
361B ALA* 3.7 4.8 - - - +
362B ALA* 4.3 7.4 - - + -
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Residues in contact with LEU 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B PHE* 3.7 35.4 - - + -
133B ILE* 3.9 24.2 - - + -
136B PHE* 3.2 36.5 - - + +
137B ASP 3.9 0.2 + - - -
138B GLY* 3.1 20.7 + - - -
303B LYS* 2.9 36.4 + - + +
304B LEU* 3.4 11.2 - - + +
306B ARG* 1.3 76.0 - - - +
308B ILE* 1.3 62.9 + - - +
356B PHE* 4.0 20.4 - - + -
359B ILE* 4.2 17.5 - - + -
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Residues in contact with ILE 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B LEU* 4.2 14.8 - - + -
136B PHE* 4.2 11.4 - - + -
137B ASP* 5.2 1.4 + - - +
138B GLY* 4.1 2.6 + - - +
261B TRP* 3.9 26.7 - - + +
264B LEU* 3.3 48.5 - - + +
265B ARG* 4.3 18.6 + - + +
268B ARG* 3.3 36.2 + - + +
304B LEU 2.8 19.2 + - - +
305B TYR* 3.7 6.5 - - + +
307B LEU* 1.3 76.5 - - - +
309B GLY* 1.3 57.6 + - - +
310B ILE* 4.5 4.3 - - + -
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Residues in contact with GLY 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138B GLY 3.1 30.1 - - - -
139B PRO* 3.2 13.8 - - - +
140B ALA 4.2 2.1 + - - -
268B ARG* 4.2 6.2 + - - +
278B ILE* 4.1 9.0 - - - +
305B TYR 3.0 3.6 + - - -
306B ARG 3.0 4.4 + - - -
308B ILE* 1.3 79.7 - - - +
310B ILE* 1.3 69.1 + - - +
311B ASP* 3.1 9.7 + - - +
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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