Contacts of the helix formed by residues 297 - 309 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122I ARG* 3.5 31.3 + - - +
123I LEU 2.9 21.9 + - - -
124I GLU* 3.7 16.5 + - - -
289I THR* 4.5 0.2 - - - -
296I ILE* 1.3 77.7 - - - +
298I MET* 1.3 64.1 + - - +
299I PHE* 2.8 24.1 + - - +
300I VAL* 3.0 15.6 + - - +
301I LEU* 3.5 7.6 + - - +
333I PHE* 4.6 4.3 - - - -
351I HIS* 5.0 2.1 + - - -
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Residues in contact with MET 298 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122I ARG* 4.8 0.4 - - - +
282I ARG* 3.4 38.6 - - + +
285I HIS* 4.4 4.3 - - + -
289I THR* 4.0 18.6 + - - +
296I ILE 3.6 2.8 + - - -
297I SER* 1.3 73.4 + - - +
299I PHE* 1.3 56.0 + - - +
301I LEU* 3.7 25.4 - - + -
302I ALA* 2.9 32.1 + - + +
305I TYR* 5.2 0.4 - - + -
313I LEU* 4.0 24.2 - - + -
314I HIS 3.4 24.7 - - - +
315I VAL* 4.8 4.5 - - + -
333I PHE* 3.6 33.0 - - + -
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Residues in contact with PHE 299 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124I GLU 3.6 7.4 - - - +
125I ASP* 3.3 38.1 - - - -
297I SER* 2.8 17.7 + - - +
298I MET* 1.3 79.0 - - - +
300I VAL* 1.3 60.0 + - - +
302I ALA* 3.4 1.6 + - - -
303I LYS* 3.3 18.3 + - - +
332I GLY* 4.1 17.3 - - - -
333I PHE* 3.6 24.6 - + + -
336I LEU* 3.3 41.1 - - + +
342I TYR* 3.8 22.4 - + - -
351I HIS* 3.4 47.1 - + + +
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Residues in contact with VAL 300 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105I LEU* 5.3 1.8 - - + -
123I LEU* 3.7 34.5 - - + +
124I GLU 3.8 1.1 - - - +
125I ASP* 3.7 32.8 - - - +
126I LEU* 4.0 20.0 - - + +
296I ILE* 3.9 13.7 - - + -
297I SER 3.0 9.1 + - - +
299I PHE* 1.3 75.1 - - - +
301I LEU* 1.3 66.8 + - + +
303I LYS* 3.3 6.2 + - - +
304I LEU* 3.0 43.3 + - + +
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Residues in contact with LEU 301 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257I VAL* 4.3 4.7 - - + -
261I TRP* 4.2 17.5 - - + -
282I ARG* 5.8 0.2 - - + -
285I HIS* 4.3 8.7 - - + -
288I PHE* 3.7 31.2 - - + -
289I THR* 3.9 13.5 - - + -
296I ILE* 3.9 26.5 - - + -
297I SER 3.5 1.5 + - - +
298I MET* 3.3 23.0 + - - +
300I VAL* 1.3 83.5 - - + +
302I ALA* 1.3 62.8 + - - +
304I LEU* 4.6 3.8 - - + -
305I TYR* 2.9 61.0 + - + +
313I LEU* 4.9 0.2 - - - -
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Residues in contact with ALA 302 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298I MET* 2.9 22.5 + - + +
299I PHE* 3.6 7.2 - - - +
300I VAL 3.2 0.2 - - - -
301I LEU* 1.3 76.7 - - - +
303I LYS* 1.3 63.1 + - - +
305I TYR* 4.2 1.0 - - - +
306I ARG* 3.1 17.7 + - - +
313I LEU* 3.9 15.3 - - + -
315I VAL* 5.6 0.2 - - + -
333I PHE* 4.7 14.4 - - + +
336I LEU* 4.2 9.9 - - + -
337I LEU* 3.2 32.5 - - + +
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Residues in contact with LYS 303 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125I ASP* 3.4 19.8 + - - +
126I LEU* 2.8 33.3 + - + +
127I TYR* 4.3 1.0 - - - +
128I PHE* 5.4 3.4 - - + -
133I ILE* 5.9 0.2 - - + -
299I PHE* 3.3 8.7 + - - +
300I VAL* 3.3 9.9 + - - +
302I ALA* 1.3 77.7 - - - +
304I LEU* 1.3 64.3 + - + +
306I ARG* 3.1 6.8 + - - +
307I LEU* 2.8 52.7 + - + +
336I LEU* 4.0 28.0 - - + +
337I LEU* 5.4 0.2 - - - -
342I TYR* 6.1 0.2 - - - -
352I LEU* 5.3 1.6 + - - +
354I GLN* 3.0 42.9 - - + +
356I PHE* 4.2 8.9 - - + -
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Residues in contact with LEU 304 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101I LEU* 3.9 23.6 - - + -
105I LEU* 4.0 24.2 - - + -
126I LEU* 4.5 7.6 - - + -
128I PHE* 4.1 22.9 - - + -
136I PHE* 5.4 1.1 - - + -
261I TRP* 3.7 35.9 - - + -
300I VAL* 3.0 38.6 + - + +
301I LEU* 4.0 0.7 - - + +
303I LYS* 1.3 79.9 - - + +
305I TYR* 1.3 58.3 + - - +
307I LEU* 3.3 10.2 + - + +
308I ILE* 2.8 35.4 + - - +
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Residues in contact with TYR 305 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256I VAL* 3.6 23.5 + - + -
257I VAL* 3.3 31.6 - - + +
261I TRP* 3.7 30.6 - + - -
264I LEU* 3.4 34.8 - - + -
282I ARG* 5.6 1.1 - - + -
288I PHE* 5.9 0.2 - - - -
298I MET* 5.2 2.2 - - + -
301I LEU* 2.9 49.6 + - + +
304I LEU* 1.3 72.1 - - - +
306I ARG* 1.3 63.9 + - - +
308I ILE* 3.5 1.9 + - + +
309I GLY 3.0 6.1 + - - -
310I ILE* 2.9 42.4 + - + +
313I LEU* 4.0 30.5 - - + -
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Residues in contact with ARG 306 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138I GLY* 3.5 0.5 - - - -
139I PRO* 3.2 27.6 - - + +
302I ALA 3.1 20.5 + - - +
303I LYS* 3.5 4.5 - - - +
305I TYR* 1.3 76.7 - - - +
307I LEU* 1.3 63.6 + - - +
309I GLY 3.3 3.8 + - - -
310I ILE 4.6 8.3 - - - -
336I LEU 2.6 36.8 + - - -
337I LEU* 3.2 32.9 + - + +
339I GLU 2.8 33.5 + - - -
340I SER* 4.1 2.4 - - - +
356I PHE* 3.5 31.5 - - + +
359I ILE* 3.2 26.0 + - + +
360I LYS 3.0 24.0 + - - +
361I ALA* 3.9 4.0 - - - +
362I ALA* 4.2 10.3 - - + -
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Residues in contact with LEU 307 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128I PHE* 3.7 35.0 - - + -
133I ILE* 3.9 22.7 - - + -
136I PHE* 3.2 34.9 - - + +
137I ASP 3.9 0.2 + - - -
138I GLY* 3.0 22.5 + - - -
303I LYS* 2.8 37.4 + - + +
304I LEU* 3.3 9.4 + - + +
306I ARG* 1.3 74.3 - - - +
308I ILE* 1.3 67.1 + - - +
356I PHE* 4.2 20.9 - - + -
359I ILE* 4.3 17.5 - - + -
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Residues in contact with ILE 308 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101I LEU* 4.0 15.7 - - + -
136I PHE* 4.1 13.0 - - + -
137I ASP* 5.0 1.9 + - - +
138I GLY 4.1 3.5 + - - +
261I TRP* 3.8 25.1 - - + +
264I LEU* 3.7 42.0 - - + +
265I ARG* 4.3 22.1 + - + +
268I ARG* 3.3 39.0 + - + +
304I LEU 2.8 22.5 + - - +
305I TYR* 3.8 5.8 - - + +
307I LEU* 1.3 75.8 - - - +
309I GLY* 1.3 58.6 + - - +
310I ILE* 4.7 3.8 - - + -
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Residues in contact with GLY 309 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138I GLY 3.2 27.6 - - - -
139I PRO* 3.4 10.7 - - - +
140I ALA 4.5 0.9 + - - -
268I ARG* 4.0 10.6 + - - +
278I ILE* 3.8 15.4 - - - +
305I TYR 3.0 3.8 + - - -
306I ARG 3.6 1.8 - - - -
307I LEU 3.2 1.4 - - - -
308I ILE* 1.3 80.5 - - - +
310I ILE* 1.3 64.7 - - - +
311I ASP* 3.3 6.4 + - - +
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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
------------------------------------------------------------
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