Contacts of the helix formed by residues 297 - 309 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122F ARG* 3.7 31.5 + - - +
123F LEU 3.0 22.1 + - - -
124F GLU* 3.9 16.1 + - - -
289F THR* 4.3 0.2 - - - -
296F ILE* 1.3 78.6 - - - +
298F MET* 1.3 65.5 + - - +
299F PHE* 2.9 22.0 + - - +
300F VAL* 3.2 14.0 + - - +
301F LEU* 3.6 8.5 + - - +
333F PHE* 4.6 4.3 - - - -
351F HIS* 5.1 1.7 + - - -
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Residues in contact with MET 298 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122F ARG* 4.9 0.6 - - - +
282F ARG* 3.4 37.0 - - + +
285F HIS* 4.4 7.0 - - + -
289F THR* 3.9 19.5 + - - +
296F ILE 3.7 1.6 + - - -
297F SER* 1.3 73.5 + - - +
299F PHE* 1.3 57.8 + - - +
300F VAL 3.3 0.2 - - - -
301F LEU* 3.4 21.5 + - + -
302F ALA* 2.9 34.3 + - + +
305F TYR* 5.3 1.1 - - + -
313F LEU* 3.9 22.2 - - + -
314F HIS 3.4 26.0 - - - +
315F VAL* 4.7 4.3 - - + -
333F PHE* 3.4 30.9 - - + -
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Residues in contact with PHE 299 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124F GLU 3.7 7.6 - - - +
125F ASP* 3.6 30.3 - - - -
297F SER* 2.9 14.8 + - - +
298F MET* 1.3 80.0 - - - +
300F VAL* 1.3 60.5 + - - +
302F ALA* 3.5 1.4 + - - -
303F LYS* 3.3 7.5 + - - +
332F GLY* 4.2 19.5 - - - -
333F PHE* 3.5 26.1 - + + -
336F LEU* 3.1 52.9 - - + +
342F TYR* 3.6 22.4 - + - -
351F HIS* 3.2 51.6 - + + +
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Residues in contact with VAL 300 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105F LEU* 5.5 1.1 - - + -
123F LEU* 3.8 26.5 - - + +
124F GLU 3.8 2.9 - - - +
125F ASP* 3.7 36.3 - - - +
126F LEU* 3.9 22.7 - - + +
296F ILE* 4.1 12.6 - - + -
297F SER* 3.2 7.9 + - - +
299F PHE* 1.3 74.8 - - - +
301F LEU* 1.3 66.3 + - + +
303F LYS* 3.2 7.1 + - - +
304F LEU* 3.0 43.7 + - + +
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Residues in contact with LEU 301 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257F VAL* 4.2 12.6 - - + -
261F TRP* 4.1 16.8 - - + -
282F ARG* 5.9 0.2 - - + -
285F HIS* 4.4 2.2 - - + -
288F PHE* 3.7 31.2 - - + -
289F THR* 4.2 10.8 - - + -
296F ILE* 3.8 28.3 - - + -
297F SER 3.6 1.7 + - - +
298F MET* 3.4 21.9 + - - +
300F VAL* 1.3 83.3 - - + +
302F ALA* 1.3 62.6 + - - +
304F LEU* 3.2 5.1 + - + +
305F TYR* 2.8 60.6 + - + +
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Residues in contact with ALA 302 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298F MET* 2.9 23.1 + - + +
299F PHE* 3.6 8.5 - - - +
300F VAL 3.2 0.4 - - - -
301F LEU* 1.3 76.3 - - - +
303F LYS* 1.3 62.2 + - - +
305F TYR* 4.0 1.0 - - - +
306F ARG* 3.1 17.8 + - - +
313F LEU* 3.9 15.0 - - + -
315F VAL* 5.8 0.2 - - + -
333F PHE* 4.8 12.6 - - + +
336F LEU* 4.0 10.5 - - + -
337F LEU* 3.3 31.9 - - + +
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Residues in contact with LYS 303 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125F ASP* 3.5 19.4 + - - -
126F LEU* 2.9 31.8 + - + +
127F TYR* 4.3 0.8 - - - +
128F PHE* 5.3 3.4 - - + -
133F ILE* 5.5 0.2 - - + -
299F PHE* 3.3 3.3 + - - +
300F VAL* 3.2 9.4 + - - +
302F ALA* 1.3 79.8 - - - +
304F LEU* 1.3 62.9 + - + +
306F ARG* 3.3 6.3 + - - +
307F LEU* 2.8 51.7 + - + +
336F LEU* 3.8 27.7 - - + +
337F LEU* 5.3 0.2 - - - -
352F LEU 5.2 0.6 + - - -
354F GLN* 2.9 37.1 - - + +
356F PHE* 3.9 22.8 - - + -
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Residues in contact with LEU 304 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101F LEU* 4.1 16.6 - - + -
105F LEU* 3.9 23.3 - - + -
126F LEU* 4.6 6.5 - - + -
128F PHE* 3.7 35.7 - - + -
136F PHE* 5.1 0.8 - - + -
261F TRP* 3.8 32.8 - - + -
300F VAL* 3.0 38.9 + - + +
301F LEU* 3.9 3.1 - - + +
303F LYS* 1.3 78.5 - - + +
305F TYR* 1.3 58.3 + - - +
307F LEU* 3.3 8.8 + - + +
308F ILE* 2.8 35.5 + - - +
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Residues in contact with TYR 305 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256F VAL* 3.7 20.3 + - + -
257F VAL* 3.4 30.7 - - + +
261F TRP* 3.5 33.8 - + - -
264F LEU* 3.5 33.7 - - + -
282F ARG* 5.7 1.3 - - + -
288F PHE* 5.9 0.2 - - - -
298F MET* 5.3 1.8 - - + -
301F LEU* 2.8 53.0 + - + +
302F ALA 4.1 2.7 - - - +
304F LEU* 1.3 70.0 - - - +
306F ARG* 1.3 62.7 + - - +
308F ILE* 3.9 2.9 - - + +
309F GLY 3.1 5.0 + - - -
310F ILE* 2.9 43.3 + - + +
313F LEU* 4.0 27.8 - - + -
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Residues in contact with ARG 306 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138F GLY* 3.4 0.2 - - - -
139F PRO* 3.2 27.8 - - + +
302F ALA 3.1 19.1 + - - +
303F LYS* 3.6 4.9 - - - +
305F TYR* 1.3 73.2 - - - +
307F LEU* 1.3 66.9 - - - +
309F GLY 3.3 4.0 + - - -
310F ILE 4.5 7.9 - - - -
336F LEU 2.7 36.0 + - - -
337F LEU* 3.2 33.2 + - + +
338F ARG 4.1 1.0 + - - -
339F GLU 2.9 31.7 + - - -
340F SER* 4.3 2.2 - - - +
356F PHE* 3.5 26.9 - - - +
359F ILE* 3.1 29.2 + - + +
360F LYS 2.9 25.2 + - - +
361F ALA* 3.7 4.9 - - - +
362F ALA* 4.1 9.2 - - + -
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Residues in contact with LEU 307 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128F PHE* 3.5 37.2 - - + -
133F ILE* 3.9 25.1 - - + -
136F PHE* 3.1 36.4 - - + +
138F GLY* 3.0 22.4 + - - -
303F LYS* 2.8 37.7 + - + +
304F LEU* 3.5 8.1 - - + +
306F ARG* 1.3 77.4 - - - +
308F ILE* 1.3 63.2 + - - +
356F PHE* 4.1 12.8 - - + -
359F ILE* 4.0 23.6 - - + -
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Residues in contact with ILE 308 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101F LEU* 4.1 7.6 - - + -
136F PHE* 4.1 20.9 - - + -
137F ASP* 5.0 2.3 + - - +
138F GLY 3.9 2.9 + - - +
261F TRP* 4.0 31.2 - - + +
264F LEU* 4.1 27.6 - - + +
265F ARG* 4.2 26.9 + - + +
268F ARG* 3.4 38.4 + - + +
304F LEU 2.8 21.6 + - - +
305F TYR* 3.9 6.1 - - + +
307F LEU* 1.3 76.9 - - - +
309F GLY* 1.3 58.2 + - - +
310F ILE* 4.8 5.2 - - + -
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Residues in contact with GLY 309 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138F GLY 3.2 27.1 - - - -
139F PRO* 3.4 12.0 - - - +
140F ALA 4.4 0.9 + - - -
268F ARG* 4.1 12.2 + - - +
278F ILE* 3.9 9.2 - - - +
305F TYR 3.1 3.6 + - - -
306F ARG 3.3 1.8 + - - -
307F LEU 3.3 2.0 - - - -
308F ILE* 1.3 80.2 - - - +
310F ILE* 1.3 68.0 + - - +
311F ASP* 3.3 10.9 + - - +
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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