Contacts of the helix formed by residues 263 - 274 (chain F) in PDB entry 5OOM
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 LEU 263 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47F VAL* 3.8 30.1 - - + -
49F ARG* 3.8 32.9 + - + +
66F VAL* 3.8 16.2 - - + -
80F ALA* 3.6 25.1 - - + -
189F ILE* 3.7 12.8 - - + -
190F MET 3.0 15.8 + - - +
191F ASP* 4.5 6.9 + - + +
262F THR* 1.3 73.6 - - - +
264F PRO* 1.3 68.6 - - + +
266F VAL* 3.2 9.0 + - + +
267F ALA* 3.0 22.5 + - - +
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Residues in contact with PRO 264 (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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191F ASP 4.4 10.5 - - - +
220F ASP* 5.1 3.4 - - - +
221F LEU* 3.3 27.9 - - + +
262F THR* 3.4 15.7 - - - +
263F LEU* 1.3 92.0 - - + +
265F THR* 1.3 54.6 + - - +
267F ALA* 3.5 6.3 + - + +
268F PHE* 2.9 27.9 + - - +
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Residues in contact with THR 265 (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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219F VAL* 3.5 20.4 - - + +
220F ASP 3.4 32.3 - - - +
221F LEU* 3.4 7.6 - - - +
245F ALA* 4.1 5.6 - - + -
261F LEU* 3.5 10.7 - - - +
262F THR* 2.3 48.7 + - - +
264F PRO* 1.3 73.9 - - - +
266F VAL* 1.3 59.8 + - - +
268F PHE* 3.4 8.1 - - - +
269F LEU* 2.9 35.1 + - - +
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Residues in contact with VAL 266 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49F ARG* 3.5 24.5 - - - +
82F LEU* 3.6 17.5 - - + -
87F PHE* 4.0 13.9 - - + -
189F ILE* 4.3 18.6 - - + -
261F LEU* 3.7 29.2 - - + -
262F THR 3.0 19.9 + - - +
263F LEU* 3.2 11.6 + - + +
265F THR* 1.3 75.0 - - - +
267F ALA* 1.3 60.8 + - - +
269F LEU* 3.3 4.9 + - - +
270F GLU* 3.0 29.6 + - - +
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Residues in contact with ALA 267 (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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49F ARG* 4.8 15.2 - - - +
52F GLU* 5.0 11.7 - - + +
53F LEU* 5.3 1.9 - - - +
263F LEU 3.0 16.0 + - - +
264F PRO* 4.0 5.8 - - + +
266F VAL* 1.3 76.5 - - - +
268F PHE* 1.3 57.1 + - - +
270F GLU* 3.9 10.7 - - - +
271F ASP* 3.0 30.3 + - - +
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Residues in contact with PHE 268 (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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221F LEU* 4.1 23.6 - - + -
245F ALA* 3.6 28.0 - - + -
246F VAL* 4.5 10.3 - - + -
264F PRO 2.9 19.5 + - - +
265F THR* 3.4 8.3 - - - +
267F ALA* 1.3 76.6 - - - +
269F LEU* 1.3 59.2 - - + +
271F ASP* 3.2 5.1 + - - +
272F LYS* 2.9 66.0 + - + +
63i LEU* 3.2 47.8 - - + -
64i GLY* 5.4 0.4 - - - -
65i ASN* 5.7 0.4 - - - -
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Residues in contact with LEU 269 (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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86F VAL* 4.4 3.0 - - + +
87F PHE* 5.1 3.6 - - + -
174F LEU* 5.6 1.6 - - + -
178F LEU* 4.1 16.2 - - + -
219F VAL* 5.9 0.9 - - + -
245F ALA* 4.9 3.1 - - + +
248F LEU* 3.8 28.5 - - + -
261F LEU* 4.1 26.9 - - + -
265F THR* 2.9 23.0 + - - +
266F VAL* 3.3 4.2 + - - +
268F PHE* 1.3 76.6 - - + +
270F GLU* 1.3 62.0 + - - +
272F LYS* 4.4 1.8 - - - +
273F LEU* 3.0 52.4 + - + +
63i LEU* 3.6 29.6 - - + -
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Residues in contact with GLU 270 (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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49F ARG* 2.8 42.1 + - - -
51F VAL* 4.6 4.3 - - - +
52F GLU* 5.0 0.9 + - - +
53F LEU* 4.6 10.7 - - + +
82F LEU* 3.4 4.2 - - - +
83F HIS* 2.7 35.3 + - + -
86F VAL* 3.7 24.7 - - + -
87F PHE* 4.2 5.8 - - + -
266F VAL* 3.0 20.2 + - - +
267F ALA* 3.9 5.9 - - - +
269F LEU* 1.3 76.1 - - - +
271F ASP* 1.3 58.0 + - - +
274F LEU* 2.9 44.4 + - + +
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Residues in contact with ASP 271 (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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53F LEU* 4.4 20.7 - - + +
267F ALA 3.0 19.2 + - - +
268F PHE* 3.2 6.0 + - - +
270F GLU* 1.3 78.1 - - - +
272F LYS* 1.3 75.1 + - + +
274F LEU* 4.2 0.7 - - - -
275F TRP* 3.4 24.8 + - - +
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Residues in contact with LYS 272 (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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268F PHE* 2.9 61.2 + - + +
269F LEU* 4.4 3.6 - - - +
271F ASP* 1.3 91.8 + - - +
273F LEU* 1.3 63.5 + - + +
275F TRP* 3.9 15.5 - - + +
276F GLN* 4.2 8.3 - - - +
293F PHE* 6.1 3.6 - - + -
62i ILE 4.0 12.4 - - - +
63i LEU* 3.9 31.6 - - + -
65i ASN* 3.7 36.7 + - - +
66i PHE* 6.5 0.9 - - + -
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Residues in contact with LEU 273 (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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86F VAL* 4.0 24.7 - - + -
171F ALA* 3.6 38.4 - - + +
174F LEU* 4.0 30.1 - - + -
175F LYS* 3.5 28.0 + - + +
178F LEU* 4.3 11.4 - - + -
269F LEU* 3.0 33.4 + - + +
272F LYS* 1.3 85.0 - - + +
274F LEU* 1.3 58.9 + - - +
275F TRP 3.1 6.1 + - - -
276F GLN* 3.6 13.0 + - + +
277F ASP 4.2 0.7 + - - -
62i ILE* 4.8 5.2 - - + +
63i LEU* 5.8 1.8 - - + -
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Residues in contact with LEU 274 (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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53F LEU* 3.8 27.0 - - + +
83F HIS* 3.5 57.0 - - + +
85F ASP* 3.9 20.9 - - + +
86F VAL* 4.8 5.2 - - + +
175F LYS* 5.3 0.4 - - - +
270F GLU* 2.9 27.6 + - + +
271F ASP 4.2 0.4 - - - +
273F LEU* 1.3 76.3 - - - +
275F TRP* 1.3 58.9 + - - +
276F GLN 3.4 0.2 - - - -
277F ASP* 3.0 32.8 + - + +
278F SER* 4.2 3.5 + - - -
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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