Contacts of the helix formed by residues 248 - 266 (chain I) in PDB entry 5U07
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 ASP 248 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243I VAL* 4.6 2.7 - - - +
246I THR* 3.3 18.1 + - - +
247I GLY* 1.3 75.7 - - - +
249I ALA* 1.3 84.3 + - - +
250I GLN* 2.2 48.2 + - - +
251I THR* 3.2 26.7 + - + +
252I ALA* 3.4 4.5 + - - +
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Residues in contact with ALA 249 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243I VAL* 4.6 13.2 - - + +
247I GLY 4.0 1.0 + - - -
248I ASP* 1.3 83.5 + - - +
250I GLN* 1.3 60.8 + - - +
252I ALA* 3.3 7.1 + - - +
253I ARG* 2.9 45.3 + - + +
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Residues in contact with GLN 250 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248I ASP* 2.2 48.7 + - - +
249I ALA* 1.3 77.0 - - - +
251I THR* 1.3 68.5 + - + +
253I ARG* 2.9 11.4 + - + +
254I THR* 2.9 33.0 + - + +
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Residues in contact with THR 251 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246I THR* 3.9 16.9 + - - +
248I ASP* 3.2 22.3 + - + +
250I GLN* 1.3 93.0 - - + +
252I ALA* 1.3 58.7 + - - +
254I THR* 2.7 24.8 + - - +
255I ALA* 2.9 17.2 + - - +
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Residues in contact with ALA 252 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242I LEU* 4.4 7.8 - - + +
243I VAL* 3.7 27.6 - - + +
246I THR* 3.7 14.6 - - - +
248I ASP 3.4 12.0 + - - +
249I ALA 3.3 9.7 + - - +
250I GLN 3.1 0.6 - - - -
251I THR* 1.3 83.4 + - - +
253I ARG* 1.3 59.4 + - - +
255I ALA* 3.2 7.1 + - - +
256I VAL* 2.9 36.7 + - + +
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Residues in contact with ARG 253 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239I LEU* 4.8 16.6 - - - +
243I VAL* 4.2 20.2 - - - +
249I ALA* 2.9 38.7 + - + +
250I GLN* 2.9 11.2 + - - +
252I ALA* 1.3 77.4 - - - +
254I THR* 1.3 64.0 + - + +
256I VAL* 3.2 8.2 + - - +
257I ALA* 2.9 26.1 + - - +
364I VAL* 4.1 24.2 + - + +
367I ALA* 2.3 45.5 + - - +
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Residues in contact with THR 254 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55I LEU* 5.0 11.7 - - - +
250I GLN* 2.9 14.0 + - + +
251I THR* 2.7 27.6 + - - +
253I ARG* 1.3 76.3 - - + +
255I ALA* 1.3 62.7 + - - +
257I ALA* 3.9 4.4 - - - +
258I GLU* 2.9 36.2 + - - +
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Residues in contact with ALA 255 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55I LEU* 5.7 0.4 - - - -
165I VAL* 4.1 23.1 - - + -
169I LEU* 4.5 7.9 - - + +
242I LEU* 4.6 13.7 - - + -
246I THR* 5.3 5.4 - - + -
251I THR 2.9 17.9 + - - +
252I ALA* 3.5 8.3 - - - +
254I THR* 1.3 77.9 + - - +
256I VAL* 1.3 56.9 + - - +
258I GLU* 3.3 14.2 - - - +
259I PHE* 2.9 30.4 + - - +
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Residues in contact with VAL 256 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4I VAL* 5.1 11.0 - - + -
169I LEU* 5.4 0.7 - - - -
237I VAL* 4.0 18.6 - - + -
239I LEU* 5.4 8.5 - - + -
242I LEU* 3.6 23.1 - - + -
252I ALA* 2.9 23.9 + - + +
253I ARG* 3.7 9.4 - - - +
255I ALA* 1.3 73.7 - - - +
257I ALA* 1.3 66.8 - - - +
259I PHE* 3.0 6.0 + - - +
260I LEU* 2.9 46.8 + - + +
364I VAL* 4.2 18.8 - - + -
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Residues in contact with ALA 257 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253I ARG 2.9 17.4 + - - +
254I THR* 3.9 5.6 - - - +
256I VAL* 1.3 77.8 - - - +
258I GLU* 1.3 63.7 + - - +
260I LEU* 3.2 2.3 + - - +
261I ARG* 2.9 28.5 + - - +
360I ILE* 4.4 19.0 - - + +
361I ASP* 5.2 7.6 - - - +
364I VAL* 4.3 15.0 - - + +
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Residues in contact with GLU 258 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50I GLU* 4.6 2.1 - - - +
51I VAL* 3.5 26.7 - - + +
54I ARG* 4.7 20.6 - - + +
55I LEU* 3.0 57.7 + - - +
165I VAL* 3.6 9.5 - - - +
254I THR* 2.9 27.7 + - - +
255I ALA* 3.3 8.8 - - - +
257I ALA* 1.3 76.0 - - - +
259I PHE* 1.3 60.9 + - - +
261I ARG* 3.8 7.7 - - - +
262I ALA* 2.9 29.1 + - - +
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Residues in contact with PHE 259 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6I ILE* 5.4 3.1 - - + -
47I VAL* 3.6 27.1 - - + -
51I VAL* 4.0 8.3 - - - -
169I LEU* 3.6 28.5 - - + -
170I PHE* 3.8 13.9 - + - -
186I VAL* 3.7 21.3 - - + -
188I PHE* 5.0 4.9 - + - -
235I ALA* 4.6 16.6 - - + -
237I VAL* 3.6 26.2 - - + -
255I ALA 2.9 20.2 + - - +
256I VAL* 3.0 4.5 + - - +
258I GLU* 1.3 78.2 - - - +
260I LEU* 1.3 75.9 + - + +
262I ALA* 3.2 2.8 + - - +
263I PHE* 2.9 37.8 + + + +
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Residues in contact with LEU 260 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4I VAL* 4.5 10.1 - - + -
6I ILE* 4.0 29.6 - - + -
237I VAL* 4.4 7.0 - - + -
256I VAL* 2.9 35.1 + - + +
257I ALA 3.7 3.6 - - - +
259I PHE* 1.3 92.4 - - + +
261I ARG* 1.3 64.2 + - - +
263I PHE* 3.0 16.8 + - - +
264I LEU* 3.0 18.2 + - + +
286I ILE* 4.5 9.0 - - + -
360I ILE* 4.0 25.8 - - + -
363I MET* 6.0 0.4 - - + -
364I VAL* 3.9 25.6 - - + -
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Residues in contact with ARG 261 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50I GLU* 6.1 1.1 - - - +
54I ARG* 3.7 43.1 - - - +
257I ALA* 2.9 19.8 + - - +
258I GLU* 3.8 6.5 - - - +
260I LEU* 1.3 77.8 - - - +
262I ALA* 1.3 57.3 + - - +
264I LEU* 3.3 2.6 + - - +
265I SER* 2.9 47.0 + - - +
357I PRO* 3.9 38.3 - - - +
360I ILE* 4.1 20.7 - - + +
361I ASP* 4.2 18.6 + - - -
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Residues in contact with ALA 262 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47I VAL* 4.1 12.2 - - + +
50I GLU* 3.2 37.9 + - + +
51I VAL* 3.9 14.8 - - + -
258I GLU 2.9 17.5 + - - +
259I PHE 3.2 5.1 + - - +
261I ARG* 1.3 75.7 - - - +
263I PHE* 1.3 63.6 + - - +
265I SER* 4.8 0.4 - - - -
266I THR* 3.0 32.9 + - - -
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Residues in contact with PHE 263 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6I ILE* 3.2 35.2 - - + -
8I ALA* 4.0 12.6 - - + -
47I VAL* 4.1 15.8 - - + +
188I PHE* 3.3 36.1 - + - -
233I ARG* 3.1 76.1 + - + -
234I TYR 4.6 1.3 - - - -
235I ALA* 4.6 5.8 - - + -
259I PHE* 2.9 23.4 + + + +
260I LEU* 3.0 11.6 + - - +
262I ALA* 1.3 78.5 - - - +
264I LEU* 1.3 78.1 + - + +
266I THR 4.1 4.3 - - - +
281I PRO* 6.0 0.2 - - + -
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Residues in contact with LEU 264 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6I ILE* 5.0 2.2 - - + -
8I ALA* 4.5 0.7 - - + -
10I GLN* 4.6 0.9 - - - +
260I LEU* 3.0 14.1 + - + +
261I ARG* 3.9 3.6 - - - +
263I PHE* 1.3 103.2 - - + +
265I SER* 1.3 67.6 + - - +
266I THR 3.6 3.8 + - - +
279I THR 4.6 1.6 - - - +
280I LEU* 4.5 2.3 - - - +
281I PRO* 3.4 33.4 - - + +
284I VAL* 3.6 45.3 - - + -
286I ILE* 5.3 0.7 - - + -
356I TYR* 4.4 24.0 - - + -
359I LEU* 6.1 0.2 - - + -
360I ILE* 3.7 28.0 - - + -
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Residues in contact with SER 265 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50I GLU* 5.9 3.1 - - - -
261I ARG* 2.9 29.8 + - - +
262I ALA* 4.8 0.4 - - - -
264I LEU* 1.3 79.9 - - - +
266I THR* 1.3 65.5 + - - +
267I VAL* 4.0 5.2 + - - +
279I THR 4.7 4.5 + - - +
280I LEU* 4.7 13.5 - - - +
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Residues in contact with THR 266 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10I GLN* 4.7 2.4 + - - -
46I ALA* 4.4 25.6 - - + +
47I VAL* 5.2 5.6 - - + +
50I GLU* 3.2 29.2 - - + +
233I ARG* 4.9 5.9 + - - -
262I ALA* 3.0 20.5 + - - -
263I PHE 4.1 7.6 - - - +
264I LEU 3.9 5.5 - - - +
265I SER* 1.3 81.0 - - - +
267I VAL* 1.3 86.0 + - - +
268I PRO* 5.0 0.3 - - - +
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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
------------------------------------------------------------
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