Contacts of the helix formed by residues 247 - 262 (chain A) in PDB entry 1S0V
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 ALA 247 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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225A GLY 3.1 19.3 - - - +
226A MET* 2.4 34.3 + - - +
228A SER* 4.6 10.1 - - - +
245A GLU 3.5 2.6 + - - -
246A LEU* 1.3 68.2 - - - +
248A PRO* 1.3 72.8 - - - +
249A GLU* 2.7 19.6 + - - +
250A TYR* 2.8 23.6 + - + +
251A ALA 2.9 9.7 + - - -
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Residues in contact with PRO 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A SER* 5.2 3.8 - - - +
245A GLU* 4.2 17.3 - - - +
246A LEU 3.0 10.8 - - - +
247A ALA* 1.3 79.8 - - - -
249A GLU* 1.3 73.2 + - - +
251A ALA* 3.4 9.8 + - + +
252A GLU* 3.1 27.4 + - - +
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Residues in contact with GLU 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A GLY 5.0 1.0 - - - +
247A ALA* 2.7 20.8 + - - +
248A PRO* 1.3 88.8 - - - +
250A TYR* 1.3 77.1 + - + +
252A GLU* 3.1 21.8 + - - +
253A ALA* 3.1 10.9 + - - +
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Residues in contact with TYR 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A LEU* 4.3 17.3 - - + +
77A LEU* 4.4 12.3 - - + -
80A LYS* 4.3 14.7 + - - -
224A THR* 5.5 1.1 - - - -
225A GLY* 4.9 5.3 + - - -
226A MET* 3.2 48.8 + - + -
246A LEU* 4.2 12.3 - - + -
247A ALA* 2.8 15.3 + - + +
249A GLU* 1.3 86.1 - - + +
251A ALA* 1.3 65.8 + - - +
253A ALA* 3.2 18.9 + - + +
254A ILE* 3.3 17.3 + - - +
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Residues in contact with ALA 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A ASN* 5.1 8.9 + - - +
246A LEU* 3.5 27.7 - - + +
247A ALA 2.9 9.2 + - - +
248A PRO* 3.6 14.4 - - + +
249A GLU 3.2 0.2 - - - -
250A TYR* 1.3 77.8 - - - +
252A GLU* 1.4 56.6 + - + +
254A ILE* 3.4 7.0 + - - +
255A ALA* 2.9 29.3 + - - +
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Residues in contact with GLU 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A ASN* 6.1 0.2 - - - +
248A PRO 3.1 19.2 + - - +
249A GLU* 3.1 13.5 + - - +
251A ALA* 1.4 75.4 - - - +
253A ALA* 1.3 57.5 - - - +
255A ALA* 4.4 6.1 - - - -
256A THR* 2.6 42.2 + - - +
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Residues in contact with ALA 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A LEU* 3.8 25.4 - - + -
249A GLU 3.1 9.6 + - - +
250A TYR* 3.3 17.5 - - + +
252A GLU* 1.3 74.8 - - - +
254A ILE* 1.3 53.5 + - - +
256A THR* 3.6 3.8 - - - -
257A ARG* 2.8 36.4 + - - +
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Residues in contact with ILE 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A PHE* 4.1 26.2 - - + -
59A LEU* 6.2 0.2 - - + -
64A VAL* 5.2 9.0 - - + -
69A ALA* 4.1 20.2 - - + +
70A ALA* 4.0 17.5 - - + -
73A LEU* 3.6 30.1 - - + -
123A LEU* 5.0 11.9 - - + -
246A LEU* 5.0 12.6 - - + -
250A TYR 3.3 5.5 + - - +
251A ALA* 3.5 8.5 - - - +
252A GLU 3.2 0.2 - - - -
253A ALA* 1.3 75.8 - - - +
255A ALA* 1.3 74.2 + - - +
256A THR 2.6 3.4 + - - -
257A ARG* 2.8 12.3 + - - +
258A ALA* 2.8 13.3 + - + +
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Residues in contact with ALA 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A ASN* 3.0 38.6 - - - +
3A THR* 3.3 13.7 - - - +
4A ILE* 3.3 16.3 - - + +
55A PHE* 6.1 0.4 - - - -
251A ALA 2.9 20.2 + - - +
252A GLU* 4.0 6.5 - - - +
254A ILE* 1.3 76.1 - - - +
256A THR* 1.3 57.1 + - - +
258A ALA* 4.5 2.9 - - - -
259A GLY 3.1 17.8 + - - -
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Residues in contact with THR 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A ILE* 2.9 28.7 - - + +
252A GLU* 2.6 28.6 + - - +
253A ALA* 3.6 4.9 - - - -
254A ILE 2.6 5.3 + - - -
255A ALA* 1.3 71.8 - - - +
257A ARG* 1.3 64.6 + - - +
258A ALA 3.1 1.6 - - - -
259A GLY* 3.0 10.2 + - - -
260A ALA* 3.0 17.4 + - + +
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Residues in contact with ARG 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A ALA* 3.6 17.1 + - - +
69A ALA 3.4 21.3 - - - +
72A PRO* 3.9 29.2 - - + +
253A ALA 2.8 21.0 + - - +
254A ILE 2.8 0.8 + - - +
256A THR* 1.3 72.7 - - - +
258A ALA* 1.3 57.5 + - - +
260A ALA* 3.8 4.2 + - - +
261A LEU* 3.1 47.5 + - - +
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Residues in contact with ALA 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A THR* 3.6 17.9 - - + +
51A PHE* 3.2 20.8 - - + -
55A PHE* 4.2 15.5 - - + -
69A ALA* 3.6 24.1 - - + +
254A ILE 2.8 13.8 + - - +
255A ALA* 3.9 0.9 - - - +
257A ARG* 1.3 75.0 - - - +
259A GLY* 1.3 67.1 + - - +
261A LEU* 4.0 0.7 - - - -
262A ALA* 3.0 21.8 + - - +
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Residues in contact with GLY 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A THR* 3.3 15.7 - - - +
4A ILE* 3.8 7.0 - - - -
6A ILE* 2.8 37.7 - - - +
255A ALA 3.1 11.3 + - - -
256A THR 3.0 9.0 + - - -
258A ALA* 1.3 79.0 - - - +
260A ALA* 1.3 59.4 + - - -
261A LEU 3.2 0.2 + - - -
262A ALA* 3.3 8.2 + - - +
263A GLY 3.7 0.5 + - - -
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Residues in contact with ALA 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A ILE* 3.7 7.6 - - - +
10A ASP* 5.6 3.1 - - - -
256A THR* 3.0 15.7 + - + +
257A ARG* 4.3 4.7 - - - +
259A GLY* 1.3 72.3 - - - +
261A LEU* 1.3 64.8 + - + +
263A GLY* 3.3 9.9 + - - -
264A ILE* 3.6 19.5 - - + +
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Residues in contact with LEU 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A PHE* 3.3 34.2 - - + -
68A ALA* 3.6 18.8 - - + -
69A ALA* 3.5 32.5 - - + +
257A ARG* 3.1 43.8 + - - +
258A ALA 3.4 1.1 - - - +
259A GLY 3.1 0.2 - - - -
260A ALA* 1.3 74.2 - - + +
262A ALA* 1.3 54.8 + - - +
263A GLY 2.5 17.8 + - - -
264A ILE* 2.8 26.4 + - + +
265A SER* 4.0 5.4 + - - -
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Residues in contact with ALA 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A THR* 5.7 2.5 - - + -
6A ILE* 4.6 0.9 - - + -
11A PHE* 4.3 1.4 - - - -
47A GLY 3.9 3.6 - - - -
48A GLU* 3.3 44.0 + - + +
51A PHE* 3.4 41.2 - - + -
52A ARG* 5.3 2.9 - - + +
258A ALA 3.0 9.2 + - - +
259A GLY* 3.5 8.1 - - - +
261A LEU* 1.3 76.9 - - - +
263A GLY* 1.3 57.0 + - - +
264A ILE 3.5 0.8 + - - -
265A SER* 4.5 4.0 + - - -
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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