Contacts of the helix formed by residues 247 - 255 (chain A) in PDB entry 1WMA
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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16A ILE* 4.4 2.0 - - - +
19A ALA* 3.9 8.7 - - + +
20A ILE* 3.8 37.5 - - + +
23A ASP* 3.9 11.7 - - - +
243A PRO 2.9 16.5 + - - +
244A GLU 3.7 7.2 - - - +
245A GLU 3.2 0.4 - - - -
246A GLY* 1.3 75.7 - - - +
248A GLU* 1.3 64.0 + - - +
249A THR 3.5 0.7 - - - -
250A PRO* 3.3 4.1 - - - +
251A VAL* 2.9 25.1 + - + +
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Residues in contact with GLU 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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23A ASP* 5.5 4.0 - - - +
244A GLU 3.6 9.9 - - - +
245A GLU* 3.2 39.3 + - - +
246A GLY 3.2 0.4 - - - -
247A ALA* 1.3 75.9 - - - +
249A THR* 1.3 59.9 + - - +
251A VAL* 3.4 4.3 + - - +
252A TYR* 2.9 29.5 + - - +
271A LYS* 4.3 25.8 + - - +
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Residues in contact with THR 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 CYS* 3.9 13.7 - - + -
226A CYS 4.2 10.1 - - - +
227A PRO* 5.2 1.6 - - - -
241A LYS* 5.7 2.9 + - - -
245A GLU 4.8 0.6 + - - -
246A GLY 4.2 1.0 + - - -
248A GLU* 1.3 78.1 - - - +
250A PRO* 1.3 71.3 - - + +
252A TYR* 3.2 8.4 + - + +
253A LEU* 3.0 23.6 + - + +
268A VAL* 3.9 38.8 - - + +
270A GLU* 3.3 10.0 + - - -
271A LYS* 3.0 28.4 + - - +
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Residues in contact with PRO 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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16A ILE* 4.8 0.9 - - + -
20A ILE* 3.6 31.6 - - + -
87A VAL* 4.9 2.7 - - + +
135A VAL* 3.8 23.7 - - + +
137A VAL* 4.6 7.6 - - + -
225A CYS* 3.9 16.2 - - - -
227A PRO* 4.6 10.8 - - + -
246A GLY 3.3 21.1 - - - +
247A ALA 3.3 4.5 - - - +
249A THR* 1.3 94.8 - - + +
251A VAL* 1.3 57.0 + - - +
253A LEU* 3.3 3.5 + - - +
254A ALA* 3.0 27.3 + - - +
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Residues in contact with VAL 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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20A ILE* 4.1 27.1 - - + +
23A ASP* 3.8 34.3 - - + +
24A LEU* 4.6 6.5 - - + -
27A LEU* 4.4 9.2 - - + -
247A ALA 2.9 22.4 + - - +
248A GLU* 4.0 4.0 - - - +
250A PRO* 1.3 73.0 - - - +
252A TYR* 1.3 67.9 + - - +
254A ALA* 3.1 6.3 + - - +
255A LEU* 3.1 45.9 + - + +
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Residues in contact with TYR 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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248A GLU 2.9 18.3 + - - +
249A THR* 3.4 5.6 - - - +
251A VAL* 1.3 77.3 - - - +
253A LEU* 1.3 85.7 + - + +
255A LEU* 3.3 3.4 + - - -
256A LEU* 3.2 44.1 + - + +
263A PRO* 3.9 17.9 - - + +
268A VAL* 4.4 3.4 - - + -
271A LYS* 3.9 57.4 + - + -
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Residues in contact with LEU 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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133A ARG* 3.6 17.7 - - - +
134A VAL 5.2 0.9 - - - +
135A VAL* 3.6 17.3 - - + +
221A LEU 5.4 0.3 - - - +
223A ASN* 4.0 24.9 + - + +
225A CYS* 3.6 35.4 - - + -
249A THR* 3.0 24.6 + - + +
250A PRO 3.7 4.0 - - - +
252A TYR* 1.3 98.9 - - + +
254A ALA* 1.3 61.0 + - - +
255A LEU 3.5 0.3 + - - -
256A LEU* 3.6 13.9 - - + +
263A PRO* 3.8 23.3 - - + -
268A VAL* 4.0 13.5 - - + -
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Residues in contact with ALA 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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20A ILE* 6.2 0.2 - - + -
24A LEU* 4.2 17.7 - - + -
85A VAL* 3.6 34.3 - - + +
87A VAL* 4.4 5.8 - - + -
133A ARG* 3.5 23.2 - - - +
135A VAL* 3.5 11.8 - - + +
250A PRO 3.0 13.7 + - - +
251A VAL* 3.1 8.9 + - - +
253A LEU* 1.3 77.6 - - - +
255A LEU* 1.3 61.1 + - - +
256A LEU 3.6 0.9 - - - -
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Residues in contact with LEU 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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24A LEU* 3.9 15.7 - - + -
27A LEU* 3.5 39.7 - - + +
28A PHE* 3.8 33.4 - - + -
85A VAL* 5.3 0.2 - - + -
133A ARG* 5.1 0.4 - - - +
251A VAL* 3.1 31.6 + - + +
252A TYR* 3.7 4.7 - - - +
254A ALA* 1.3 85.2 - - + +
256A LEU* 1.3 66.5 + - - +
257A PRO* 3.2 6.1 - - - +
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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