Contacts of the helix formed by residues 253 - 260 (chain H) in PDB entry 2WWB
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 253 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20H LEU* 5.3 1.1 - - - -
209H TYR* 3.9 7.4 - - + +
210H ALA* 4.0 7.4 - - + -
211H GLU* 3.5 25.8 - - + +
252H GLU* 1.4 88.2 + - - +
254H ALA* 1.4 60.2 + - - +
255H PHE 3.4 2.5 - - - -
256H THR* 3.4 16.7 - - + +
257H LYS* 3.3 24.1 + - + +
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Residues in contact with ALA 254 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23H PRO* 5.6 0.7 - - - -
208H VAL 5.8 0.2 - - - +
209H TYR 5.0 4.5 - - - +
210H ALA* 4.5 6.0 - - + +
230H VAL* 3.9 26.9 - - + +
250H TRP* 4.6 14.1 - - + -
251H THR 3.3 20.9 - - - +
252H GLU* 3.1 3.2 + - - +
253H ALA* 1.4 75.5 - - - +
255H PHE* 1.4 64.2 + - - +
257H LYS* 3.7 2.4 + - - +
258H LEU* 3.1 26.4 + - - +
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Residues in contact with PHE 255 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20H LEU* 3.7 26.2 - - + -
21H PRO* 3.1 56.3 - - + +
22H LEU 4.8 0.2 - - - -
23H PRO* 3.8 36.9 - - + +
24H ALA 5.0 1.3 - - - -
252H GLU* 5.4 3.5 + - - +
253H ALA 3.4 1.0 - - - +
254H ALA* 1.4 77.9 - - - +
256H THR* 1.4 77.4 + - - +
258H LEU* 3.3 3.8 + - - +
259H ASP* 3.0 56.5 + - - +
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Residues in contact with THR 256 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20H LEU* 4.3 16.8 - - + -
253H ALA* 3.4 19.3 - - + +
255H PHE* 1.4 92.0 - - - +
257H LYS* 1.4 63.0 + - + +
259H ASP* 3.4 18.1 + - - +
260H GLN* 3.6 11.4 + - - +
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Residues in contact with LYS 257 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210H ALA* 3.0 40.6 + - + +
211H GLU* 4.5 15.5 + - + +
229H ASN* 3.8 1.0 + - - -
230H VAL* 4.0 14.3 - - + +
231H ALA* 3.8 24.2 - - - +
253H ALA* 3.3 17.2 + - + +
254H ALA 4.1 3.1 - - - +
255H PHE 3.3 0.2 - - - -
256H THR* 1.4 78.9 - - + +
258H LEU* 1.4 59.5 + - - +
260H GLN* 3.6 15.4 + - - +
261H VAL* 5.6 0.2 - - - +
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Residues in contact with LEU 258 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23H PRO* 3.9 25.4 - - + -
25H VAL* 4.0 30.6 - - + +
26H PHE* 4.2 3.4 - - + -
126H ILE* 3.9 37.2 - - + -
230H VAL* 5.0 19.4 - - + +
250H TRP* 6.3 2.5 - - + -
254H ALA 3.1 20.3 + - - +
255H PHE 3.6 4.0 - - - +
257H LYS* 1.4 74.4 - - - +
259H ASP* 1.4 64.9 + - - +
260H GLN 3.4 0.7 + - - -
261H VAL* 3.8 17.3 - - + +
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Residues in contact with ASP 259 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23H PRO* 5.3 0.9 - - - +
24H ALA* 5.0 11.1 + - - +
25H VAL* 5.1 10.0 - - - +
255H PHE* 3.0 44.8 + - + +
256H THR* 3.4 12.9 + - - +
258H LEU* 1.4 77.3 - - - +
260H GLN* 1.4 58.5 + - + +
261H VAL* 3.8 11.6 + - - +
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Residues in contact with GLN 260 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256H THR 3.6 11.6 + - - +
257H LYS* 3.6 12.8 + - - +
258H LEU 3.4 0.4 - - - -
259H ASP* 1.4 76.4 - - + +
261H VAL* 1.4 94.0 + - - +
262H TRP* 5.3 2.1 - - - +
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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