Contacts of the helix formed by residues 250 - 258 (chain H) in PDB entry 4D1Q
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 GLY 250 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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248H ASP* 3.1 26.5 + - - -
249H ARG* 1.3 74.7 - - - +
251H ALA* 1.3 68.2 + - - -
252H ASN* 2.9 4.9 + - - -
253H VAL* 3.1 9.6 + - - +
254H VAL* 3.1 19.6 + - - +
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Residues in contact with ALA 251 (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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249H ARG 3.1 6.2 + - - -
250H GLY* 1.3 68.8 - - - -
252H ASN* 1.3 68.3 + - - +
254H VAL* 3.1 23.6 - - - +
255H LYS* 3.4 9.4 + - - +
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Residues in contact with ASN 252 (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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181H LEU* 3.9 18.0 - - + +
219H SER* 3.9 18.8 + - - +
220H THR* 5.1 2.1 - - - -
221H ALA* 4.5 7.3 + - - +
224H ILE* 3.8 19.1 - - + -
250H GLY 2.9 4.0 + - - -
251H ALA* 1.3 81.0 - - - +
253H VAL* 1.3 69.2 + - + +
254H VAL 3.0 1.6 + - - -
255H LYS* 3.1 4.5 + - - +
256H SER* 3.0 21.9 + - - -
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Residues in contact with VAL 253 (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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179H ILE* 3.4 33.0 - - + +
180H ASP* 5.0 6.1 - - - +
181H LEU* 4.6 24.0 - - + +
224H ILE* 4.8 4.5 - - + -
247H THR* 3.5 24.2 - - + +
248H ASP* 4.4 13.7 - - - +
250H GLY* 3.1 9.6 + - - +
252H ASN* 1.3 80.4 - - + +
254H VAL* 1.3 59.1 + - - +
256H SER* 2.4 24.5 + - - +
257H LEU* 3.2 14.5 + - + +
262H ARG* 4.2 0.9 - - - -
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Residues in contact with VAL 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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248H ASP 4.1 3.6 - - - +
249H ARG* 3.7 20.2 - - + +
250H GLY 3.1 11.4 + - - +
251H ALA* 3.1 23.3 - - - +
252H ASN 3.0 0.2 + - - -
253H VAL* 1.3 71.9 - - - +
255H LYS* 1.3 74.5 + - + +
256H SER 3.1 0.7 + - - -
257H LEU* 3.1 2.1 + - - +
258H ALA* 2.8 30.0 + - - +
262H ARG* 3.4 40.1 + - - +
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Residues in contact with LYS 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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221H ALA* 3.8 22.4 - - + +
222H GLU* 5.1 4.5 - - - +
251H ALA 3.9 7.2 - - - +
252H ASN* 3.1 7.9 + - - +
254H VAL* 1.3 84.7 - - + +
256H SER* 1.3 62.4 - - - +
258H ALA* 3.5 18.0 - - + +
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Residues in contact with SER 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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179H ILE* 5.8 0.2 - - - +
221H ALA* 3.6 28.7 - - - +
224H ILE* 3.8 20.3 - - - +
225H TYR* 3.5 27.5 - - - +
228H LEU* 6.5 0.7 - - - -
252H ASN 3.0 9.8 + - - -
253H VAL* 2.4 35.9 + - - +
255H LYS* 1.3 80.6 - - - +
257H LEU* 1.3 65.3 + - - +
258H ALA* 4.9 0.3 - - - +
259H ASN 5.1 0.2 + - - -
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Residues in contact with LEU 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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179H ILE* 4.1 12.1 - - + -
225H TYR* 4.6 2.9 - - + -
228H LEU* 3.9 25.6 - - + -
245H PHE* 3.5 53.8 - - + -
247H THR* 4.4 10.3 - - - +
253H VAL* 3.7 13.7 - - + +
254H VAL 3.1 1.8 + - - -
256H SER* 1.3 87.9 + - - +
258H ALA* 1.3 51.7 + - - +
259H ASN* 2.5 21.2 + - - +
260H ASN* 2.8 33.0 + - + +
262H ARG* 3.9 22.2 - - + -
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Residues in contact with ALA 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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254H VAL 2.8 17.3 + - - +
255H LYS* 3.5 20.9 - - + +
256H SER 4.9 0.2 - - - +
257H LEU* 1.3 66.1 - - - +
259H ASN* 1.3 67.0 + - - +
260H ASN 3.2 12.7 + - - +
262H ARG* 5.1 3.6 - - - +
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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