Contacts of the helix formed by residues 250 - 257 (chain E) in PDB entry 6DWZ
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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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248E ASP* 3.3 13.5 + - - -
249E ARG* 1.3 77.1 - - - +
251E ALA* 1.3 60.6 + - - -
252E ASN* 3.2 7.1 + - - -
253E VAL* 3.4 7.3 + - - +
254E VAL* 2.9 24.8 + - - +
6H A 3.9 5.6 - - - -
7H C 3.7 27.5 + - - -
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Residues in contact with ALA 251 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249E ARG 3.3 5.4 + - - +
250E GLY* 1.3 73.3 - - - -
252E ASN* 1.3 66.0 + - - +
254E VAL* 4.1 8.1 - - + -
255E LYS* 2.9 27.9 + - - +
21G C 3.8 17.6 + - - +
22G A 3.9 27.3 - - + +
23G C 6.1 0.9 - - - -
5H G 4.5 7.6 - - - +
6H A 5.0 5.6 + - - +
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Residues in contact with ASN 252 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181E LEU* 5.3 6.8 - - + +
219E SER* 3.2 26.7 + - - +
221E ALA* 3.5 13.7 - - - +
224E ILE* 3.7 17.9 - - + +
250E GLY* 3.2 2.7 - - - -
251E ALA* 1.3 78.0 + - - +
253E VAL* 1.3 63.1 + - + +
256E SER* 3.1 27.9 + - - -
20G T 5.2 2.2 + - - +
21G C 3.4 36.5 + - - +
22G A 4.7 5.6 + - - -
6H A 5.6 3.1 - - - -
7H C 6.1 0.7 + - - -
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Residues in contact with VAL 253 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179E ILE* 4.4 13.9 - - + -
180E ASP* 5.1 4.7 - - - +
181E LEU* 3.5 33.7 - - + +
224E ILE* 4.6 3.4 - - + -
247E THR* 3.1 40.6 - - + +
248E ASP* 3.7 19.7 - - - +
250E GLY* 3.4 4.8 + - - +
252E ASN* 1.3 77.9 - - + +
254E VAL* 1.3 71.9 + - - +
256E SER* 2.9 23.5 + - - +
257E LEU* 3.0 11.5 + - + +
262E ARG* 4.3 0.4 - - - -
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Residues in contact with VAL 254 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248E ASP 3.7 6.7 - - - +
249E ARG* 3.5 30.5 - - + +
250E GLY 2.9 22.2 + - - +
251E ALA* 3.9 7.2 - - - +
253E VAL* 1.3 79.0 - - - +
255E LYS* 1.3 68.3 + - - +
257E LEU 3.4 1.2 + - - -
258E ALA* 3.3 15.9 + - - +
262E ARG* 3.9 33.7 + - - +
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Residues in contact with LYS 255 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221E ALA* 3.8 11.7 - - + -
222E GLU* 4.0 19.5 + - - +
251E ALA 2.9 17.5 + - - +
254E VAL* 1.3 78.4 - - - +
256E SER* 1.3 65.4 + - - +
258E ALA* 2.8 27.1 + - + +
22G A 3.2 28.2 + - - +
23G C 2.7 40.4 + - - +
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Residues in contact with SER 256 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179E ILE* 5.1 1.7 - - - +
221E ALA* 3.3 33.6 - - - +
224E ILE* 4.2 13.9 - - - +
225E TYR* 3.2 36.0 - - - -
252E ASN 3.1 18.6 + - - -
253E VAL* 2.9 17.2 + - - +
255E LYS* 1.3 77.2 - - - +
257E LEU* 1.3 67.2 + - - +
258E ALA 3.5 0.9 + - - -
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Residues in contact with LEU 257 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179E ILE* 4.6 18.8 - - + -
225E TYR* 5.4 3.4 - - + -
228E LEU* 4.8 11.9 - - + -
245E PHE* 3.6 44.6 - - + -
247E THR* 5.1 6.5 - - + -
253E VAL* 3.0 14.0 + - + +
254E VAL 3.9 0.9 - - - -
256E SER* 1.3 83.5 + - - +
258E ALA* 1.3 66.4 + - - +
259E ASN* 2.8 5.9 + - - -
260E ASN* 3.0 47.0 + - + +
262E ARG* 3.7 23.4 - - + +
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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