Contacts of the helix formed by residues 250 - 260 (chain A) in PDB entry 4DX2
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 CYS 250 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199A LEU* 6.0 0.2 - - - -
202A LEU* 3.4 33.0 - - - -
205A GLY* 3.9 18.6 - - - -
245A ALA* 2.9 12.4 + - - +
248A ARG* 3.7 15.0 - - - -
249A ARG* 1.3 76.4 - - - +
251A LYS* 1.3 65.2 + - - +
252A HIS* 3.3 23.8 - - + +
253A TYR* 3.1 18.5 + - + -
254A VAL* 3.2 15.5 + - - +
300A ILE* 4.8 0.4 - - - +
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Residues in contact with LYS 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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249A ARG 3.7 5.1 + - - -
250A CYS* 1.3 71.4 - - - +
252A HIS* 1.3 57.6 + - + +
254A VAL* 3.0 10.9 + - + +
255A GLU* 2.5 69.5 + - + +
299A HIS* 3.9 35.0 - - + +
300A ILE* 3.9 28.6 - - + +
303A TYR* 4.6 13.0 - - + +
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Residues in contact with HIS 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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205A GLY* 2.9 30.4 + - - -
206A ARG* 5.1 1.6 - - + -
250A CYS* 3.4 14.2 - - + +
251A LYS* 1.3 81.4 - - - +
253A TYR* 1.3 92.4 + + + -
255A GLU* 3.6 9.9 + - - +
256A LEU* 3.1 26.0 + - - +
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Residues in contact with TYR 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A LEU* 4.1 11.9 - - + -
202A LEU* 4.0 8.5 - - + -
205A GLY 3.3 20.0 - - - -
206A ARG* 3.4 7.4 + - - +
207A ASN 2.7 29.5 + - - -
208A ASP* 4.6 3.8 + - - -
210A ILE* 3.6 45.8 - - + -
211A PRO* 4.6 8.0 - - + +
245A ALA* 4.1 15.0 - - + -
250A CYS* 3.1 18.6 + - + +
252A HIS* 1.3 99.8 - + - +
254A VAL* 1.3 57.3 + - - +
256A LEU* 3.6 11.2 - - + +
257A LEU* 2.7 43.2 + - + +
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Residues in contact with VAL 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A LEU* 4.1 16.4 - - + -
245A ALA* 3.6 21.0 - - + +
246A ILE* 3.7 25.6 - - + +
250A CYS 3.2 15.0 + - - +
251A LYS* 3.0 12.7 + - + +
253A TYR* 1.3 76.7 - - - +
255A GLU* 1.3 65.3 + - + +
257A LEU* 3.7 0.5 - - - +
258A VAL* 2.8 27.9 + - + +
300A ILE* 4.4 16.6 - - + -
303A TYR* 4.1 20.0 - - + -
304A LEU* 4.5 8.7 - - + -
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Residues in contact with GLU 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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251A LYS* 2.5 58.6 + - + +
252A HIS* 3.9 7.1 - - - +
254A VAL* 1.3 71.3 - - - +
256A LEU* 1.3 64.5 + - - +
259A ALA* 2.8 29.4 + - - +
303A TYR* 3.6 42.1 + - + +
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Residues in contact with LEU 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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210A ILE* 4.2 19.5 - - + -
211A PRO* 4.4 17.7 - - + -
214A LEU* 3.7 21.3 - - + -
252A HIS 3.1 18.3 + - - +
253A TYR* 3.6 14.8 - - + +
255A GLU* 1.3 75.6 - - - +
257A LEU* 1.3 64.4 + - + +
259A ALA* 3.8 4.2 - - - +
260A GLN* 3.0 44.5 + - + +
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Residues in contact with LEU 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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195A LEU* 4.3 25.6 - - + -
199A LEU* 4.4 7.9 - - + -
210A ILE* 5.4 4.9 - - + -
214A LEU* 4.4 13.2 - - + -
227A ILE* 4.4 19.9 - - + +
241A ALA* 3.6 15.3 - - + +
242A LEU* 3.6 35.9 - - + +
245A ALA* 4.1 10.3 - - + -
253A TYR* 2.7 28.6 + - + +
254A VAL 3.7 2.7 - - - +
256A LEU* 1.3 74.6 - - + +
258A VAL* 1.3 62.0 + - - +
260A GLN* 3.2 11.9 + - - +
261A GLY 3.3 1.2 + - - -
262A ALA* 3.1 28.5 + - + +
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Residues in contact with VAL 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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242A LEU* 4.2 18.4 - - + -
254A VAL* 2.8 22.8 + - + +
257A LEU* 1.3 68.8 - - - +
259A ALA* 1.3 58.0 + - - +
261A GLY* 2.8 27.4 + - - -
262A ALA* 3.6 7.0 + - - +
264A VAL* 4.1 21.1 - - + -
303A TYR* 3.5 29.6 - - + +
304A LEU* 4.2 9.9 - - + -
307A ASN* 3.7 22.7 - - - +
309A HIS* 4.0 12.4 - - + +
310A LYS* 4.4 9.1 - - + +
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Residues in contact with ALA 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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255A GLU 2.8 20.9 + - - +
256A LEU* 3.8 6.1 - - + +
258A VAL* 1.3 73.1 - - - +
260A GLN* 1.3 74.0 + - - +
261A GLY 3.3 1.0 + - - -
303A TYR* 4.8 0.2 - - - +
309A HIS* 3.4 41.9 + - + +
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Residues in contact with GLN 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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214A LEU* 3.9 2.7 - - + -
218A GLU* 5.4 2.1 - - - +
223A MET* 3.4 37.4 - - + +
224A ARG* 4.3 10.2 + - - +
227A ILE* 3.5 29.7 - - + +
256A LEU* 3.0 40.5 + - + +
257A LEU 3.6 2.7 - - - +
258A VAL 3.0 0.6 + - - -
259A ALA* 1.3 89.3 + - - +
261A GLY* 1.3 56.3 + - - +
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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