Contacts of the helix formed by residues 247 - 258 (chain A) in PDB entry 3UDB
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 SER 247 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114A GLU* 2.7 32.4 + - - -
246A ILE* 1.3 76.7 - - - +
248A PRO* 1.3 69.7 - - - +
249A GLU* 3.4 24.2 + - - -
250A CYS* 3.1 19.6 + - - +
251A ARG* 3.1 10.2 + - - +
276A TRP* 3.8 1.9 - - - -
279A LYS* 5.5 4.1 + - - -
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Residues in contact with PRO 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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246A ILE 3.6 2.2 - - - +
247A SER* 1.3 83.5 - - - +
249A GLU* 1.3 76.1 + - + +
251A ARG* 3.1 13.1 + - + +
252A HIS* 2.9 28.8 + - - +
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Residues in contact with GLU 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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247A SER* 3.2 15.5 + - - +
248A PRO* 1.3 99.3 - - + +
250A CYS* 1.3 62.0 + - - +
252A HIS* 3.4 5.6 + - - +
253A LEU* 3.2 8.3 + - - +
274A HIS* 3.2 29.3 - - + -
275A GLU* 3.6 25.7 - - + +
276A TRP* 3.9 19.9 - - + +
279A LYS* 4.7 11.1 + - - -
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Residues in contact with CYS 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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114A GLU* 3.7 4.9 - - - +
207A LEU* 5.3 2.0 - - - -
211A LEU* 3.5 31.9 - - - -
246A ILE* 4.2 16.8 - - + -
247A SER* 3.1 16.0 + - - +
249A GLU* 1.3 80.9 - - - +
251A ARG* 1.3 60.9 + - - +
253A LEU* 3.4 3.3 + - - +
254A ILE* 3.2 26.7 + - - +
276A TRP* 3.2 42.8 - - + +
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Residues in contact with ARG 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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238A TYR* 5.3 0.7 + - - -
240A ILE* 4.3 29.0 + - + +
244A VAL 4.3 10.7 + - - -
245A HIS* 5.3 2.6 + - - +
246A ILE* 3.9 44.9 + - + +
247A SER 3.1 10.8 + - - +
248A PRO* 3.1 14.3 + - + +
250A CYS* 1.3 76.7 - - - +
252A HIS* 1.3 62.0 + - - +
254A ILE* 4.0 5.9 - - - +
255A SER* 3.4 19.9 + - - -
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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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248A PRO 2.9 15.0 + - - +
249A GLU* 3.6 8.5 - - - +
250A CYS 3.1 0.2 - - - -
251A ARG* 1.3 76.0 - - - +
253A LEU* 1.3 64.8 + - - +
255A SER* 2.5 30.9 + - - -
256A ARG* 3.0 35.1 + - + +
274A HIS* 3.0 27.2 + + - +
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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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121A PHE* 4.0 20.0 - - + -
207A LEU* 4.4 6.7 - - + -
249A GLU 3.2 7.5 + - - +
250A CYS* 3.4 8.7 + - - +
252A HIS* 1.3 76.8 - - - +
254A ILE* 1.3 64.3 + - - +
256A ARG* 2.9 13.6 + - - +
257A ILE* 3.1 31.7 + - + +
266A ILE* 4.3 15.9 - - + -
271A ILE* 4.3 13.9 - - + -
274A HIS* 3.6 32.2 + - + +
276A TRP* 3.7 33.2 - - + -
277A PHE* 5.2 1.6 - - + -
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Residues in contact with ILE 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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204A GLY* 5.7 2.9 - - - +
207A LEU* 4.0 22.4 - - + -
208A TYR* 5.1 12.6 - - + +
211A LEU* 4.0 26.2 - - + -
238A TYR* 3.9 17.0 - - + +
240A ILE* 4.2 21.3 - - + -
246A ILE* 4.8 1.1 - - + -
250A CYS* 3.2 19.5 + - - +
251A ARG* 4.0 5.2 - - + +
253A LEU* 1.3 77.4 - - - +
255A SER* 1.3 63.9 + - - +
257A ILE* 3.1 9.3 + - + +
258A PHE* 3.0 49.1 + - + +
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Residues in contact with SER 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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238A TYR* 3.6 17.5 - - - -
251A ARG 3.4 10.8 + - - -
252A HIS* 2.5 34.2 + - - -
254A ILE* 1.3 78.7 - - - +
256A ARG* 1.3 61.5 + - - +
258A PHE* 3.9 7.8 + - - +
259A VAL* 3.4 16.6 - - - +
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Residues in contact with ARG 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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252A HIS* 3.0 45.3 + - + +
253A LEU* 2.9 10.6 + - - +
255A SER* 1.3 79.3 + - - +
257A ILE* 1.3 61.3 + - - +
259A VAL* 3.6 15.7 - - - +
264A LYS 3.1 24.7 + - - -
265A ARG* 3.9 0.2 - - - -
266A ILE* 3.1 66.7 + - + +
270A GLU* 4.2 12.5 + - - -
274A HIS* 5.5 0.2 - - + -
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Residues in contact with ILE 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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121A PHE* 4.3 16.4 - - + -
200A VAL* 3.5 28.3 - - + +
201A TRP* 3.8 10.8 - - - -
203A CYS* 5.8 0.4 - - + -
204A GLY* 3.7 28.0 - - - +
207A LEU* 4.8 3.4 - - + -
253A LEU* 3.1 33.2 + - + +
254A ILE* 3.1 8.9 + - + +
256A ARG* 1.3 76.9 - - - +
258A PHE* 1.3 63.3 + - + +
259A VAL 2.8 11.8 + - - -
265A ARG* 3.2 22.5 + - - +
266A ILE* 3.7 19.7 - - + -
271A ILE* 4.5 5.8 - - + -
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Residues in contact with PHE 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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201A TRP* 3.7 38.8 - + + -
204A GLY* 3.6 25.4 - - - -
205A VAL* 3.7 29.2 - - + -
208A TYR* 4.4 12.1 - + + -
216A PRO* 4.2 19.7 - - + -
217A PHE* 4.3 5.6 - + - -
236A VAL* 3.3 20.8 - - + +
238A TYR* 3.7 35.6 - + + +
254A ILE* 3.0 33.4 + - + +
255A SER* 3.9 4.8 - - - +
256A ARG 3.6 0.4 - - - -
257A ILE* 1.3 75.5 - - + +
259A VAL* 1.3 62.3 + - - +
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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