Contacts of the helix formed by residues 242 - 254 (chain A) in PDB entry 5UM9
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 242 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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229A LEU 5.3 1.1 - - - +
230A LEU* 4.3 8.7 - - - -
241A ILE* 1.3 73.8 - - - +
243A PRO* 1.3 76.9 - - - +
244A LYS 3.6 1.6 - - - -
246A ALA* 3.0 26.9 + - - +
4D C 3.1 25.5 + - - -
5D T 4.9 2.2 - - - -
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Residues in contact with PRO 243 (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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5A GLY 5.8 1.1 - - - +
9A LEU* 4.1 21.5 - - + -
230A LEU* 3.6 23.7 - - + -
242A GLY* 1.3 81.7 - - - +
244A LYS* 1.3 79.2 + - + +
245A ARG 3.1 0.2 + - - -
246A ALA* 3.8 0.5 - - - +
247A VAL* 2.9 31.3 + - + +
4D C 3.2 17.5 - - + +
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Residues in contact with LYS 244 (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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9A LEU* 5.8 5.7 - - + +
12A ASP* 5.1 16.7 + - - +
13A VAL* 5.1 10.2 - - + +
243A PRO* 1.3 88.5 - - + +
245A ARG* 1.3 61.0 + - + +
247A VAL* 3.9 4.0 + - - +
248A ASP* 2.9 29.5 + - - +
3D T 3.6 50.4 + - - +
4D C 3.2 16.7 + - - +
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Residues in contact with ARG 245 (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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240A GLY 3.5 19.6 + - - -
241A ILE* 4.2 15.3 - - + -
242A GLY 4.6 0.4 - - - +
243A PRO 3.2 0.2 - - - -
244A LYS* 1.3 73.4 - - + +
246A ALA* 1.3 61.0 + - - +
248A ASP* 3.3 6.1 + - - +
249A LEU* 2.9 38.3 + - + +
268A TYR* 3.7 23.7 + - - -
3D T 4.1 22.0 + - - +
4D C 2.7 43.0 + - - +
16E G 4.7 5.3 + - - +
17E T 3.8 38.2 + - - +
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Residues in contact with ALA 246 (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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226A LEU* 4.0 12.1 - - + -
229A LEU* 3.9 28.5 - - + -
230A LEU* 5.1 1.3 - - + -
241A ILE* 3.8 16.2 - - + +
242A GLY 3.0 22.2 + - - +
243A PRO* 3.9 1.8 - - + +
245A ARG* 1.3 76.9 - - - +
247A VAL* 1.3 63.7 + - - +
249A LEU* 4.1 5.8 - - - -
250A ILE* 2.9 29.5 + - - +
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Residues in contact with VAL 247 (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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9A LEU* 4.0 35.7 - - + -
13A VAL* 5.4 7.9 - - + -
216A LEU* 4.8 13.2 - - + -
218A LEU* 6.1 0.2 - - - +
226A LEU* 4.1 17.5 - - + -
243A PRO 2.9 21.2 + - - +
244A LYS* 4.0 2.9 - - - +
246A ALA* 1.3 76.2 - - - +
248A ASP* 1.3 65.4 + - - +
250A ILE* 4.0 1.5 - - - +
251A GLN* 2.9 57.9 + - + +
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Residues in contact with ASP 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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244A LYS 2.9 17.7 - - - +
245A ARG* 3.3 7.3 + - - +
247A VAL* 1.3 84.2 - - - +
249A LEU* 1.3 64.4 + - + +
251A GLN* 3.4 11.3 + - - +
252A LYS* 2.9 28.5 + - - +
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Residues in contact with LEU 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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229A LEU* 5.2 1.8 - - + -
241A ILE* 3.7 37.5 - - + -
245A ARG* 2.9 26.6 + - + +
246A ALA* 3.2 6.5 + - - +
248A ASP* 1.3 78.0 - - + +
250A ILE* 1.3 58.1 + - - +
252A LYS* 4.8 0.7 - - + -
253A HIS* 2.9 54.3 + - + +
259A ILE* 3.8 27.2 - - + +
263A LEU* 4.5 19.3 - - + -
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Residues in contact with ILE 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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218A LEU* 4.0 20.4 - - + -
222A GLN* 3.8 24.9 - - + +
225A ASP* 3.7 7.9 - - + -
226A LEU* 3.0 52.0 - - + +
229A LEU* 3.5 17.9 - - + -
246A ALA 2.9 11.6 + - - +
247A VAL 4.2 1.8 - - - +
249A LEU* 1.3 73.1 - - - +
251A GLN* 1.3 64.8 + - - +
252A LYS 3.0 1.6 - - - -
254A LYS* 2.8 38.7 + - - +
255A SER 5.3 2.2 - - - +
256A ILE* 5.9 0.2 - - + -
259A ILE* 3.8 18.2 - - + -
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Residues in contact with GLN 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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13A VAL* 6.0 1.8 - - - +
215A GLU 4.9 2.4 + - - -
216A LEU* 3.2 35.4 + - + +
217A GLY 5.5 0.7 - - - +
218A LEU* 4.3 14.4 - - + -
247A VAL* 2.9 42.5 + - + +
248A ASP* 3.8 11.9 - - - +
250A ILE* 1.3 77.0 - - - +
252A LYS* 1.3 55.9 + - - +
254A LYS* 3.1 19.5 - - - +
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Residues in contact with LYS 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 ASP 2.9 16.9 + - - +
249A LEU* 6.1 0.4 - - + -
251A GLN* 1.3 79.7 - - - +
253A HIS* 1.3 89.5 + - + +
254A LYS* 3.7 8.2 + - - +
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Residues in contact with HIS 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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249A LEU* 2.9 44.6 + - + +
252A LYS* 1.3 108.7 + - + +
254A LYS* 1.3 67.5 + - - +
255A SER* 3.0 10.6 + - - -
258A GLU* 3.6 31.0 - - + +
259A ILE* 3.9 22.0 - - + -
262A ARG* 3.6 42.3 + - + +
263A LEU* 6.1 0.6 - - + +
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Residues in contact with LYS 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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217A GLY 5.3 6.5 - - - -
218A LEU* 5.1 0.2 - - + -
222A GLN* 3.3 49.2 - - - +
225A ASP* 4.2 3.5 - - - +
250A ILE* 2.8 30.8 + - - +
251A GLN* 3.1 28.3 - - - +
252A LYS 4.3 5.1 + - - +
253A HIS* 1.3 80.5 - - - +
255A SER* 1.3 60.8 + - - +
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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