Contacts of the helix formed by residues 241 - 254 (chain A) in PDB entry 1U75
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 ASP 241 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151A ALA* 3.8 13.3 - - + +
155A ARG* 2.7 39.3 + - - -
237A SER 3.3 13.2 + - - +
238A LEU 3.7 0.7 - - - +
239A ILE 3.2 1.3 - - - -
240A GLN* 1.3 79.8 - - - +
242A PRO* 1.4 67.6 - - - +
243A LYS* 3.3 9.5 + - - +
244A TYR* 3.2 28.3 + - + +
245A LEU* 2.9 31.9 + - - +
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Residues in contact with PRO 242 (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 GLN 4.3 4.0 - - - +
241A ASP* 1.4 89.9 - - - +
243A LYS* 1.3 68.7 + - + +
245A LEU* 3.9 10.5 - - + +
246A SER* 3.3 23.4 + - - -
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Residues in contact with LYS 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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155A ARG* 3.8 17.0 - - - +
165A ASP* 4.1 11.7 + - + +
241A ASP* 3.3 11.4 + - - +
242A PRO* 1.3 79.8 - - + +
244A TYR* 1.3 66.2 + - - +
246A SER* 3.5 13.4 + - - -
247A ILE* 3.5 21.7 - - + +
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Residues in contact with TYR 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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151A ALA* 3.7 27.4 - - + -
154A VAL* 3.7 4.8 - - + -
155A ARG* 3.2 42.9 + - - +
165A ASP* 3.2 31.3 + - + -
168A VAL* 3.6 31.5 - - + +
169A VAL* 3.6 19.5 - - + +
237A SER 4.6 0.2 - - - -
238A LEU* 3.3 35.0 - - + +
241A ASP* 3.2 24.9 + - + +
243A LYS* 1.3 80.5 - - - +
245A LEU* 1.3 55.7 + - - +
247A ILE* 3.2 7.4 + - - +
248A VAL* 3.0 29.1 + - - +
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Residues in contact with LEU 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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207A LEU* 3.8 28.9 - - + -
238A LEU 3.1 8.2 + - - +
239A ILE* 3.7 32.5 - - + +
241A ASP 2.9 18.7 + - - +
242A PRO* 3.9 10.5 - - + +
244A TYR* 1.3 72.8 - - - +
246A SER* 1.3 61.6 + - - +
248A VAL* 3.7 2.2 - - + +
249A LYS* 3.0 54.5 + - - +
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Residues in contact with SER 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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242A PRO 3.3 12.5 + - - -
243A LYS* 3.5 12.8 - - - -
245A LEU* 1.3 78.1 - - - +
247A ILE* 1.3 61.2 + - - +
249A LYS* 3.8 8.0 + - - +
250A GLU* 3.3 26.2 + - - +
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Residues in contact with ILE 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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165A ASP* 3.9 35.2 - - + +
166A ARG* 3.9 31.6 - - + +
169A VAL* 3.9 12.3 - - + -
243A LYS* 3.5 18.2 - - + +
244A TYR* 3.2 8.2 + - - +
245A LEU 3.2 0.2 - - - -
246A SER* 1.3 78.5 - - - +
248A VAL* 1.3 63.2 + - - +
249A LYS 3.3 1.1 - - - -
250A GLU* 3.3 8.0 + - - +
251A TYR* 3.0 55.8 + - + +
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Residues in contact with VAL 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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169A VAL* 3.9 13.9 - - + -
203A TYR* 3.7 35.3 - - + +
206A LEU* 4.3 4.3 - - + -
207A LEU* 4.1 19.1 - - + -
238A LEU* 3.8 33.0 - - + +
239A ILE* 4.2 13.0 - - + -
244A TYR 3.0 20.2 + - - +
245A LEU* 3.3 8.7 + - + +
247A ILE* 1.3 74.6 - - - +
249A LYS* 1.3 57.9 + - - +
251A TYR* 3.3 1.7 + - - -
252A ALA* 2.9 27.9 + - - +
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Residues in contact with LYS 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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207A LEU* 3.9 30.3 - - + -
245A LEU* 3.0 43.4 + - + +
246A SER* 3.8 8.5 - - - +
248A VAL* 1.3 73.6 - - - +
250A GLU* 1.3 65.0 + - - +
252A ALA* 4.0 1.4 - - - +
253A ASN* 3.3 24.3 + - - +
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Residues in contact with GLU 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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166A ARG* 2.5 44.5 + - - -
246A SER 3.3 14.1 + - - +
247A ILE* 3.3 13.5 + - - +
249A LYS* 1.3 79.9 - - - +
251A TYR* 1.3 60.6 + - + +
253A ASN* 4.0 3.8 - - - +
254A ASP* 3.2 27.2 + - - +
257A LYS* 3.8 15.4 - - + +
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Residues in contact with TYR 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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166A ARG* 3.2 36.4 + - - +
169A VAL* 3.9 5.2 - - + -
170A ALA* 3.7 23.6 - - + -
200A ASN* 2.9 22.5 + - - +
203A TYR* 3.7 37.2 - + + -
247A ILE* 3.0 34.6 + - + +
248A VAL 3.9 3.6 - - - +
250A GLU* 1.3 78.3 - - + +
252A ALA* 1.3 60.1 + - - +
253A ASN 3.2 2.2 - - - -
254A ASP 3.1 14.3 - - - +
255A GLN* 4.3 0.2 - - - -
257A LYS* 4.1 8.3 - - + -
258A PHE* 3.7 29.2 - + + -
261A ASP* 2.6 38.1 + - + +
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Residues in contact with ALA 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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200A ASN* 3.1 18.7 + - - +
203A TYR* 3.8 19.9 - - + +
204A LEU* 3.4 31.0 - - + +
207A LEU* 3.9 21.8 - - + -
248A VAL 2.9 17.2 + - - +
249A LYS 4.0 2.9 - - - +
250A GLU 3.5 0.2 - - - -
251A TYR* 1.3 76.8 - - - +
253A ASN* 1.3 58.7 + - - +
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Residues in contact with ASN 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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200A ASN* 4.8 0.4 - - - -
249A LYS 3.3 15.6 + - - +
250A GLU* 4.0 5.2 - - - +
251A TYR 3.2 0.4 - - - -
252A ALA* 1.3 81.0 - - - +
254A ASP* 1.3 62.3 + - - +
255A GLN 4.2 1.3 + - - -
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Residues in contact with ASP 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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250A GLU 3.2 10.3 + - - +
251A TYR* 3.1 16.2 - - - +
253A ASN* 1.3 84.2 - - - +
255A GLN* 1.3 63.7 + - - +
256A ASP* 3.4 11.4 + - - +
257A LYS* 2.8 40.9 + - + +
258A PHE 3.5 13.3 + - - -
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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