Contacts of the helix formed by residues 235 - 247 (chain A) in PDB entry 1P45
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 ALA 235 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A ILE* 5.1 11.3 - - + +
24A HIS* 3.6 37.6 + - + +
194A ILE* 4.0 32.3 - - + +
234A ASP* 1.3 71.6 + - - +
236A THR* 1.3 58.4 + - - +
237A PRO* 3.5 2.0 - - - -
238A VAL* 3.2 8.3 + - + +
239A ALA* 3.0 25.6 + - - +
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Residues in contact with THR 236 (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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24A HIS* 5.5 0.4 - - - -
27A ARG* 3.7 29.4 + - - +
28A VAL* 5.1 4.8 - - + +
234A ASP* 3.3 16.1 + - - -
235A ALA* 1.3 78.7 + - - +
237A PRO* 1.3 60.3 - - + +
239A ALA* 3.0 5.8 + - - +
240A LYS* 2.6 57.1 + - + +
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Residues in contact with PRO 237 (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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230A TRP* 5.1 12.8 - - + -
234A ASP* 3.6 26.9 - - - +
235A ALA 3.6 2.0 - - - -
236A THR* 1.3 97.8 - - + +
238A VAL* 1.3 62.8 + - + +
240A LYS* 3.7 12.1 - - + +
241A THR* 2.7 30.1 + - - -
260A ALA* 5.3 1.8 - - + -
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Residues in contact with VAL 238 (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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21A ILE* 4.4 21.5 - - + -
147A MET* 4.6 7.6 - - - -
189A VAL* 4.2 15.3 - - + -
191A ALA* 4.1 22.7 - - + -
194A ILE* 4.2 15.0 - - + -
230A TRP* 3.7 29.8 - - + -
235A ALA* 3.2 10.0 + - + +
237A PRO* 1.3 77.8 - - + +
239A ALA* 1.3 60.6 + - - +
241A THR* 2.9 16.8 + - - -
242A VAL* 3.1 12.8 + - + +
260A ALA* 4.0 11.0 - - + +
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Residues in contact with ALA 239 (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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21A ILE* 5.3 1.1 - - + +
24A HIS* 3.3 37.0 - - + +
25A ILE* 3.8 16.7 - - + +
28A VAL* 3.5 12.6 - - + -
235A ALA 3.0 11.5 + - - +
236A THR* 3.0 6.7 + - - +
238A VAL* 1.3 70.8 - - - +
240A LYS* 1.3 68.3 + - - +
241A THR 2.9 2.6 + - - -
242A VAL* 3.3 4.2 + - - +
243A CYS* 3.1 25.8 + - - -
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Residues in contact with LYS 240 (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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28A VAL* 4.5 19.7 - - + +
236A THR* 2.6 42.1 + - + +
237A PRO* 3.7 11.0 - - + +
239A ALA* 1.3 73.8 - - - +
241A THR* 1.3 60.9 + - - +
243A CYS* 3.4 5.7 + - - +
244A ALA* 3.2 19.6 + - - +
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Residues in contact with THR 241 (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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189A VAL* 4.1 12.6 - - + -
237A PRO 2.7 20.1 + - - -
238A VAL 2.9 7.8 + - - -
240A LYS* 1.3 75.0 - - - +
242A VAL* 1.3 69.7 + - - +
244A ALA* 2.9 24.1 + - + +
245A LEU* 3.3 8.7 + - + +
258A ILE* 4.0 24.5 - - + -
259A TYR 5.8 0.2 - - - +
260A ALA* 3.7 27.7 - - + +
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Residues in contact with VAL 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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25A ILE* 3.7 24.7 - - + -
92A VAL* 4.1 10.5 - - + -
145A VAL* 3.9 14.8 - - + -
147A MET* 3.4 32.3 - - + -
189A VAL* 3.9 14.8 - - + +
238A VAL* 3.1 13.6 + - + +
239A ALA 3.6 6.7 - - - +
241A THR* 1.3 78.0 - - - +
243A CYS* 1.3 61.6 + - - +
245A LEU* 3.2 4.3 + - - +
246A LEU* 2.9 39.5 + - + +
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Residues in contact with CYS 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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4A LEU* 3.9 19.2 - - + +
5A LEU* 4.2 12.7 - - + +
25A ILE* 4.7 4.7 - - - -
28A VAL* 4.1 14.8 - - + -
29A ALA* 3.9 33.7 - - - -
32A GLN* 5.7 1.8 - - + -
239A ALA 3.1 14.9 + - - -
240A LYS* 3.9 8.5 - - - +
241A THR 3.2 0.2 - - - -
242A VAL* 1.3 75.4 - - - +
244A ALA* 1.3 65.6 + - - +
246A LEU* 2.8 22.0 + - - +
247A SER* 2.8 14.7 + - - -
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Residues in contact with ALA 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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4A LEU* 4.1 7.5 - - + +
240A LYS 3.2 9.6 + - - +
241A THR* 2.9 15.3 + - + +
243A CYS* 1.3 77.2 - - - +
245A LEU* 1.3 62.3 + - + +
247A SER* 3.0 27.4 + - - +
249A TRP* 4.6 1.7 - - + -
250A LEU* 3.9 26.7 - - + +
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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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143A SER* 2.6 19.7 + - - +
145A VAL* 3.8 15.7 - - + -
185A ARG* 2.8 21.5 + - - +
187A ASN* 4.0 35.0 - - + +
188A LEU 4.4 1.3 - - - +
189A VAL* 3.8 25.6 - - + -
241A THR* 3.3 7.0 + - + +
242A VAL 3.2 8.8 + - - +
244A ALA* 1.3 79.0 - - - +
246A LEU* 1.4 53.6 + - - +
247A SER 3.4 0.2 - - - +
250A LEU* 3.2 33.6 - - + +
253A THR* 4.8 1.8 - - - +
258A ILE* 3.7 33.2 - - + -
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Residues in contact with LEU 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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5A LEU* 4.3 11.9 - - + -
8A LYS* 4.2 18.7 + - - +
10A ILE* 4.4 19.7 - - + -
25A ILE* 5.0 5.2 - - + -
29A ALA* 5.8 2.2 - - + -
89A ASP 5.1 2.1 - - - +
90A GLY* 4.0 8.3 - - - -
91A VAL 3.8 14.6 - - - +
92A VAL* 3.4 25.6 - - + -
141A GLY 5.3 0.2 - - - +
143A SER* 3.4 36.8 - - - +
145A VAL* 3.6 15.9 - - + -
185A ARG* 4.0 1.4 + - - -
242A VAL* 2.9 28.2 + - + +
243A CYS* 2.8 17.1 + - - +
245A LEU* 1.4 72.2 - - - +
247A SER* 1.3 59.4 - - - +
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Residues in contact with SER 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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4A LEU* 3.9 26.6 - - - +
5A LEU* 4.0 12.5 - - - +
8A LYS* 5.0 2.0 - - - -
141A GLY 5.8 0.2 - - - -
185A ARG* 2.7 27.5 + - - -
243A CYS 2.8 13.3 + - - -
244A ALA* 3.0 13.2 + - - +
245A LEU 3.1 2.5 - - - +
246A LEU* 1.3 79.7 - - - +
248A ASP* 1.3 61.5 + - - +
249A TRP* 2.7 29.9 + - - +
250A LEU 4.0 1.4 + - - -
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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