Contacts of the helix formed by residues 244 - 253 (chain A) in PDB entry 4I5L
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 VAL 244 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209A PHE* 4.4 7.4 - - + -
228A CYS* 3.6 31.3 - - - +
231A ILE* 3.8 30.5 - - + -
232A ALA* 4.2 16.6 - - + +
235A LEU* 4.1 11.0 - - + -
240A LEU* 2.9 20.2 + - + +
243A LEU* 1.3 81.1 - - - +
245A MET* 1.3 77.2 + - - +
246A PRO* 3.4 3.1 - - - -
247A THR* 3.0 16.2 + - - -
248A LEU* 3.1 12.1 + - + -
274A VAL* 5.3 2.5 - - + -
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Residues in contact with MET 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 LEU* 3.0 19.1 + - + +
241A GLU* 3.6 35.4 - - + +
244A VAL* 1.3 81.3 - - - +
246A PRO* 1.3 62.3 - - + +
248A LEU* 3.7 28.8 - - + +
249A ARG* 2.8 49.0 + - + +
274A VAL* 3.7 25.1 - - - -
278A ILE* 3.8 14.1 - - + -
282A ASP* 3.7 23.3 - - + +
283A LEU* 4.3 6.1 - - + -
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Residues in contact with PRO 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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241A GLU 3.2 21.1 - - - +
242A ALA* 3.7 16.8 - - - +
243A LEU 4.4 0.9 - - - -
244A VAL 3.4 6.1 - - - +
245A MET* 1.3 89.7 - - + +
247A THR* 1.3 57.4 + - - +
249A ARG* 3.8 18.6 - - + +
250A GLN* 3.1 27.5 + - - +
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Residues in contact with THR 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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209A PHE* 3.4 38.1 - - + -
210A SER* 4.5 13.3 + - - -
213A ALA* 3.3 33.1 - - + +
224A ALA* 5.1 2.9 - - + +
228A CYS* 5.3 0.9 - - - -
243A LEU 4.7 3.5 + - - -
244A VAL 3.0 8.5 + - - -
246A PRO* 1.3 78.7 - - - +
248A LEU* 1.3 59.6 + - - +
250A GLN* 3.3 10.1 + - - +
251A ALA* 2.9 28.4 + - + +
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Residues in contact with LEU 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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225A VAL* 5.0 4.0 - - + -
228A CYS* 3.8 27.9 - - + -
244A VAL* 3.1 10.9 + - + +
245A MET* 3.7 35.4 - - + +
247A THR* 1.3 75.1 - - - +
249A ARG* 1.3 65.3 + - - +
251A ALA* 3.1 10.0 + - + +
252A ALA* 3.0 23.8 + - + +
263A VAL* 4.5 14.6 - - + -
267A PHE* 6.4 0.2 - - + -
270A LEU* 3.7 38.4 - - + -
274A VAL* 5.3 4.0 - - + -
283A LEU* 4.0 18.8 - - + -
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Residues in contact with ARG 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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241A GLU* 3.4 13.7 + - - -
245A MET* 2.8 42.8 + - + +
246A PRO* 3.8 24.0 - - - +
248A LEU* 1.3 72.7 - - - +
250A GLN* 1.3 61.8 + - - +
252A ALA* 3.4 15.4 + - - +
253A GLU* 3.4 25.4 + - - +
282A ASP* 2.7 35.7 + - + +
286A ALA* 6.4 1.8 - - + -
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Residues in contact with GLN 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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210A SER 5.3 0.3 - - - +
213A ALA* 3.4 33.9 - - - +
214A SER* 4.1 11.7 - - - -
246A PRO 3.1 19.6 + - - +
247A THR* 3.5 7.9 - - - +
248A LEU 3.3 0.2 - - - -
249A ARG* 1.3 77.2 - - - +
251A ALA* 1.3 63.3 + - - +
253A GLU* 3.3 10.2 + - - +
254A ASP* 3.1 26.2 + - - +
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Residues in contact with ALA 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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213A ALA* 6.5 0.4 - - + -
221A ARG 5.8 1.6 - - - +
224A ALA* 6.1 3.1 - - + -
225A VAL* 4.4 13.5 - - + +
247A THR* 2.9 16.7 + - + +
248A LEU* 3.1 14.3 + - + +
250A GLN* 1.3 76.9 - - - +
252A ALA* 1.3 62.2 + - - +
253A GLU 3.2 0.7 + - - -
254A ASP* 3.3 10.6 + - - +
259A VAL* 3.3 30.9 - - + +
260A ARG* 3.9 3.6 - - - +
263A VAL* 3.8 15.6 - - + +
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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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248A LEU* 3.0 16.4 + - + +
249A ARG* 3.7 9.0 - - - +
250A GLN 3.3 0.2 - - - -
251A ALA* 1.3 76.4 - - - +
253A GLU* 1.3 59.2 + - - +
254A ASP 3.6 0.4 - - - -
260A ARG* 3.4 18.9 - - - +
263A VAL* 3.8 26.2 - - + +
286A ALA* 5.0 16.8 - - + -
289A ASN* 6.2 0.5 - - - +
290A LEU* 4.1 14.4 - - + +
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Residues in contact with GLU 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 ARG* 3.4 22.0 - - - +
250A GLN* 3.3 8.4 + - - +
252A ALA* 1.3 78.7 - - - +
254A ASP* 1.3 66.0 + - - +
255A LYS 3.7 1.0 + - - -
260A ARG* 4.0 4.9 - - - +
289A ASN* 5.6 4.2 + - - -
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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