Contacts of the helix formed by residues 241 - 249 (chain B) in PDB entry 3Q37
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 PRO 241 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B LEU* 4.7 3.6 - - + -
28B LEU* 3.7 30.9 - - + -
29B PHE* 5.8 0.2 - - + -
239B LEU 4.7 0.7 - - - +
240B LYS* 1.3 89.0 - - + +
242B GLU* 1.3 59.5 + - - +
243B PHE 3.0 0.4 - - - -
244B VAL* 3.0 25.2 + - + +
245B GLU* 4.2 2.1 + - - +
71D ARG* 6.4 0.2 - - - +
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Residues in contact with GLU 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216B THR* 3.2 16.6 - - - +
217B ALA* 2.7 40.7 + - + +
237B ALA* 4.1 21.0 - - + +
240B LYS* 3.0 24.0 + - + +
241B PRO* 1.3 79.4 - - - +
243B PHE* 1.3 61.7 + - - +
245B GLU* 3.0 24.2 + - - +
246B ILE* 3.2 11.3 + - + +
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Residues in contact with PHE 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B ALA* 3.7 33.7 - - + -
10B ALA 3.9 16.2 - - - -
11B ALA* 3.8 20.6 - - + -
29B PHE* 3.6 24.7 - + + -
41B VAL 4.6 0.2 - - - -
61B PHE* 4.2 16.2 - + - -
234B VAL* 3.9 20.4 - - + -
237B ALA 3.7 9.9 + - - +
238B SER* 4.0 18.6 - - - -
240B LYS 3.0 14.5 + - - +
241B PRO 3.0 0.8 - - - -
242B GLU* 1.3 79.2 - - - +
244B VAL* 1.3 62.2 + - - +
246B ILE* 3.1 11.8 + - + +
247B ILE* 3.0 43.4 + - + +
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Residues in contact with VAL 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B LEU* 4.3 20.6 - - + -
29B PHE* 4.8 10.5 - - + -
32B THR* 3.7 39.3 - - + +
241B PRO* 3.0 15.0 + - + +
243B PHE* 1.3 78.1 - - - +
245B GLU* 1.3 65.5 + - + +
247B ILE* 3.3 14.9 + - + +
248B GLU* 3.2 20.1 + - + +
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Residues in contact with GLU 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217B ALA* 3.5 33.4 - - + +
220B ALA* 5.2 0.2 - - - +
241B PRO 5.2 0.9 - - - +
242B GLU* 3.0 20.1 + - - +
244B VAL* 1.3 78.7 - - + +
246B ILE* 1.3 64.6 + - - +
248B GLU* 3.3 10.0 + - - +
249B ALA* 3.2 20.1 + - - +
119D ALA* 6.0 2.3 - - - +
156D SER* 4.7 9.9 + - - -
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Residues in contact with ILE 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B ALA* 5.2 2.7 - - + -
215B VAL* 3.8 35.2 - - + +
216B THR* 4.0 22.7 - - - +
217B ALA 4.0 1.3 - - - +
220B ALA* 4.4 5.6 - - + -
232B PHE* 3.7 25.9 - - + -
234B VAL* 3.9 28.3 - - + -
237B ALA* 3.9 11.9 - - + -
242B GLU* 3.2 12.9 + - + +
243B PHE* 3.1 18.0 + - + +
245B GLU* 1.3 74.9 - - - +
247B ILE* 1.3 66.9 + - - +
249B ALA* 3.1 15.8 + - - +
250B THR* 3.8 8.0 + - - +
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Residues in contact with ILE 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B ALA* 4.0 17.7 - - + -
29B PHE* 5.7 1.1 - - + -
32B THR* 5.5 4.3 - - + -
34B ILE* 4.1 23.1 - - + -
36B HIS* 3.7 16.9 - - + -
38B VAL* 4.3 4.7 - - + -
40B CYS* 3.9 26.7 - - - -
61B PHE* 3.9 10.5 - - + -
243B PHE* 3.0 48.7 + - + +
244B VAL* 3.6 15.3 - - + +
246B ILE* 1.3 74.8 - - - +
248B GLU* 1.3 62.7 + - - +
250B THR* 2.6 28.0 + - - +
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Residues in contact with GLU 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B HIS* 4.7 6.4 - - - -
221B ARG* 5.4 0.3 - - - -
244B VAL* 3.2 10.6 + - + +
245B GLU* 3.5 13.5 - - - +
246B ILE 3.2 0.6 - - - -
247B ILE* 1.3 79.2 - - - +
249B ALA* 1.3 60.3 + - - +
250B THR 3.1 0.4 - - - -
251B LYS* 3.2 46.8 + - - +
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Residues in contact with ALA 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217B ALA 5.7 1.1 - - - +
220B ALA* 3.5 31.2 - - + +
221B ARG* 2.6 49.6 + - + +
224B TYR* 3.5 9.9 - - - +
232B PHE* 4.6 1.6 - - + -
245B GLU 3.2 8.3 + - - +
246B ILE 3.1 11.6 + - - +
247B ILE 3.1 1.2 - - - -
248B GLU* 1.3 76.6 - - - +
250B THR* 1.3 54.4 + - - +
251B LYS 3.2 1.3 - - - -
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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