Contacts of the strand formed by residues 241 - 246 (chain B) in PDB entry 3JWE
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 PHE 241 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B MET* 3.1 36.3 - - + +
154B LEU* 4.5 8.3 - - + -
237B LEU* 4.6 6.1 - - + -
239B VAL 3.3 18.1 + - - +
240B PRO* 1.3 73.4 - - - +
242B LEU* 1.3 61.4 + - - +
243B LEU* 4.2 18.4 - - + -
260B LEU* 4.1 20.9 - - + -
261B MET* 3.8 22.0 - - - -
264B ALA* 3.7 27.4 - - + -
266B SER* 3.4 21.3 - - - -
268B ASP 2.9 11.5 + - - +
269B LYS* 3.4 21.7 - - + -
270B THR 3.0 24.3 + - - -
299B TRP* 3.6 10.6 + - - -
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Residues in contact with LEU 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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152B MET 3.0 5.5 + - - +
153B VAL* 3.5 13.9 - - + +
154B LEU* 2.8 33.4 + - - +
241B PHE* 1.3 73.4 - - - +
243B LEU* 1.3 59.0 + - - +
244B LEU* 4.0 27.6 - - + -
270B THR* 3.6 22.7 - - + +
272B LYS* 5.3 4.3 - - + -
295B GLU* 4.0 17.9 - - + +
296B ILE* 4.2 17.9 - - + -
299B TRP* 3.7 50.4 - - + +
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Residues in contact with LEU 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B LEU* 3.6 12.6 - - + +
157B PRO* 3.6 36.8 - - + -
241B PHE* 4.2 11.0 - - + -
242B LEU* 1.3 74.2 - - - +
244B LEU* 1.3 66.1 + - - +
245B GLN* 5.3 0.2 - - + -
257B ALA* 3.4 35.0 - - + +
260B LEU* 3.9 19.7 - - + -
261B MET* 3.9 11.7 - - + -
270B THR 2.8 16.0 + - - +
271B LEU* 3.5 18.2 - - + +
272B LYS* 2.9 27.4 + - - -
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Residues in contact with LEU 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B VAL* 4.9 1.8 - - + -
154B LEU 2.9 11.8 + - - +
155B ILE* 4.3 12.1 - - + -
156B SER 2.8 27.9 + - - -
242B LEU* 4.0 24.0 - - + +
243B LEU* 1.3 75.4 - - - +
245B GLN* 1.3 60.8 + - - +
272B LYS* 3.6 26.0 - - + -
274B TYR* 4.2 14.6 - - + +
281B LEU* 3.4 16.8 - - + +
292B VAL* 3.9 33.0 - - + +
295B GLU* 4.6 6.1 - - + -
296B ILE* 3.9 24.2 - - + -
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Residues in contact with GLN 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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156B SER* 3.6 21.8 - - - +
157B PRO* 4.4 4.2 - - - +
243B LEU* 4.2 1.8 - - + -
244B LEU* 1.3 73.5 - - - +
246B GLY* 1.3 84.2 + - - +
249B ASP* 3.4 12.5 + - - +
252B CYS* 3.2 26.7 + - - +
253B ASP 4.6 2.1 - - - +
254B SER* 3.9 22.1 - - - +
257B ALA* 3.7 29.4 + - + +
271B LEU* 4.5 2.7 - - + -
272B LYS 3.0 6.9 + - - +
273B ILE* 3.3 21.3 - - + +
274B TYR* 2.9 24.5 + - - -
281B LEU* 3.6 8.4 - - - +
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Residues in contact with GLY 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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245B GLN* 1.3 98.5 + - - +
247B SER* 1.4 64.2 + - - -
248B ALA 3.3 3.9 + - - -
249B ASP* 3.4 7.9 + - - +
254B SER* 4.1 2.8 - - - -
273B ILE* 5.1 0.2 - - - -
274B TYR 3.5 7.4 - - - -
277B ALA 3.5 14.6 - - - -
278B TYR 3.9 5.0 + - - -
281B LEU* 3.8 18.9 - - - +
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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