Contacts of the strand formed by residues 241 - 246 (chain A) in PDB entry 3CFV
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 LEU 241 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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234A TRP* 3.3 8.5 - - - -
235A HIS* 2.9 47.0 + - + +
238A HIS* 3.3 35.5 + - + +
240A SER* 1.3 79.4 - - - +
242A PHE* 1.3 63.7 + - - +
253A ILE* 4.1 17.7 - - + -
254A TRP 3.4 17.0 - - - +
255A ASP* 4.5 15.5 - - + +
257A ARG* 5.4 2.7 - - - +
265A SER* 5.7 3.1 - - - +
280A PHE* 6.2 0.4 - - + -
302A LEU* 4.8 9.2 - - + -
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Residues in contact with PHE 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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193A LEU* 3.4 39.0 - - + -
201A VAL* 4.2 7.0 - - + -
222A PHE* 3.9 38.8 - + - -
232A VAL* 3.8 17.7 - - + -
233A ALA 3.4 12.8 - - - +
234A TRP* 3.7 16.8 - + + -
235A HIS 4.1 2.5 - - - +
240A SER 4.3 1.3 - - - -
241A LEU* 1.3 77.4 - - - +
243A GLY* 1.3 59.8 + - - +
244A SER* 4.7 1.6 - - - -
253A ILE* 3.5 3.6 - - - +
254A TRP* 2.7 79.5 + + + -
255A ASP 4.9 0.2 - - - -
256A THR* 4.1 11.9 - - + -
280A PHE* 4.5 3.6 - - - -
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Residues in contact with GLY 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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232A VAL* 3.5 5.2 - - - +
233A ALA 2.9 34.4 + - - -
242A PHE* 1.3 75.7 - - - +
244A SER* 1.3 60.7 + - - -
251A LEU* 4.9 0.4 - - - -
252A MSE 3.1 10.8 - - - -
253A ILE* 4.3 4.5 - - - -
278A LEU* 3.6 19.6 - - - +
280A PHE* 3.8 10.2 - - - -
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Residues in contact with SER 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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201A VAL* 4.2 17.9 - - - -
225A HIS* 2.8 26.5 - - - -
229A VAL* 4.4 0.7 - - - -
231A ASP 3.6 8.5 - - - -
232A VAL* 4.5 5.4 - - - -
242A PHE* 4.7 0.7 - - - -
243A GLY* 1.3 75.2 - - - -
245A VAL* 1.3 63.3 + - - +
250A LYS 4.1 0.3 - - - +
251A LEU* 3.3 7.1 - - - +
252A MSE 2.8 31.4 + - - +
254A TRP* 2.7 31.7 + - - -
278A LEU* 4.7 0.4 - - - -
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Residues in contact with VAL 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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225A HIS* 4.3 0.4 - - - -
229A VAL* 3.2 6.7 - - - +
230A GLU 2.6 28.9 + - - -
231A ASP 3.0 15.2 + - - +
244A SER* 1.3 82.3 - - - +
246A ALA* 1.3 54.7 + - - +
250A LYS 3.9 2.9 - - - -
251A LEU* 3.7 23.6 - - + -
275A VAL* 2.9 54.7 - - + +
276A ASN 4.0 2.9 - - - -
277A CYS* 3.8 11.7 - - - +
278A LEU* 4.1 19.5 - - + -
290A THR* 4.5 1.8 - - - +
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Residues in contact with ALA 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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225A HIS* 3.2 34.5 - - + -
227A ALA 4.3 1.1 - - - +
228A VAL 3.4 15.9 - - - +
229A VAL* 3.4 10.3 - - - -
230A GLU 3.8 1.6 - - - +
245A VAL* 1.3 74.2 - - - +
247A ASP* 1.3 63.3 + - - +
248A ASP* 3.1 11.2 + - - +
249A GLN* 3.4 6.6 + - - -
250A LYS 3.6 7.5 + - - -
275A VAL* 3.2 28.3 + - - +
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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