Contacts of the strand formed by residues 238 - 243 (chain A) in PDB entry 5FFO
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 ASP 238 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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228A VAL* 3.5 9.2 - - - +
229A GLY 2.9 32.0 + - - +
230A ASP* 3.4 0.9 - - - +
231A PHE* 3.0 26.0 + - + +
232A ASN* 2.5 31.0 + - - +
234A ASP* 4.6 0.3 - - - +
236A ILE* 3.1 13.1 - - - +
237A ASP* 1.3 73.3 - - - +
239A PHE* 1.3 65.4 + - - +
240A VAL* 3.8 2.3 + - - +
255A ILE* 4.9 2.2 - - + -
256A TYR 3.5 10.3 - - - +
257A ASP* 3.2 10.0 - - - +
258A GLY* 3.1 20.9 + - - +
264A LEU* 4.1 8.4 - - + +
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Residues in contact with PHE 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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164A THR* 4.1 22.4 - - + -
168A ARG* 4.8 4.3 - - - -
170A LEU* 3.7 35.9 - - + -
183A LEU* 4.4 12.3 - - + -
185A SER* 3.1 38.1 - - - -
208A LEU* 4.5 3.6 - - + -
227A ALA 4.2 2.2 - - - -
228A VAL* 4.8 2.2 - - + -
237A ASP 4.1 6.7 - - - -
238A ASP* 1.3 74.8 - - - +
240A VAL* 1.3 61.8 + - - +
254A TYR 3.9 0.9 - - - +
255A ILE* 3.5 4.0 - - - +
256A TYR* 2.9 42.2 + - + +
257A ASP 4.1 3.4 - - - -
258A GLY* 3.7 30.1 - - - -
261A MET* 3.9 29.2 - - + -
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Residues in contact with VAL 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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170A LEU* 4.7 0.7 - - - +
226A VAL* 3.2 6.4 - - - +
227A ALA* 2.9 47.4 + - + +
228A VAL* 5.2 0.2 - - - -
231A PHE* 3.5 35.7 - - + -
238A ASP 4.4 2.7 - - - +
239A PHE* 1.3 76.4 - - - +
241A SER* 1.3 66.1 + - - +
253A VAL* 3.8 22.2 - - + -
254A TYR 3.8 2.5 - - - -
255A ILE* 4.1 16.6 - - + -
280A VAL* 4.8 11.9 - - + -
281A ALA 6.0 1.1 - - - +
282A ALA* 5.2 3.1 - - + -
293A VAL* 4.5 15.3 - - + -
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Residues in contact with SER 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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183A LEU* 3.8 27.2 - - - +
222A LEU* 4.0 7.2 - - - -
223A GLY* 3.2 28.4 + - - -
225A SER 2.7 19.3 + - - -
226A VAL* 4.2 1.6 - - - -
240A VAL* 1.3 78.1 - - - +
242A GLY* 1.3 61.0 + - - +
243A VAL* 3.9 1.6 - - - +
253A VAL* 3.4 6.4 - - - +
254A TYR 3.0 35.4 + - - -
280A VAL* 4.7 1.8 - - - -
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Residues in contact with GLY 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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221A TYR 3.5 8.5 - - - +
223A GLY 3.7 0.9 + - - -
224A TYR* 3.6 12.6 + - - +
225A SER* 3.2 14.4 + - - -
241A SER* 1.3 75.7 + - - +
243A VAL* 1.3 62.0 + - - +
244A PRO* 3.5 12.2 - - - +
252A MET 3.7 5.6 - - - -
253A VAL* 3.9 10.5 - - - -
277A GLY 3.5 19.7 - - - -
280A VAL* 4.3 3.5 - - - +
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Residues in contact with VAL 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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220A SER* 3.2 26.5 - - - +
221A TYR 3.9 0.2 - - - -
222A LEU* 3.7 26.9 - - + +
241A SER 3.9 4.7 - - - +
242A GLY* 1.3 78.1 - - - +
244A PRO* 1.3 64.2 - - - +
245A ARG 3.3 1.1 - - - -
246A ALA* 3.1 26.2 + - + -
252A MET 2.6 34.2 + - - +
254A TYR* 3.4 41.7 - - + +
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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