Contacts of the strand formed by residues 249 - 252 (chain A) in PDB entry 3HF8
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 249 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112A ILE* 3.3 41.1 - - + -
115A LEU* 3.6 22.9 - - + -
227A PHE* 3.9 2.2 - - - -
228A SER* 3.5 14.6 - - - +
229A ILE 4.7 0.4 - - - -
230A ARG* 3.8 29.2 - - + +
241A PHE 4.9 0.2 - - - +
244A GLY* 2.9 31.3 + - - +
245A LEU* 3.3 7.4 + - - +
247A PHE* 3.6 7.4 - - + +
248A ARG* 1.3 78.6 - - - +
250A PHE* 1.3 63.2 + - - +
251A HIS* 4.0 6.9 + - + -
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Residues in contact with PHE 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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227A PHE* 4.2 4.0 - + + -
228A SER 3.0 13.0 + - - +
229A ILE* 3.4 8.8 - - + +
230A ARG 3.1 21.1 + - - -
241A PHE* 3.5 13.0 - + - -
245A LEU* 3.7 20.6 - - + -
248A ARG 4.1 0.4 - - - -
249A VAL* 1.3 74.0 - - - +
251A HIS* 1.3 76.8 + - - +
252A CYS* 3.4 15.8 + - - -
273A GLU* 3.7 21.3 - - - -
277A HIS* 3.3 41.5 - + + -
281A LEU* 3.7 36.8 - - + -
290A SER* 6.4 0.2 - - - -
312A TYR* 3.5 21.1 - + - -
316A VAL* 4.9 1.6 - - + -
400A FE 4.6 0.2 - - - -
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Residues in contact with HIS 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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115A LEU* 4.4 15.6 - - + +
118A CYS* 5.5 1.3 - - - -
119A ALA* 3.5 23.4 - - + +
230A ARG* 3.3 30.5 - - + -
232A VAL* 3.9 22.4 - - + +
236A LEU* 3.5 28.8 - - + +
240A ASP 4.3 7.4 - - - -
241A PHE* 3.5 37.7 + - + -
244A GLY* 4.1 22.7 - - - -
249A VAL* 4.3 8.2 + - + -
250A PHE* 1.3 80.2 - - - +
252A CYS* 1.3 58.3 + - - +
273A GLU* 4.2 4.0 - - - +
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Residues in contact with CYS 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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214A LEU* 4.0 9.6 - - + +
229A ILE* 3.6 42.6 - - + -
230A ARG 2.9 9.7 + - - -
231A PRO* 3.4 7.1 - - - +
232A VAL* 2.9 24.3 + - - +
250A PHE* 3.4 24.9 + - - -
251A HIS* 1.3 72.4 - - - +
253A THR* 1.3 65.2 + - - +
254A GLN 3.9 0.3 + - - -
273A GLU* 3.8 27.6 - - + -
277A HIS* 6.0 0.4 - - - -
278A VAL* 5.4 2.5 - - - -
281A LEU* 5.9 0.9 - - - -
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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