Contacts of the strand formed by residues 247 - 251 (chain A) in PDB entry 3HYW
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 247 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121A THR* 3.6 32.5 - - + -
132A THR* 4.0 2.5 - - + -
135A LYS* 4.2 30.5 - - + +
136A LEU* 3.6 34.1 - - + -
139A LEU* 4.1 25.4 - - + -
145A PRO 3.3 2.9 + - - +
146A VAL* 3.3 23.4 - - + -
147A VAL 3.1 22.9 + - - -
163A PHE* 3.7 28.9 - + - -
167A LEU* 4.3 2.9 - - + -
245A ALA* 4.4 0.2 - - - +
246A LYS* 1.3 80.8 - - - +
248A THR* 1.3 77.7 + - - +
249A MET* 4.1 0.7 - - + -
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Residues in contact with THR 248 (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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119A ASN 4.1 3.7 + - - -
120A SER* 2.7 34.2 + - - +
121A THR* 2.7 31.9 + - - +
135A LYS* 6.4 0.4 - - - +
147A VAL* 3.1 33.4 - - + -
226A ILE* 3.6 10.9 - - + +
227A GLU 5.6 1.1 - - - +
231A VAL* 3.7 12.8 - - + -
245A ALA* 3.6 11.7 - - + -
246A LYS 5.6 0.2 - - - -
247A PHE* 1.3 88.4 - - - +
249A MET* 1.3 54.5 + - - +
250A PHE* 4.0 7.2 - - - -
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Residues in contact with MET 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A THR* 3.4 24.2 - - - +
122A SER* 3.9 10.1 - - - -
123A ILE* 3.9 39.3 - - + -
132A THR* 4.6 0.2 - - + -
147A VAL 3.2 5.9 + - - -
148A ILE* 3.2 24.6 - - + +
149A GLY 3.0 22.2 + - - -
160A ALA* 4.1 13.5 - - + -
163A PHE* 3.6 37.9 - - + -
247A PHE* 4.1 2.2 - - + -
248A THR* 1.3 74.9 - - - +
250A PHE* 1.3 72.8 + - - +
251A MET* 4.1 9.4 - - - +
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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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116A GLN* 3.8 20.8 + - + +
120A SER* 3.5 9.9 + - - +
121A THR 3.1 16.3 + - - +
122A SER* 3.9 5.0 - - - -
147A VAL* 3.6 41.1 - - + -
148A ILE 4.1 0.7 - - - -
149A GLY* 3.3 36.1 - - - -
150A ALA* 3.5 11.0 - - - -
151A ILE* 4.2 7.0 - - + -
185A ILE* 3.7 4.9 - - + -
223A VAL* 3.6 28.0 - - + -
226A ILE* 3.7 19.3 - - + -
231A VAL* 4.0 21.5 - - + -
248A THR* 4.0 3.8 - - - -
249A MET* 1.3 85.9 - - - +
251A MET* 1.3 62.6 + - - +
252A PRO* 3.7 6.2 - - - +
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Residues in contact with MET 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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116A GLN* 3.4 8.6 + - - -
123A ILE* 4.7 3.6 - - - -
124A CYS* 3.5 30.3 - - - -
149A GLY 2.9 21.5 + - - +
150A ALA* 4.4 3.6 - - + -
151A ILE* 3.5 19.1 + - - +
154A VAL* 3.6 18.1 - - + +
156A CSS 3.3 30.1 - - + +
157A PHE* 5.0 0.2 - - - -
159A PRO* 4.1 13.9 - - + -
160A ALA* 3.8 28.3 - - + -
249A MET* 4.1 16.8 - - - +
250A PHE* 1.3 71.9 - - - +
252A PRO* 1.3 69.2 - - + +
254A PHE* 5.2 0.4 - - + -
441A FAD 5.1 0.2 - - + -
700A H2S 3.7 12.3 - - - -
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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