Contacts of the strand formed by residues 239 - 246 (chain H) in PDB entry 1S9C
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 239 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58H PRO* 3.4 35.7 - - + -
59H THR* 4.5 4.9 - - + -
94H LEU* 5.7 1.6 - - + -
96H LEU* 3.4 25.6 - - + +
224H ALA* 3.9 33.4 - - + -
228H LEU* 4.0 26.0 - - + +
235H ASP 3.9 0.8 + - - -
236H VAL 3.2 17.5 + - - +
237H SER 3.2 3.1 - - - +
238H ARG* 1.3 76.7 - - - +
240H LYS* 1.3 59.2 + - - +
241H ALA* 4.3 5.2 - - - -
242H VAL* 2.8 39.0 - - + -
286H VAL* 3.7 21.1 - - + -
288H LEU* 4.2 7.4 - - + -
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Residues in contact with LYS 240 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95H GLU* 3.4 4.6 - - + +
96H LEU* 2.7 37.4 + - - +
237H SER 5.3 2.9 - - - +
238H ARG 3.2 8.0 + - - +
239H PHE* 1.3 75.5 - - - +
241H ALA* 1.3 62.5 + - + +
287H ASP* 3.0 25.5 + - + +
288H LEU 4.5 8.2 + - - +
289H ALA* 3.8 27.9 - - + +
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Residues in contact with ALA 241 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93H TYR* 3.9 14.6 - - + +
94H LEU 3.2 13.9 - - - +
95H GLU* 3.7 16.6 - - + +
96H LEU* 5.8 0.4 - - - -
239H PHE* 3.9 2.5 - - - -
240H LYS* 1.3 84.6 - - + +
242H VAL* 1.3 66.6 + - - +
285H TYR* 5.0 2.7 - - + -
286H VAL* 3.0 5.2 - - - +
287H ASP* 2.7 43.8 + - + +
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Residues in contact with VAL 242 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59H THR* 4.7 4.5 - - + -
93H TYR* 3.4 8.4 - - - -
94H LEU* 2.9 36.0 + - + +
220H PHE* 3.0 41.3 - - + -
224H ALA* 5.1 4.0 - - + -
239H PHE* 2.8 45.8 - - + -
241H ALA* 1.3 73.6 - - - +
243H LYS* 1.3 60.1 + - - +
269H PHE* 5.3 4.0 - - + -
285H TYR* 3.2 14.1 - - - +
286H VAL* 4.1 3.8 - - + -
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Residues in contact with LYS 243 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91H GLU* 3.1 34.0 + - - +
92H GLN 3.5 10.6 + - - +
93H TYR* 3.9 17.5 - - + +
141H GLN* 4.6 9.1 + - - -
143H SER* 5.6 0.8 - - - -
161H VAL* 4.8 0.4 - - - +
162H LYS 3.0 26.8 + - - +
163H VAL 3.5 15.0 - - - +
164H ALA* 3.6 29.4 - - - +
242H VAL* 1.3 75.5 - - - +
244H ALA* 1.3 73.0 + - - +
269H PHE* 4.4 0.2 - - - -
283H ASN 4.7 0.7 - - - +
284H ALA* 2.9 5.1 - - - +
285H TYR* 2.9 60.2 + - + +
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Residues in contact with ALA 244 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91H GLU* 3.3 6.4 - - - +
92H GLN 3.1 31.4 + - - +
220H PHE* 3.6 31.2 - - + -
243H LYS* 1.3 83.4 - - - +
245H ARG* 1.3 61.5 + - - +
246H PHE* 5.1 4.5 - - + -
269H PHE* 4.4 2.7 - - + -
281H ILE* 3.8 12.6 - - + -
283H ASN 5.1 0.9 - - - -
284H ALA* 3.5 17.7 - - + +
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Residues in contact with ARG 245 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90H GLY 3.9 3.6 - - - +
91H GLU* 2.7 34.5 + - + +
163H VAL* 5.8 2.6 - - - +
164H ALA* 3.5 26.8 - - + +
244H ALA* 1.3 74.9 - - - +
246H PHE* 1.3 73.8 + - - +
247H ALA* 6.0 0.2 - - + -
281H ILE* 3.2 6.1 - - - +
282H SER* 2.8 57.1 + - - +
283H ASN* 3.8 16.3 - - - +
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Residues in contact with PHE 246 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89H HIS* 3.7 43.7 - + + +
90H GLY* 2.8 37.2 + - - +
91H GLU* 3.8 12.1 - - - -
92H GLN* 3.9 8.3 - - + -
216H GLY* 3.3 35.9 - - - -
217H LEU* 3.9 22.9 - - + -
220H PHE* 4.1 14.8 - + + -
244H ALA* 5.0 4.0 - - + -
245H ARG* 1.3 82.9 - - - +
247H ALA* 1.3 62.3 + - - +
280H VAL 3.7 3.4 - - - +
281H ILE* 4.2 18.4 - - + -
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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