Contacts of the strand formed by residues 85 - 91 (chain H) in PDB entry 1O5F
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 85 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33H LEU* 6.0 0.2 - - + -
59H PHE* 6.2 0.2 - - + -
65H TRP* 4.0 59.8 + - - +
66H VAL* 3.8 25.8 - - + -
84H GLY* 1.3 76.1 - - - +
86H GLN* 1.3 63.5 + - - +
87H ALA 3.8 14.6 - - - +
88H VAL* 4.0 14.6 - - + -
106H VAL* 3.8 25.6 - - + -
107H HIS 3.6 3.4 - - - -
108H LEU* 4.9 0.2 - - + -
109H SER* 3.3 7.1 + - - -
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Residues in contact with GLN 86 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65H LEU* 3.3 6.4 - - - +
85H VAL* 1.3 75.3 - - - +
87H ALA* 1.3 60.8 + - + +
107H HIS* 2.9 23.4 + - + +
108H LEU 4.3 2.7 - - - +
109H SER* 3.5 27.3 + - - +
246H SER 3.7 19.6 + - - -
247H GLU* 4.0 6.9 + - - +
248H ALA 2.9 25.9 + - - +
249H SER* 3.2 13.9 + - - +
250H GLY 2.9 19.9 + - - -
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Residues in contact with ALA 87 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51H TRP* 6.2 0.2 - - + -
65H LEU* 3.7 1.8 - - - -
85H VAL* 3.7 2.6 - - - +
86H GLN* 1.3 85.9 - - + +
88H VAL* 1.3 69.0 + - - +
89H VAL* 4.2 4.9 - - + +
106H VAL* 3.6 0.9 - - - -
107H HIS* 3.0 36.5 + - + +
245H HIS 5.4 1.3 - - - +
248H ALA* 3.5 32.5 - - + +
249H SER 4.0 0.2 - - - -
250H GLY 3.1 13.5 - - - +
252H VAL* 4.5 3.8 - - + -
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Residues in contact with VAL 88 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59H PHE* 3.8 47.3 - - + -
65H LEU* 3.8 22.4 - - - -
85H VAL* 4.0 10.1 - - + -
87H ALA* 1.3 80.2 - - - +
89H VAL* 1.3 70.4 + - - +
90H TYR* 4.7 1.8 - - + +
104H ALA* 4.3 4.0 - - + -
105H LEU 3.3 11.4 - - - +
106H VAL* 4.4 5.2 - - + -
250H GLY 2.8 5.3 + - - -
251H MET* 3.4 23.0 - - + +
252H VAL* 2.8 26.9 + - - +
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Residues in contact with VAL 89 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51H TRP* 4.6 16.4 - - + -
87H ALA* 5.2 4.0 - - + -
88H VAL* 1.3 79.1 - - - +
90H TYR* 1.3 61.8 + - - +
104H ALA* 3.3 2.1 - - - -
105H LEU* 2.9 37.2 + - + +
237H TRP* 3.8 5.9 - - + -
241H ALA* 4.1 12.3 - - + +
245H HIS* 4.0 24.9 - - + -
252H VAL* 3.2 33.7 - - + +
254H GLN* 4.0 25.4 - - + +
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Residues in contact with TYR 90 (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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56H ALA* 4.2 11.9 - - + +
59H PHE* 5.7 1.1 - - + -
64H ARG* 3.9 28.6 + - - -
88H VAL* 4.8 3.4 - - + -
89H VAL* 1.3 76.7 - - - +
91H HIS* 1.3 75.2 + - - +
92H GLY* 4.7 3.1 - - - -
94H TYR 5.7 0.2 - - - -
97H PHE* 3.8 34.3 + + + +
103H ILE 3.9 4.9 - - - -
104H ALA* 4.0 12.6 - - + -
237H TRP* 3.7 4.3 - - - -
251H MET* 3.8 29.6 - - + -
252H VAL 2.9 23.0 + - - -
253H THR* 3.0 35.2 - - + +
254H GLN 2.9 23.4 + - - -
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Residues in contact with HIS 91 (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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56H ALA* 4.7 0.6 - - - +
90H TYR* 1.3 80.6 - - - +
92H GLY* 1.3 61.1 + - - +
93H GLY* 2.9 35.7 + - - -
94H TYR* 3.1 17.5 + - - +
101H ASN* 3.4 35.3 + - + +
103H ILE* 3.3 15.6 + - + -
234H PHE* 3.7 34.1 - + - -
237H TRP* 3.5 26.7 - + + +
254H GLN 3.3 3.6 - - - -
255H LEU* 3.3 32.3 + - + -
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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