Contacts of the strand formed by residues 120 - 127 (chain F) in PDB entry 5FHK
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 ILE 120 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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214C ARG* 4.3 9.0 + - - +
89F ALA 3.5 27.8 - - - +
90F SER* 3.7 10.1 - - - -
91F GLY 3.2 9.4 - - - +
93F ILE* 3.9 18.6 - - + -
113F PHE* 3.9 28.2 - - + -
114F MET* 4.9 8.0 - - - +
117F TYR* 3.2 45.9 + - + +
118F PRO 4.4 2.9 - - - +
119F GLU* 1.3 80.9 - - - +
121F ASN* 1.3 77.1 + - - +
122F ILE* 4.4 0.8 + - + -
277F LYS* 4.3 8.7 - - + -
280F LEU* 4.3 9.9 - - + -
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Residues in contact with ASN 121 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187C PHE* 6.1 1.2 - - - -
212C ARG* 2.8 30.3 + - - +
213C GLY 3.9 12.1 + - - +
214C ARG* 3.2 30.2 - - - +
91F GLY* 2.8 16.6 + - - +
92F LYS* 4.2 7.9 - - + -
93F ILE* 2.7 32.1 + - - -
118F PRO 5.2 2.6 + - - -
119F GLU 4.9 4.5 + - - +
120F ILE* 1.3 84.8 + - - +
122F ILE* 1.3 61.4 + - - +
123F GLU 4.2 0.4 - - - -
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Residues in contact with ILE 122 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213C GLY 5.1 0.3 - - - +
214C ARG 3.1 6.5 + - - +
215C PHE* 3.3 25.3 - - + -
216C GLN* 2.8 27.9 + - - +
92F LYS* 5.6 0.2 - - - -
93F ILE* 3.5 9.4 - - + +
95F ILE* 3.9 28.3 - - + -
110F LEU* 4.0 24.9 - - + -
113F PHE* 4.1 20.6 - - + -
114F MET* 3.8 31.2 - - + -
120F ILE* 5.1 1.8 - - + -
121F ASN* 1.3 79.1 - - - +
123F GLU* 1.3 63.9 + - - +
124F LEU* 4.3 0.9 - - + +
281F PHE* 4.4 6.5 - - + -
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Residues in contact with GLU 123 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132A GLN* 3.6 19.9 + - - +
216C GLN* 3.4 15.3 - - + +
92F LYS* 3.0 39.5 + - + +
93F ILE 3.0 9.7 + - - +
94F LYS* 3.5 35.2 - - + +
95F ILE 3.0 25.8 + - - +
121F ASN 4.2 0.4 - - - -
122F ILE* 1.3 72.3 - - - +
124F LEU* 1.3 63.1 + - - +
125F THR* 4.8 6.4 + - - +
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Residues in contact with LEU 124 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215C PHE* 4.1 21.8 - - + -
216C GLN 2.8 14.7 + - - +
217C ALA* 3.3 29.2 - - + -
218C ASN* 3.4 7.1 + - - +
222C VAL* 4.5 3.8 - - + -
95F ILE* 3.4 14.6 - - + -
97F THR* 3.5 29.8 - - + +
102F THR* 4.0 13.2 - - + -
110F LEU* 3.5 31.6 - - + -
122F ILE* 3.9 0.6 - - + -
123F GLU* 1.3 74.3 - - - +
125F THR* 1.3 68.6 + - - +
126F THR* 3.5 22.7 - - + +
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Residues in contact with THR 125 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218C ASN* 3.3 20.0 - - + +
94F LYS* 5.2 0.7 - - - -
95F ILE 3.0 6.5 + - - -
96F SER* 3.3 7.1 + - - -
97F THR 3.1 19.6 + - - +
123F GLU* 4.8 10.7 + - - +
124F LEU* 1.3 78.3 + - - +
126F THR* 1.3 68.4 + - - +
127F GLU* 3.6 12.4 + - - +
138F TRP* 3.6 31.5 - - + -
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Residues in contact with THR 126 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218C ASN* 2.8 35.3 + - - +
219C ALA* 4.9 8.5 - - + +
222C VAL* 5.1 8.7 - - + -
97F THR* 3.2 15.0 - - - +
99F TYR* 4.0 32.0 - - - +
102F THR* 3.9 14.8 - - + +
124F LEU* 3.5 20.9 - - + -
125F THR* 1.3 76.6 - - - +
127F GLU* 1.3 59.9 + - - +
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Residues in contact with GLU 127 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96F SER* 4.1 16.1 + - - +
97F THR 2.8 6.4 + - - +
98F PRO* 3.3 9.5 - - - +
99F TYR* 3.0 21.4 + - - -
125F THR* 4.4 14.5 - - - +
126F THR* 1.3 74.9 - - - +
128F SER* 1.3 64.4 + - - +
129F ASN* 3.5 22.9 - - + +
130F ALA* 5.3 2.4 + - + +
132F GLN* 5.4 1.4 - - - +
133F LEU* 3.2 29.7 - - + +
138F TRP* 4.9 8.0 - - - -
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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