Contacts of the strand formed by residues 120 - 127 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89C ALA* 3.3 31.4 - - + +
90C SER* 3.6 4.7 - - - -
91C GLY 3.3 11.0 - - - +
93C ILE* 3.7 25.6 - - + -
113C PHE* 3.7 33.2 - - + -
114C MET* 4.8 7.5 - - + +
117C TYR* 3.0 27.4 + - + +
118C PRO 4.2 4.9 - - - +
119C GLU* 1.3 79.4 - - - +
121C ASN* 1.3 68.4 + - - +
122C ILE* 4.9 2.9 - - + -
277C LYS* 3.8 22.9 - - + -
280C LEU* 5.1 2.2 - - + -
214F ARG* 4.3 11.8 + - - +
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Residues in contact with ASN 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91C GLY* 2.9 24.4 + - - -
92C LYS* 3.2 18.9 - - - +
93C ILE* 2.8 31.7 + - - +
114C MET* 5.7 0.2 - - - -
119C GLU 4.9 2.0 + - - -
120C ILE* 1.3 77.6 - - - +
122C ILE* 1.3 58.3 + - - +
123C GLU* 4.7 3.3 - - - +
212F ARG* 3.2 45.6 + - - +
213F GLY 3.8 9.8 - - - +
214F ARG* 3.3 17.0 - - - +
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Residues in contact with ILE 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93C ILE* 3.3 14.1 - - + +
95C ILE* 3.9 24.0 - - + -
110C LEU* 4.1 27.4 - - + +
113C PHE* 4.4 13.7 - - + -
114C MET* 3.5 35.4 - - + -
120C ILE* 4.9 6.3 - - + -
121C ASN* 1.3 76.9 - - - +
123C GLU* 1.3 72.2 + - - +
124C LEU* 4.3 4.3 - - + +
281C PHE* 5.1 0.7 - - + -
213F GLY 5.3 0.5 - - - +
214F ARG 3.1 7.1 + - - +
215F PHE* 3.6 23.8 - - + -
216F GLN 3.0 25.3 + - - +
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Residues in contact with GLU 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C LYS* 3.5 38.3 + - + +
93C ILE 3.0 8.9 + - - +
94C LYS* 3.1 35.5 + - - +
95C ILE* 2.9 27.4 + - - +
121C ASN* 4.2 4.0 + - - +
122C ILE* 1.3 76.1 - - - +
124C LEU* 1.3 59.0 + - - +
138C TRP* 5.0 0.2 - - - -
212F ARG* 4.2 11.9 + - - +
216F GLN* 3.3 32.1 + - + +
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Residues in contact with LEU 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95C ILE* 3.4 11.7 - - + +
97C THR* 3.3 38.8 - - + +
102C THR* 4.1 17.3 - - + -
107C MET* 4.2 6.5 - - - -
110C LEU* 4.2 11.2 - - + -
122C ILE* 4.1 4.0 - - + -
123C GLU* 1.3 72.1 - - - +
125C THR* 1.3 68.3 + - - +
126C THR* 4.1 5.8 - - + -
215F PHE* 3.8 36.6 - - + -
216F GLN 2.8 10.4 + - - +
217F ALA* 3.2 23.4 - - + -
218F ASN* 3.3 6.2 + - - +
222F VAL* 4.0 17.3 - - + -
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Residues in contact with THR 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94C LYS* 4.3 9.4 + - - -
95C ILE 3.0 6.3 + - - -
96C SER* 3.4 6.8 + - - -
97C THR 3.1 21.4 + - - +
124C LEU* 1.3 77.4 + - - +
126C THR* 1.3 66.2 + - - +
127C GLU* 4.2 14.4 - - + +
138C TRP* 3.3 33.9 - - + -
218F ASN* 3.4 24.1 - - + +
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Residues in contact with THR 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97C THR* 3.3 23.8 - - - +
99C TYR* 4.6 14.3 - - - -
102C THR* 3.8 22.2 - - + +
124C LEU* 4.2 10.8 - - + -
125C THR* 1.3 73.2 - - - +
127C GLU* 1.3 62.6 + - - +
218F ASN* 2.9 31.9 + - - +
219F ALA* 4.3 12.3 - - + +
221F ASN* 6.1 0.2 - - - +
222F VAL* 4.9 8.5 - - + -
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Residues in contact with GLU 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96C SER* 2.9 24.5 + - - +
97C THR 2.9 9.5 + - - +
98C PRO* 3.4 8.1 - - - +
99C TYR* 2.8 26.2 + - - +
125C THR* 4.2 16.1 - - + +
126C THR* 1.3 78.9 - - - +
128C SER* 1.3 65.1 + - - +
133C LEU* 3.2 30.5 - - + +
138C TRP* 4.1 7.3 - - - -
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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