Contacts of the strand formed by residues 109 - 116 (chain C) in PDB entry 3SKU
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 PRO 109 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44C LEU* 3.3 31.4 - - + -
99C TRP 3.6 6.5 - - - +
100C PHE* 3.9 5.2 - - + -
108C ILE* 1.3 91.3 - - + +
110C ILE* 1.3 60.7 + - - +
112C VAL* 4.8 3.4 - - + -
136C ASN* 3.9 9.9 + - - +
201C ALA 4.7 0.4 - - - +
203C LEU* 3.4 16.6 - - + -
208C TYR* 3.2 22.0 - - - +
217C ILE* 3.4 27.7 - - + +
219C MET* 3.7 17.6 - - + +
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Residues in contact with ILE 110 (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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99C TRP* 2.7 19.8 + - + +
100C PHE 4.0 4.9 - - - +
101C ARG* 3.5 29.8 - - + +
108C ILE* 3.9 3.4 - - + +
109C PRO* 1.3 73.9 - - - +
111C THR* 1.3 58.5 + - - +
135C TRP* 3.2 15.5 - - + -
136C ASN 3.1 32.7 + - - +
138C TYR* 3.3 68.6 - - + -
151C PHE* 4.1 9.9 - - + -
164C TYR* 3.9 13.9 - - + -
219C MET* 3.4 3.2 - - - +
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Residues in contact with THR 111 (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 ILE 5.3 1.3 - - - +
98C ALA* 3.6 2.8 - - - -
99C TRP* 2.9 60.1 + - + +
110C ILE* 1.3 81.2 - - - +
112C VAL* 1.3 67.7 + - - +
113C MET* 4.9 17.8 - - + +
134C ARG 2.9 8.8 + - - -
135C TRP* 2.9 47.2 + - + -
144C VAL* 5.1 2.0 - - + -
151C PHE* 4.5 1.6 - - + -
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Residues in contact with VAL 112 (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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44C LEU* 3.6 31.4 - - + -
45C PRO* 5.1 2.5 - - + -
96C THR* 4.6 5.6 - - + -
97C ILE 3.7 5.4 - - - +
98C ALA* 5.3 4.5 - - + -
100C PHE* 6.3 0.4 - - + -
109C PRO* 4.8 3.1 - - + -
111C THR* 1.3 81.3 + - - +
113C MET* 1.3 68.4 + - - +
114C GLU* 4.1 25.8 - - + +
131C THR* 4.2 1.3 + - - -
133C PRO* 3.6 1.4 - - - +
134C ARG* 2.7 49.6 + - + +
214C VAL* 4.1 4.0 - - + -
219C MET* 3.6 29.8 - - + -
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Residues in contact with MET 113 (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 THR* 3.3 6.4 - - - +
97C ILE* 2.9 49.4 + - + +
111C THR* 4.9 11.7 - - + +
112C VAL* 1.3 81.9 - - - +
114C GLU* 1.3 62.4 + - - +
115C TYR* 4.0 29.8 - - + +
131C THR* 3.4 6.1 - - - +
133C PRO* 3.8 33.0 - - + -
135C TRP* 5.7 1.1 - - - -
144C VAL* 3.6 33.4 - - + -
148C ASN* 4.0 14.8 - - - +
225C PRO* 4.6 13.7 - - - -
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Residues in contact with GLU 114 (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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40C ILE* 3.1 14.4 + - + +
41C GLN* 2.6 53.1 + - + +
43C GLY 3.8 18.4 - - - +
44C LEU* 5.0 1.2 - - - +
45C PRO* 5.0 2.6 - - - +
95C LEU 3.6 7.2 - - - +
96C THR* 4.2 9.2 - - + +
112C VAL* 4.1 21.8 - - + +
113C MET* 1.3 79.3 - - - +
115C TYR* 1.3 66.0 + - - +
130C ARG* 3.7 1.4 - - - -
131C THR* 2.5 52.8 + - + +
134C ARG* 6.4 0.2 - - + -
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Residues in contact with TYR 115 (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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36C ARG* 5.3 3.6 - - - -
40C ILE* 4.4 2.4 - - - +
41C GLN* 4.7 1.2 + - - -
94C ASN* 3.6 5.7 - - - +
95C LEU* 2.8 69.5 + - + +
97C ILE* 3.9 15.9 - - + +
113C MET* 4.0 36.5 - - + +
114C GLU* 1.3 79.7 - - - +
116C THR* 1.3 63.4 + - - +
118C CYS* 3.7 19.1 - - - -
125C GLY* 4.1 25.6 - - - -
127C CYS* 4.1 4.0 - - + -
129C ILE 3.8 3.8 - - - -
130C ARG* 4.4 26.5 - - + -
131C THR 5.9 0.2 - - - -
148C ASN* 4.4 14.2 + - - +
225C PRO* 5.6 1.7 - - - +
1307C NAG 4.6 2.1 + - - -
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Residues in contact with THR 116 (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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40C ILE* 4.0 21.8 - - + -
93C TYR 4.0 2.9 - - - -
94C ASN* 2.7 22.1 + - - -
115C TYR* 1.3 78.1 - - - +
117C GLU* 1.3 75.1 + - + +
118C CYS* 3.3 2.5 - - - -
127C CYS* 3.7 2.4 - - - +
128C PRO* 3.7 9.4 - - - +
129C ILE* 3.2 49.4 + - + +
1307C NAG 4.0 9.0 + - - -
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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