Contacts of the strand formed by residues 106 - 115 (chain C) in PDB entry 6P59
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 106 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8C GLN* 3.9 21.5 - - + +
11C LYS* 4.1 27.1 - - + +
12C PHE* 4.6 5.8 - - + -
17C PHE* 3.8 24.0 - - + -
102C ILE* 4.0 1.5 - - - +
103C LEU 2.8 37.4 + - - +
104C ASN* 3.5 13.2 - - + +
105C GLY* 1.3 76.8 - - - +
107C CYS* 1.3 66.8 + - - +
108C VAL* 3.4 21.6 + - + +
127C PHE* 4.4 11.9 - - + -
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Residues in contact with CYS 107 (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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8C GLN* 3.7 13.6 - - - +
101C MET 3.8 5.4 - - - -
102C ILE* 4.2 19.1 - - - +
105C GLY 4.7 1.6 - - - -
106C VAL* 1.3 71.1 - - - +
108C VAL* 1.3 61.8 + - - +
127C PHE* 4.0 11.9 - - + -
128C ASP* 3.3 34.6 + - + +
131C ARG* 3.9 28.3 - - + -
132C ALA* 3.8 26.2 - - - +
135C GLU* 4.6 4.7 - - - -
101F TYR* 5.6 1.1 - - - -
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Residues in contact with VAL 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C PHE* 4.2 7.4 - - + -
17C PHE* 3.7 28.7 - - + -
100C PRO* 4.4 0.2 - - - +
101C MET* 2.9 52.2 + - + +
103C LEU* 3.7 28.9 - - + -
106C VAL* 3.8 13.5 - - + +
107C CYS* 1.3 79.7 - - - +
109C ILE* 1.3 71.9 + - - +
110C TRP* 6.0 0.2 - - + -
125C LEU* 4.2 14.4 - - + -
126C GLU 3.1 11.2 - - - +
128C ASP* 4.3 2.1 - - - +
131C ARG* 5.1 1.4 + - - -
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Residues in contact with ILE 109 (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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98C LYS* 4.5 21.3 - - + -
99C ALA 3.7 3.6 - - - +
100C PRO* 3.5 24.5 - - + -
108C VAL* 1.3 81.9 - - - +
110C TRP* 1.3 62.2 + - - +
111C LYS* 4.0 28.0 - - + -
125C LEU* 3.4 2.4 - - - -
126C GLU* 2.5 52.8 + - + +
127C PHE 4.9 2.5 - - - +
128C ASP* 3.1 36.6 - - + +
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Residues in contact with TRP 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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21C LEU* 5.0 5.4 - - + +
25C CYS* 4.2 9.3 - - - -
27C ILE* 3.5 42.6 - - + -
57C PHE* 6.1 0.4 - - + -
66C LEU* 3.6 26.4 - - + +
68C PHE* 5.3 2.2 - + - -
97C LEU* 3.7 24.2 - - + -
98C LYS* 3.3 6.6 - - - -
99C ALA* 2.8 49.5 + - + +
101C MET* 4.0 12.5 - - + +
108C VAL* 6.0 0.2 - - + -
109C ILE* 1.3 74.7 - - - +
111C LYS* 1.3 64.7 + - - +
112C GLY* 3.4 24.5 - - - -
123C GLY* 3.6 25.9 - - - -
124C CYS 3.8 5.2 - - - -
125C LEU* 3.5 32.3 - - + +
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Residues in contact with LYS 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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96C TYR* 6.4 1.1 - - + -
97C LEU 3.3 7.9 - - - +
98C LYS* 5.2 8.7 - - + +
109C ILE* 4.0 22.9 - - + -
110C TRP* 1.3 82.7 - - - +
112C GLY* 1.3 58.5 + - - +
123C GLY* 3.2 2.6 - - - -
124C CYS* 3.2 36.6 + - - +
126C GLU* 4.0 30.0 + - + +
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Residues in contact with GLY 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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96C TYR* 3.2 10.9 - - - +
97C LEU* 2.6 41.8 + - - +
110C TRP* 3.4 13.8 - - - -
111C LYS* 1.3 75.8 - - - +
113C TRP* 1.3 65.1 + - - +
122C MET 3.2 13.9 - - - -
123C GLY* 4.0 0.4 - - - -
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Residues in contact with TRP 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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27C ILE* 3.9 1.6 - - - +
94C LYS* 4.9 23.8 - - + -
95C VAL 3.0 13.9 - - - +
96C TYR* 4.2 34.5 - + + -
97C LEU* 4.7 2.5 - - - +
112C GLY* 1.3 78.8 - - - +
114C ILE* 1.3 78.1 + - - +
115C ASP* 4.1 13.2 - - + -
118C ARG* 4.6 11.9 - - - -
120C ASP* 4.1 5.4 - - - -
121C GLY* 3.1 37.2 - - - -
122C MET* 3.2 50.4 + - + +
123C GLY* 6.1 0.2 - - - -
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Residues in contact with ILE 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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27C ILE* 3.4 33.4 - - + +
28C LYS* 4.8 1.1 - - - -
29C TYR* 5.3 1.1 - - + -
44C PHE* 4.4 13.0 - - + -
57C PHE* 3.7 30.7 - - + -
94C LYS* 3.5 4.0 - - - -
95C VAL* 2.9 45.0 + - + +
97C LEU* 4.3 6.3 - - + -
113C TRP* 1.3 86.8 - - - +
115C ASP* 1.3 77.4 + - - +
119C LEU* 3.8 19.3 - - + +
120C ASP 3.3 16.2 - - - +
121C GLY 3.8 0.2 - - - +
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Residues in contact with ASP 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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93C GLY* 3.2 11.7 - - - +
94C LYS* 4.8 7.6 - - + +
113C TRP* 3.9 13.8 - - + -
114C ILE* 1.3 72.8 - - - +
116C LEU* 1.3 65.7 + - - +
117C GLN* 3.6 9.5 + - - +
118C ARG* 3.4 41.8 + - + +
119C LEU* 2.7 34.1 + - - -
120C ASP 2.7 16.7 + - - +
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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