Contacts of the strand formed by residues 123 - 131 (chain C) in PDB entry 3Q2S
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 SER 123 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164B HIS* 3.1 36.6 + - - -
89C THR 4.4 1.7 + - - -
90C TRP* 3.5 29.1 + - - +
114C PHE* 3.3 28.2 - - - -
115C PHE 3.7 5.3 + - - -
117C ASN* 4.8 0.3 - - - +
122C GLN* 1.3 87.6 + - - +
124C LYS* 1.3 61.9 + - - +
125C GLY* 3.1 12.1 + - - -
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Residues in contact with LYS 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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115C PHE* 2.6 31.3 + - + +
116C GLU 3.6 28.1 + - - +
117C ASN* 3.2 24.5 - - - +
122C GLN 3.2 1.8 + - - -
123C SER* 1.3 71.4 - - - +
125C GLY* 1.3 57.1 + - - +
126C PHE* 3.4 17.7 + - + -
167C PHE 5.1 0.2 - - - +
168C GLU* 3.1 37.8 + - - +
170C GLN* 5.2 2.8 - - - +
171C SER* 3.2 36.1 + - - +
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Residues in contact with GLY 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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86C GLY* 3.6 2.6 - - - -
87C ASN 3.7 1.2 + - - -
88C LEU* 3.0 54.1 + - - +
89C THR 4.5 2.9 - - - -
90C TRP* 5.3 0.7 - - - -
114C PHE* 5.8 0.7 - - - -
123C SER* 3.1 14.9 + - - -
124C LYS* 1.3 79.5 - - - +
126C PHE* 1.3 60.1 + - - +
170C GLN* 5.5 4.7 - - - -
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Residues in contact with PHE 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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84C TYR* 5.1 5.6 - + - -
85C ILE 3.1 13.7 - - - +
86C GLY* 3.7 10.1 - - - -
87C ASN 5.2 0.2 - - - +
88C LEU* 5.0 1.1 - - - -
114C PHE* 4.7 3.8 - - - -
115C PHE* 3.0 78.7 + + + +
123C SER* 4.7 0.8 + - - -
124C LYS* 3.8 31.0 - - + -
125C GLY* 1.3 81.1 - - - +
127C ALA* 1.3 61.8 + - - +
164C LEU* 4.9 8.3 - - + -
167C PHE* 3.4 55.2 - + + -
168C GLU* 3.8 22.2 - - + -
170C GLN* 6.1 0.7 - - - -
171C SER* 5.2 0.2 - - - -
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Residues in contact with ALA 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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84C TYR* 3.9 0.9 - - - -
85C ILE* 3.0 34.6 + - + +
88C LEU* 4.9 1.4 - - + +
97C LEU* 4.4 10.1 - - + -
112C ILE* 3.9 15.3 - - + -
113C LYS 3.0 17.0 - - - +
114C PHE* 3.7 27.1 - - + +
115C PHE* 3.9 2.0 - - - -
126C PHE* 1.3 75.9 - - - +
128C LEU* 1.3 60.6 + - - +
129C VAL* 3.5 3.2 + - + +
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Residues in contact with LEU 128 (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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82C ALA* 4.1 14.6 - - + -
83C LEU 3.7 8.3 - - - +
84C TYR* 3.4 33.2 - - + +
111C GLU* 4.3 12.2 - - - +
112C ILE* 4.2 0.3 - - - -
113C LYS* 2.5 45.7 + - + +
115C PHE* 3.2 27.1 - - + -
127C ALA* 1.3 71.3 - - - +
129C VAL* 1.3 73.0 + - - +
130C GLY 4.3 1.2 + - - +
159C VAL* 4.9 6.5 - - + -
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Residues in contact with VAL 129 (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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82C ALA* 3.3 3.1 - - - +
83C LEU* 2.9 53.2 + - + +
85C ILE* 3.4 42.0 - - + -
97C LEU* 6.2 1.6 - - + -
101C VAL* 5.9 5.4 - - + -
109C ILE* 5.2 9.0 - - + -
111C GLU 4.7 7.0 - - - +
112C ILE* 5.3 7.0 - - + +
127C ALA* 4.3 3.6 - - + +
128C LEU* 1.3 78.5 - - - +
130C GLY* 1.3 71.7 + - - +
131C VAL* 5.6 2.0 - - + -
140C LEU* 5.5 10.3 - - + -
156C VAL* 5.4 0.4 - - + -
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Residues in contact with GLY 130 (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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82C ALA* 4.0 10.1 - - - -
108C ASP 4.0 0.9 - - - +
109C ILE* 4.0 2.8 - - - -
110C LEU* 3.1 42.0 + - - +
111C GLU* 3.7 14.5 + - - +
129C VAL* 1.3 84.6 - - - +
131C VAL* 1.3 65.2 + - - +
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Residues in contact with VAL 131 (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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81C ILE* 2.9 42.6 + - - +
83C LEU* 4.0 22.0 - - + -
106C VAL* 4.7 4.3 - - + -
108C ASP* 3.2 36.1 - - - +
110C LEU* 3.9 6.8 - - - +
129C VAL* 5.1 2.5 - - + +
130C GLY* 1.3 76.8 - - - +
132C GLY* 1.3 59.5 + - - +
133C SER 3.0 24.0 - - - +
134C GLU* 5.7 0.2 - - - -
136C SER* 3.4 8.7 - - - +
137C SER* 4.5 10.1 - - - +
140C LEU* 5.2 7.4 - - + -
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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