Contacts of the strand formed by residues 109 - 116 (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 ILE 109 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98C THR* 4.6 18.2 - - + +
101C VAL* 4.0 22.4 - - + -
102C HIS* 3.0 42.6 - - + +
106C VAL* 3.7 9.0 - - + +
107C ASN 3.6 12.2 + - - +
108C ASP* 1.3 69.4 - - - +
110C LEU* 1.3 61.3 + - - +
111C GLU 3.5 20.0 + - - +
112C ILE* 4.9 9.4 - - + -
129C VAL* 5.2 8.1 - - + -
130C GLY 4.1 5.2 - - - +
131C VAL* 5.7 0.2 - - - -
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Residues in contact with LEU 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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108C ASP 3.2 4.3 + - - +
109C ILE* 1.3 68.0 - - - +
111C GLU* 1.3 105.8 - - + +
130C GLY* 3.1 29.2 + - - -
131C VAL* 3.9 5.6 - - - +
132C GLY* 4.4 18.8 - - - +
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Residues in contact with GLU 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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109C ILE* 3.5 17.7 + - - +
110C LEU* 1.3 117.3 - - + +
112C ILE* 1.3 63.4 + - - +
113C LYS* 4.1 21.2 + - + +
128C LEU* 4.3 12.8 - - - +
129C VAL* 4.7 1.2 - - - +
130C GLY* 3.7 23.2 + - - -
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Residues in contact with ILE 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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94C ASP* 3.7 32.3 - - + +
97C LEU* 4.2 12.1 - - + -
98C THR* 4.9 5.6 - - - +
109C ILE* 4.9 9.6 - - + -
111C GLU* 1.3 78.6 - - - +
113C LYS* 1.3 68.6 + - - +
114C PHE* 3.3 38.2 + - + -
127C ALA* 3.9 11.9 - - + -
128C LEU 4.2 3.1 - - - +
129C VAL* 5.3 7.0 - - + +
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Residues in contact with LYS 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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68B ARG* 6.0 2.2 - - - +
152B ASN* 3.3 27.8 + - - +
154B GLU* 3.6 24.1 + - - -
111C GLU* 4.1 13.2 + - + +
112C ILE* 1.3 78.7 + - - +
114C PHE* 1.3 76.7 + - - +
115C PHE* 3.9 3.2 - - + -
116C GLU* 5.9 0.2 - - - -
127C ALA* 3.0 3.2 - - - -
128C LEU* 2.5 60.4 + - + +
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Residues in contact with PHE 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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152B ASN* 6.0 0.4 - - - +
164B HIS* 4.1 13.9 - - + +
165B ILE* 5.7 2.5 - - + -
88C LEU* 4.6 11.7 - - + -
89C THR 5.5 1.1 - - - -
92C THR* 3.1 29.4 - - - -
93C THR 4.0 1.6 - - - -
94C ASP* 3.4 31.0 - - + -
97C LEU* 4.1 14.4 - - + -
112C ILE* 3.3 35.3 + - + -
113C LYS* 1.3 93.4 - - - +
115C PHE* 1.3 64.9 + - - +
116C GLU* 3.8 24.2 - - - +
123C SER* 3.3 24.2 - - - -
126C PHE 4.7 3.8 - - - -
127C ALA* 3.7 12.8 - - + -
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Residues in contact with PHE 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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84C TYR* 4.4 8.1 - + - -
113C LYS* 3.9 3.1 - - + -
114C PHE* 1.3 74.2 - - - +
116C GLU* 1.3 58.0 + - - +
123C SER* 3.6 4.2 + - - -
124C LYS* 2.6 40.2 + - + +
126C PHE* 3.0 73.8 + + + +
128C LEU* 3.2 52.3 - - + -
164C LEU* 4.3 14.4 - - + -
168C GLU* 4.4 7.6 - - - -
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Residues in contact with GLU 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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151B PRO* 4.4 11.1 - - - +
152B ASN* 3.3 28.8 + - - -
154B GLU* 5.1 3.3 - - - +
156B PRO* 6.0 1.9 - - - +
158B TYR* 5.1 3.3 + - - -
164B HIS* 2.9 28.8 - - - -
165B ILE* 4.4 0.9 - - - +
113C LYS* 5.9 0.2 - - - -
114C PHE* 3.8 16.7 - - - +
115C PHE* 1.3 77.8 - - - +
117C ASN* 1.3 66.6 + - - +
118C ARG* 3.4 5.4 + - - +
121C GLY* 4.1 13.0 - - - +
122C GLN 3.2 19.3 - - - +
123C SER* 4.4 1.1 - - - -
124C LYS* 3.6 17.9 + - - +
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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