Contacts of the strand formed by residues 105 - 111 (chain C) in PDB entry 3QU3
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 PHE 105 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C PHE* 4.7 1.6 - + - -
13C GLY* 3.3 33.7 - - - -
16C LEU* 3.9 21.3 - - + -
17C LEU* 3.8 14.1 - - + -
38C PHE* 3.6 22.2 - + - -
99C LEU* 3.3 24.5 - - + -
102C THR* 3.2 22.8 + - + +
103C GLY* 3.2 3.6 - - - +
104C ARG* 1.3 93.3 - - + +
106C ILE* 1.3 61.1 + - - +
107C LEU 3.9 0.2 + - - -
122C TYR* 4.0 19.7 - - + -
123C GLU 3.7 3.4 - - - -
124C LEU* 3.6 23.6 - - + -
135C NA 2.9 24.9 - - - -
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Residues in contact with ILE 106 (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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103C GLY 4.4 8.3 - - - +
104C ARG 4.6 0.2 - - - +
105C PHE* 1.3 74.3 - - - +
107C LEU* 1.3 71.1 + - - +
108C ARG* 3.2 45.1 + - - +
122C TYR* 3.3 2.9 - - - -
123C GLU 2.9 41.2 + - - +
124C LEU 4.2 2.5 - - - +
125C SER* 3.9 30.1 - - - +
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Residues in contact with LEU 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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105C PHE 3.9 1.0 + - - -
106C ILE* 1.3 78.8 - - - +
108C ARG* 1.3 60.9 + - - +
109C GLN 3.6 22.2 - - - +
110C ASP* 5.0 7.4 - - + +
120C LYS* 3.8 37.7 - - + +
121C VAL 3.2 19.1 - - - +
122C TYR* 3.7 26.7 - - + +
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Residues in contact with ARG 108 (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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115A PRO* 4.5 16.6 - - + +
116A VAL* 3.4 32.0 - - + +
37C VAL* 6.4 0.2 - - + -
106C ILE* 3.2 34.7 + - - +
107C LEU* 1.3 76.6 + - - +
109C GLN* 1.3 62.6 + - - +
121C VAL* 2.8 12.2 + - + +
123C GLU* 2.5 45.9 + - + +
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Residues in contact with GLN 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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43A LYS* 4.9 15.0 - - - +
44A HIS 5.2 7.4 + - - +
115A PRO* 4.0 32.1 + - + +
107C LEU* 3.6 8.2 - - - +
108C ARG* 1.3 81.8 - - - +
110C ASP* 1.3 61.0 + - - +
111C ASN* 3.0 36.7 + - - +
120C LYS* 3.6 1.6 - - - -
121C VAL* 2.8 39.6 + - + +
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Residues in contact with ASP 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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107C LEU* 5.0 7.2 - - + -
109C GLN* 1.3 74.4 - - - +
111C ASN* 1.3 62.3 + - - +
112C SER* 2.6 35.1 + - - -
113C GLY 4.3 2.1 + - - -
120C LYS* 3.6 27.9 + - + +
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Residues in contact with ASN 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 GLN* 3.0 43.1 + - - +
110C ASP* 1.3 75.6 + - - +
112C SER* 1.3 59.6 + - - +
113C GLY 3.1 7.0 + - - -
114C ASP* 3.2 24.6 + - + +
118C PRO* 3.4 0.3 - - - +
119C HIS* 2.8 58.8 + - + +
121C VAL* 3.8 4.7 - - - +
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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