Contacts of the helix formed by residues 104 - 112 (chain C) in PDB entry 2YVX
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 ASP 104 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74C LYS* 5.3 11.4 + - + +
100C VAL* 2.8 17.4 + - + +
101C ARG* 4.1 3.1 - - - -
103C GLU* 1.3 77.0 - - + +
105C PRO* 1.3 61.2 - - - +
106C ALA* 2.8 27.0 + - - +
107C TYR* 2.5 54.1 + - + +
108C PHE* 3.2 12.6 + - - +
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Residues in contact with PRO 105 (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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101C ARG* 3.9 18.1 - - + +
103C GLU 3.8 6.1 - - - +
104C ASP* 1.3 86.2 - - - +
106C ALA* 1.3 60.2 + - + +
108C PHE* 4.3 10.6 - - + +
109C GLN* 4.3 11.6 + - - +
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Residues in contact with ALA 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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104C ASP* 2.9 8.4 + - - +
105C PRO* 1.3 80.7 - - + +
107C TYR* 1.3 69.2 + - - +
108C PHE 2.8 3.3 + - - -
109C GLN* 2.9 17.7 + - - +
110C ARG* 3.0 19.4 + - + +
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Residues in contact with TYR 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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73C LEU* 2.5 23.4 + - + -
74C LYS* 3.3 38.0 + - + -
76C LEU 5.6 0.9 + - - -
81C LEU* 4.3 8.2 - - + +
100C VAL* 4.1 12.3 - - + -
104C ASP* 2.5 35.7 + - + +
106C ALA* 1.3 71.3 - - - +
108C PHE* 1.3 53.3 + - - +
110C ARG* 4.3 7.2 - - + -
111C LEU* 2.6 75.9 + - + +
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Residues in contact with PHE 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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97C LEU* 3.1 42.4 - - + -
98C GLN* 5.9 1.6 - - + -
100C VAL* 4.4 6.6 - - + +
101C ARG* 4.4 44.6 - - + +
104C ASP 3.2 13.0 + - - +
105C PRO 4.3 9.2 - - - +
106C ALA 2.8 1.2 + - - -
107C TYR* 1.3 77.6 - - - +
109C GLN* 1.3 76.6 + - + +
110C ARG 2.8 0.3 + - - -
111C LEU* 4.8 2.0 - - - -
112C LYS* 2.8 53.4 + - + +
124C GLU* 6.2 1.3 - - + -
127C ALA* 5.6 7.0 - - + -
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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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105C PRO 4.3 8.9 + - - +
106C ALA* 2.9 11.0 + - - +
108C PHE* 1.3 85.6 - - + +
110C ARG* 1.3 63.1 + - + +
112C LYS* 3.3 27.1 + - - +
113C ASP* 3.0 21.4 - - - +
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Residues in contact with ARG 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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106C ALA* 3.0 19.3 + - + +
107C TYR* 3.6 9.2 - - + +
108C PHE 2.8 1.8 + - - -
109C GLN* 1.3 78.6 - - + +
111C LEU* 1.3 54.5 + - - +
112C LYS 2.9 4.3 - - - -
113C ASP* 2.7 42.2 + - - +
114C LEU* 4.0 3.2 + - - +
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Residues in contact with LEU 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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73C LEU* 3.2 39.3 - - + +
81C LEU* 4.1 2.2 - - + -
85C LEU* 3.4 28.1 - - + +
97C LEU* 5.0 14.8 - - + -
100C VAL* 4.9 5.2 - - + -
107C TYR* 2.6 55.2 + - + +
108C PHE* 4.1 2.2 - - - +
110C ARG* 1.3 72.5 - - - +
112C LYS* 1.3 63.8 + - - +
114C LEU* 3.2 35.2 + - + +
115C LEU 4.2 0.9 + - - -
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Residues in contact with LYS 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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97C LEU* 5.0 9.0 - - + -
108C PHE* 2.8 50.3 + - + +
109C GLN* 3.3 28.6 + - - +
111C LEU* 1.3 82.6 - - - +
113C ASP* 1.3 69.0 + - - +
115C LEU* 3.0 29.5 + - + +
120C ARG* 3.8 28.5 + - + +
124C GLU* 2.8 36.3 + - + +
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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