Contacts of the helix formed by residues 114 - 124 (chain C) in PDB entry 4FJV
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 114 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65C LEU* 4.0 7.4 - - - +
112C ASP 5.3 0.4 - - - -
113C GLY* 1.3 76.6 - - - -
115C VAL* 1.3 64.8 + - - +
116C SER* 3.5 10.4 + - - -
117C SER* 2.9 28.7 + - - -
118C LEU* 3.1 23.7 + - - +
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Residues in contact with VAL 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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43C ARG* 3.8 16.2 - - - +
58C TYR* 3.8 6.7 - - - +
62C GLU* 4.4 11.4 - - + +
65C LEU* 3.7 24.5 - - + +
114C SER* 1.3 72.6 - - - +
116C SER* 1.3 59.1 + - - +
118C LEU* 3.3 4.5 + - - +
119C LEU* 2.9 49.7 + - + +
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Residues in contact with SER 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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114C SER* 3.1 8.6 + - - -
115C VAL* 1.3 84.2 - - - +
117C SER* 1.3 60.9 + - - +
119C LEU* 3.6 8.8 + - - +
120C LYS* 3.2 20.4 + - - +
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Residues in contact with SER 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C LEU* 3.8 22.9 - - - +
113C GLY* 4.0 2.8 - - - -
114C SER* 2.9 37.2 + - - -
116C SER* 1.3 74.7 - - - +
118C LEU* 1.3 64.9 + - - +
120C LYS* 3.2 10.1 + - - +
121C VAL* 3.2 25.6 + - - +
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Residues in contact with LEU 118 (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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58C TYR* 3.6 24.0 - - + +
61C LEU* 3.9 6.1 - - + +
62C GLU* 3.4 39.0 - - + +
65C LEU* 4.3 8.5 - - + -
105C VAL* 3.6 29.4 - - + -
108C LEU* 4.1 8.7 - - + -
109C VAL* 4.1 16.2 - - + -
114C SER 3.1 17.1 + - - +
115C VAL 3.6 4.3 - - - +
117C SER* 1.3 78.5 + - - +
119C LEU* 1.3 61.6 + - - +
121C VAL* 3.1 7.0 + - - +
122C PHE* 3.1 36.1 + - + -
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Residues in contact with LEU 119 (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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5C SER 5.7 0.2 - - - -
6C PHE* 4.2 19.5 - - + -
9C ILE* 3.7 24.7 - - + +
43C ARG* 3.8 21.8 - - - +
58C TYR* 3.4 26.5 - - + +
115C VAL* 2.9 39.4 + - + +
116C SER* 3.7 8.3 - - - +
117C SER 3.3 0.2 - - - -
118C LEU* 1.3 76.8 - - - +
120C LYS* 1.3 57.9 + - - +
122C PHE* 3.3 1.6 + - - +
123C ASN* 2.8 48.7 + - - +
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Residues in contact with LYS 120 (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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3C GLU 6.0 2.4 - - - +
5C SER 6.0 0.2 - - - -
116C SER 3.2 11.3 + - - +
117C SER* 3.2 13.9 + - - +
119C LEU* 1.3 78.5 - - - +
121C VAL* 1.3 63.9 + - + +
123C ASN* 3.5 3.9 + - - +
124C ASP* 3.0 24.3 + - + +
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Residues in contact with VAL 121 (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 VAL* 3.9 21.1 - - + -
108C LEU* 3.9 23.1 - - + -
117C SER 3.2 13.4 + - - +
118C LEU 3.1 7.5 + - - +
120C LYS* 1.3 79.6 - - + +
122C PHE* 1.3 59.0 + - + +
124C ASP* 3.1 29.8 + - - +
127C ALA* 3.9 12.2 - - + +
128C SER* 3.8 4.9 + - - -
131C ILE* 3.9 25.6 - - + -
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Residues in contact with PHE 122 (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 LEU* 3.5 13.7 - - - +
9C ILE* 4.0 14.8 - - + +
54C ARG* 4.0 18.0 - - + -
57C GLY* 3.6 7.4 - - - -
58C TYR* 3.5 51.8 - + + -
61C LEU* 3.8 17.5 - - + -
105C VAL* 4.1 6.1 - - + -
118C LEU* 3.1 42.1 + - + +
119C LEU 4.1 2.7 - - - +
121C VAL* 1.3 79.2 - - + +
123C ASN* 1.3 58.6 + - - +
124C ASP 3.5 0.4 - - - -
128C SER* 2.9 34.8 + - - -
131C ILE* 3.9 33.2 - - + -
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Residues in contact with ASN 123 (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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5C SER* 3.2 39.7 + - - +
6C PHE* 3.3 7.2 - - - +
7C ASN 3.3 0.7 + - - -
8C LEU* 3.0 39.0 + - - +
9C ILE* 3.0 36.0 + - - +
119C LEU* 2.8 35.3 + - - +
120C LYS* 3.7 4.9 - - - +
121C VAL 3.1 0.2 - - - -
122C PHE* 1.3 78.0 - - - +
124C ASP* 1.3 60.0 + - - +
125C GLN* 3.5 2.9 + - - -
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Residues in contact with ASP 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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120C LYS* 3.0 13.7 + - + +
121C VAL* 3.1 12.0 + - - +
123C ASN* 1.3 75.8 - - - +
125C GLN* 1.3 59.1 + - - +
126C SER* 3.2 8.3 + - - -
127C ALA* 3.1 31.7 + - + +
128C SER* 2.8 35.3 + - - -
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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