Contacts of the helix formed by residues 131 - 140 (chain P) in PDB entry 1FQV
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 THR 131 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131O LYS* 4.3 1.8 - - - -
129P GLY 4.6 4.0 - - - +
130P LYS* 1.3 77.5 - - - +
132P PRO* 1.3 77.9 - - + +
133P GLU* 3.7 7.9 + - - +
134P GLU* 2.9 38.2 + - - +
135P ILE* 2.9 21.4 + - - +
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Residues in contact with PRO 132 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131O LYS* 3.4 31.8 - - + +
134O GLY* 3.6 27.6 - - - +
135O VAL* 4.2 11.0 - - + +
131P THR* 1.3 87.8 - - - +
133P GLU* 1.3 60.8 + - - +
135P ILE* 3.3 5.3 + - + +
136P ARG* 3.0 34.9 + - - +
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Residues in contact with GLU 133 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131P THR* 3.0 8.6 + - - +
132P PRO* 1.3 75.5 - - - +
134P GLU* 1.3 62.2 + - + +
135P ILE 3.0 5.3 + - - -
136P ARG* 2.7 50.6 + - - +
137P LYS* 2.9 49.0 + - - +
143P ASN* 5.1 1.0 + - - -
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Residues in contact with GLU 134 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129P GLY 4.4 2.0 - - - +
130P LYS* 3.6 23.3 + - + +
131P THR* 2.9 48.8 + - - +
133P GLU* 1.3 76.0 - - + +
135P ILE* 1.3 58.9 + - - +
137P LYS* 3.7 23.1 - - + +
138P THR* 3.2 31.0 + - - +
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Residues in contact with ILE 135 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131O LYS* 3.6 22.4 - - + -
132O VAL* 4.3 2.2 - - + -
135O VAL* 3.9 29.2 - - + -
139O TRP* 3.9 11.4 - - + -
127P ILE* 3.3 35.2 - - + +
130P LYS* 3.6 17.5 - - + -
131P THR 2.9 13.8 + - - +
132P PRO 3.5 7.4 - - - +
134P GLU* 1.3 76.4 - - - +
136P ARG* 1.3 67.1 + - - +
137P LYS 3.1 1.1 - - - -
138P THR* 2.8 18.8 + - - -
139P PHE* 3.2 31.3 + - + +
141P ILE* 4.5 0.6 - - + +
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Residues in contact with ARG 136 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134O GLY 3.0 23.1 + - - -
135O VAL* 2.7 30.4 + - + -
132P PRO* 3.0 18.0 + - - +
133P GLU* 2.7 61.2 + - - +
135P ILE* 1.3 76.2 - - - +
137P LYS* 1.3 52.9 + - - +
140P ASN* 2.7 38.5 + - - -
141P ILE* 2.9 28.9 + - - +
142P LYS 4.8 0.2 - - - -
143P ASN* 2.8 34.5 - - - +
145P PHE* 4.3 0.6 - - - -
150P GLU* 2.9 28.6 + - - -
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Residues in contact with LYS 137 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133P GLU* 2.9 56.2 + - + +
134P GLU* 3.7 25.8 - - + +
136P ARG* 1.3 80.6 - - - +
138P THR* 1.3 68.9 + - + +
140P ASN* 3.0 10.3 + - - +
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Residues in contact with THR 138 (chain P).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97P GLN* 2.6 37.8 + - - +
130P LYS* 3.4 33.1 - - - +
134P GLU 3.2 16.1 + - - +
135P ILE* 2.8 18.0 + - - -
137P LYS* 1.3 83.5 - - + +
139P PHE* 1.3 74.5 + - - -
140P ASN* 3.1 4.9 + - - +
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Residues in contact with PHE 139 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107O VAL 3.9 3.0 - - - +
109O TRP* 3.6 50.5 + + + -
139O TRP* 4.2 9.2 - + + -
97P GLN* 3.1 18.8 - - + -
123P VAL* 3.6 26.0 - - + -
126P MET* 3.9 34.5 - - + -
127P ILE* 3.8 26.7 - - + -
130P LYS* 5.8 1.1 - - + -
135P ILE* 3.2 22.4 + - + +
138P THR* 1.3 91.2 + - - +
140P ASN* 1.3 74.7 + - - +
141P ILE* 3.5 17.2 - - + +
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Residues in contact with ASN 140 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107O VAL 4.2 12.6 + - - +
108O SER* 3.4 31.4 + - - -
136P ARG 2.7 17.4 + - - -
137P LYS* 3.0 10.6 + - - +
138P THR 3.0 2.4 - - - +
139P PHE* 1.3 85.7 - - - +
141P ILE* 1.3 63.7 + - - +
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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