Contacts of the helix formed by residues 123 - 135 (chain C) in PDB entry 4F2N
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 PRO 123 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121C PRO 3.3 9.6 - - - +
122C MET* 1.4 88.9 - - + +
124C LYS* 1.3 67.4 + - - +
125C THR* 3.3 2.5 - - - +
126C LEU* 3.1 5.9 + - + +
127C GLU* 3.0 18.5 + - - +
218C TRP* 3.6 19.1 - - + +
219C GLU* 4.4 13.5 - - + -
222C CYS* 3.7 31.4 - - + -
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Residues in contact with LYS 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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122C MET 3.9 1.2 + - - +
123C PRO* 1.3 72.6 - - - +
125C THR* 1.3 56.7 + - - +
127C GLU* 3.0 39.6 + - - +
128C ASN* 2.9 56.1 + - - +
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Residues in contact with THR 125 (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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123C PRO* 3.3 2.4 - - - +
124C LYS* 1.3 79.1 - - - +
126C LEU* 1.3 57.6 + - - +
128C ASN* 3.7 6.2 + - - +
129C ALA* 3.2 25.5 + - - +
222C CYS* 4.2 14.4 - - - -
225C TYR* 4.5 17.9 - - + -
226C GLU* 4.1 21.0 + - + +
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Residues in contact with LEU 126 (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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122C MET* 3.9 10.5 - - + -
123C PRO 3.1 8.7 + - - +
125C THR* 1.3 77.5 - - - +
127C GLU* 1.3 67.3 + - - +
129C ALA* 3.2 3.9 + - + +
130C ILE* 2.9 45.0 + - + +
168C LEU* 5.1 0.7 - - + -
187C ILE* 4.2 11.9 - - + -
218C TRP* 3.7 33.9 - - + +
221C VAL* 3.7 13.5 - - + -
222C CYS* 3.9 27.1 - - + +
225C TYR* 4.1 30.5 - - + -
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Residues in contact with GLU 127 (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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122C MET* 3.6 27.0 - - + +
123C PRO 3.0 12.6 + - - +
124C LYS* 3.0 49.0 + - - +
126C LEU* 1.3 76.7 - - - +
128C ASN* 1.3 61.5 + - - +
131C ALA* 2.9 33.3 + - + +
137C VAL* 3.8 20.4 - - + +
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Residues in contact with ASN 128 (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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124C LYS* 2.9 40.9 + - - +
125C THR* 4.0 5.7 - - - +
127C GLU* 1.3 87.4 - - - +
129C ALA* 1.3 56.1 + - - +
131C ALA* 4.1 4.1 - - - +
132C LYS* 2.9 31.3 + - - +
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Residues in contact with ALA 129 (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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125C THR 3.2 17.5 + - - +
126C LEU* 3.2 5.6 + - + +
128C ASN* 1.3 76.5 - - - +
130C ILE* 1.3 62.8 + - - +
132C LYS* 3.5 8.2 + - - +
133C GLN* 3.2 23.9 + - - +
168C LEU* 3.8 11.3 - - + +
225C TYR* 3.4 37.0 - - + +
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Residues in contact with ILE 130 (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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122C MET* 3.9 21.1 - - + -
126C LEU* 2.9 46.5 + - + +
127C GLU 3.9 3.1 - - - +
129C ALA* 1.3 75.2 - - - +
131C ALA* 1.3 64.9 + - - +
133C GLN 3.3 0.7 + - - -
134C PHE* 3.0 29.1 + - + +
137C VAL* 4.1 16.6 - - + -
140C PHE* 3.5 38.1 - - + -
159C LEU* 4.4 17.9 - - + -
168C LEU* 4.1 15.0 - - + -
218C TRP* 4.5 5.4 - - + -
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Residues in contact with ALA 131 (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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127C GLU* 2.9 19.5 + - + +
128C ASN* 4.1 4.7 - - - +
130C ILE* 1.3 77.7 - - - +
132C LYS* 1.3 57.5 + - - +
135C GLY* 2.9 33.2 + - - +
136C SER* 3.7 26.2 - - - +
137C VAL* 4.1 7.4 - - + +
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Residues in contact with LYS 132 (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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128C ASN 2.9 18.4 + - - +
129C ALA* 3.7 8.1 - - - +
130C ILE 3.2 0.2 - - - -
131C ALA* 1.3 79.2 - - - +
133C GLN* 1.3 61.4 + - - +
135C GLY* 4.2 2.6 + - - -
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Residues in contact with GLN 133 (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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129C ALA 3.2 17.0 + - - +
132C LYS* 1.3 78.5 - - - +
134C PHE* 1.3 82.2 + - + +
135C GLY 3.5 0.6 + - - -
167C GLU* 3.4 26.7 + - - +
168C LEU* 3.1 47.4 + - + +
21F LEU* 3.2 38.2 - - + +
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Residues in contact with PHE 134 (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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130C ILE* 3.0 22.9 + - + +
133C GLN* 1.3 91.7 - - + +
135C GLY* 1.3 56.2 + - - +
136C SER 3.2 7.4 + - - +
139C ASP* 3.4 15.9 - - - +
140C PHE* 3.8 44.4 - + + +
143C SER* 5.2 3.1 - - - +
159C LEU* 3.8 20.9 - - + -
168C LEU* 3.9 15.5 - - + -
169C LEU* 4.0 14.4 - - - -
170C ILE* 3.7 27.8 - - + -
21F LEU* 3.9 43.2 - - + -
22F CYS 3.7 6.9 - - - +
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Residues in contact with GLY 135 (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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131C ALA* 2.9 17.8 + - - +
132C LYS 4.2 1.7 + - - -
133C GLN 3.5 3.0 + - - -
134C PHE* 1.3 76.7 - - - +
136C SER* 1.3 62.0 + - - +
21F LEU 4.2 1.6 + - - -
22F CYS* 3.8 4.3 - - - -
23F TYR* 3.7 38.0 - - - +
185F ARG* 5.4 0.7 + - - -
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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