Contacts of the helix formed by residues 131 - 139 (chain C) in PDB entry 5FI0
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 LEU 131 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50C ARG* 5.0 0.2 - - - +
54C LEU* 3.6 28.0 - - + -
57C ILE* 4.2 22.2 - - + -
117C LEU* 3.5 28.3 - - + -
120C CYS* 3.7 15.0 - - + -
121C LEU* 4.2 21.5 - - + -
129C HIS* 4.1 0.8 - - + -
130C GLU* 1.3 74.0 - - - +
132C GLY* 1.3 66.6 + - - +
133C ASN 3.4 2.2 - - - -
134C VAL* 3.2 39.6 + - + +
135C PHE* 3.4 14.8 + - + -
209C LEU* 4.1 13.5 - - + -
219C ASP* 2.9 10.4 + - - +
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Residues in contact with GLY 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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130C GLU 3.7 0.2 - - - -
131C LEU* 1.3 75.4 - - - +
133C ASN* 1.3 57.5 + - - +
135C PHE* 3.2 9.9 + - - +
136C LEU* 3.0 24.0 + - - +
206C LEU* 5.5 1.3 - - - -
209C LEU* 5.2 0.2 - - - +
219C ASP* 2.9 18.6 + - - -
222C ALA* 3.5 27.4 - - - -
223C VAL* 4.0 7.5 - - - +
226C ALA* 3.6 8.4 - - - +
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Residues in contact with ASN 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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153B LYS* 2.3 31.4 + - - +
155B LEU* 5.4 2.7 - - - +
167B THR* 3.9 20.6 - - - +
171B GLU* 3.0 27.8 + - - +
174B ARG* 4.2 13.0 - - - +
130C GLU* 5.2 15.5 + - - +
131C LEU 3.4 0.4 - - - -
132C GLY* 1.3 71.9 - - - +
134C VAL* 1.3 67.7 + - + +
136C LEU* 3.6 7.5 - - - +
137C LYS* 2.9 25.5 + - - +
222C ALA* 3.6 16.7 - - - +
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Residues in contact with VAL 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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47B ASP* 5.0 2.5 - - - +
174B ARG* 4.9 15.0 - - - +
113C PHE* 4.4 6.7 - - + -
116C ALA* 3.6 39.0 - - + -
117C LEU* 4.2 15.9 - - + +
120C CYS* 3.8 19.7 - - + -
130C GLU 3.8 6.5 - - - +
131C LEU* 3.2 30.4 + - + +
133C ASN* 1.3 80.5 - - + +
135C PHE* 1.3 59.8 + - + +
137C LYS* 3.6 4.3 - - - +
138C PHE* 3.2 26.6 - - + -
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Residues in contact with PHE 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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57C ILE* 4.2 28.3 - - + -
113C PHE* 3.3 34.1 - + - -
117C LEU* 5.1 3.8 - - + -
131C LEU* 3.4 17.6 + - + -
132C GLY 3.2 7.7 + - - +
134C VAL* 1.3 77.1 - - + +
136C LEU* 1.3 59.2 + - - +
138C PHE* 2.8 24.9 + - - +
139C LYS* 3.2 8.9 + - - +
142C PHE* 4.8 4.1 - + - -
202C TYR* 3.6 33.0 - + + -
205C LEU* 5.7 1.1 - - + -
206C LEU* 3.6 44.6 - - + -
226C ALA* 3.8 11.9 - - + -
229C ALA* 6.2 0.4 - - - -
230C MET* 4.0 19.5 - - + +
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Residues in contact with LEU 136 (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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153B LYS* 3.4 32.8 - - - +
132C GLY 3.0 13.4 + - - +
133C ASN* 3.3 13.4 + - - +
135C PHE* 1.3 75.5 - - - +
137C LYS* 1.3 61.6 + - - +
138C PHE 3.3 0.5 + - - -
139C LYS* 3.3 43.3 - - + +
222C ALA* 3.8 11.4 - - - +
225C SER* 3.8 25.4 - - - +
226C ALA* 3.9 13.2 - - - +
229C ALA* 3.9 26.0 - - + -
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Residues in contact with LYS 137 (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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46B VAL* 5.1 3.8 + - - +
47B ASP* 3.0 37.5 + - - +
49B LYS* 6.3 1.2 - - - +
174B ARG* 3.4 36.8 - - + +
177B LEU* 5.4 10.7 - - - +
178B CYS* 4.0 38.9 - - + +
133C ASN 2.9 16.6 + - - +
134C VAL* 3.6 7.6 - - - +
135C PHE 3.0 0.2 + - - -
136C LEU* 1.3 75.9 - - - +
138C PHE* 1.3 83.9 + - + +
139C LYS* 3.7 2.3 + - - +
140C ASP* 4.6 4.0 + - - +
141C LYS* 4.4 4.3 - - - +
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Residues in contact with PHE 138 (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 VAL* 4.0 15.7 - - + -
112C ASP* 3.8 25.1 - - + -
113C PHE* 3.7 35.9 - + + -
116C ALA* 4.1 11.9 - - + -
134C VAL 3.2 21.8 - - - -
135C PHE 2.8 8.4 + - - +
137C LYS* 1.3 103.5 - - + +
139C LYS* 1.3 57.2 + - - +
140C ASP 3.0 3.6 - - - -
141C LYS* 2.7 60.5 + - + -
142C PHE* 3.1 32.1 + - + -
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Residues in contact with LYS 139 (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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152B VAL* 6.2 3.4 - - - +
135C PHE 3.2 5.7 + - - +
136C LEU* 3.3 36.4 + - + +
137C LYS 5.1 1.4 + - - +
138C PHE* 1.3 76.5 - - - +
140C ASP* 1.3 90.0 + - - +
142C PHE* 4.1 11.3 + - - +
143C CYS 4.9 1.4 + - - -
229C ALA* 4.3 21.5 - - + +
230C MET* 5.3 1.6 - - - -
233C VAL* 3.8 22.6 - - + +
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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