Contacts of the helix formed by residues 169 - 178 (chain C) in PDB entry 1U5T
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 169 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44C TRP* 3.8 24.0 - - + -
45C TYR* 5.5 3.4 - - + -
120C ARG* 4.5 7.4 - - - +
167C ARG 4.0 5.2 - - - +
168C MET* 1.3 86.0 - - + +
170C GLU* 1.3 69.9 + - - +
171C SER* 3.8 12.8 - - - +
172C LEU* 3.0 35.8 + - + +
173C LEU* 2.7 19.4 + - - +
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Residues in contact with GLU 170 (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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150C THR* 4.2 2.1 + - - -
151C LEU* 3.8 17.4 - - + +
152C TYR* 2.7 56.1 + - - +
155C SER* 5.5 3.1 - - - +
168C MET 3.8 2.2 + - - -
169C PRO* 1.3 67.7 - - - +
171C SER* 1.3 55.4 + - - +
172C LEU 2.5 3.3 + - - -
173C LEU* 2.5 44.1 + - + +
174C TYR* 3.1 5.2 + - - +
195C LYS* 5.5 3.1 - - - -
196C VAL* 5.9 0.3 - - - +
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Residues in contact with SER 171 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C ILE* 6.5 0.9 - - - -
108C GLN 4.2 19.1 - - - -
109C SER* 5.5 1.3 - - - -
110C GLY 4.4 5.8 + - - -
120C ARG* 4.2 11.5 + - - -
169C PRO* 3.8 15.2 - - - +
170C GLU* 1.3 73.7 + - - +
172C LEU* 1.3 60.7 + - - +
174C TYR* 4.6 5.7 - - - +
175C TYR* 3.4 21.7 - - - -
195C LYS* 4.7 12.9 + - - +
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Residues in contact with LEU 172 (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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44C TRP* 4.6 4.5 - - + -
106C ILE* 4.1 7.9 - - + -
120C ARG* 2.8 37.2 - - - +
122C PHE* 2.9 66.2 - - + -
168C MET* 3.9 0.4 - - - -
169C PRO* 3.0 39.7 + - + +
170C GLU 2.5 4.9 + - - -
171C SER* 1.3 76.2 - - - +
173C LEU* 1.3 55.3 + - - +
174C TYR 2.9 1.8 - - - -
175C TYR* 2.4 45.6 + - + +
176C CYS* 3.2 4.9 - - - -
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Residues in contact with LEU 173 (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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135C ILE* 4.2 13.9 - - + -
151C LEU* 4.0 10.5 - - + +
154C LEU* 3.2 40.6 - - + -
155C SER* 3.6 17.0 - - - -
165C PHE* 5.0 2.7 - - + +
168C MET* 3.3 32.9 - - + +
169C PRO 2.7 9.9 + - - +
170C GLU* 2.5 22.8 + - - +
172C LEU* 1.3 70.2 - - - +
174C TYR* 1.3 56.5 + - - +
176C CYS* 2.9 20.0 - - - -
177C LEU* 2.5 48.6 + - + +
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Residues in contact with TYR 174 (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 SER* 6.2 0.2 - - - -
111C ARG* 3.9 15.8 + - - -
151C LEU* 3.8 11.2 - - + +
170C GLU 3.1 4.7 + - - +
171C SER 4.6 0.7 - - - +
172C LEU 2.7 4.7 + - - +
173C LEU* 1.3 73.8 - - - +
175C TYR* 1.3 91.7 + + - +
176C CYS 2.8 1.6 + - - -
177C LEU* 2.6 31.9 + - - +
178C LYS* 3.0 57.9 + - + +
188C MET* 3.8 28.3 - - + -
195C LYS* 3.4 44.0 - - + +
197C ILE* 6.0 0.7 - - - -
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Residues in contact with TYR 175 (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 LEU* 4.8 13.7 - - + -
109C SER* 4.4 3.3 + - - -
110C GLY* 2.5 57.5 + - - -
111C ARG* 3.2 27.1 + - - +
122C PHE* 4.9 7.0 - + + -
128C LEU* 4.2 18.4 - - + +
171C SER 3.4 17.3 - - - -
172C LEU* 2.4 28.2 + - + +
174C TYR* 1.3 100.7 - + - +
176C CYS* 1.3 56.3 + - - +
178C LYS* 4.1 7.6 - - + +
179C PRO* 3.1 21.2 - - - +
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Residues in contact with CYS 176 (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 PHE* 4.6 8.3 - - - -
128C LEU* 4.8 9.1 - - + +
131C TRP* 4.8 22.2 - - + +
132C ALA* 3.1 23.8 + - - +
135C ILE* 5.2 3.6 - - + -
168C MET* 3.5 26.5 - - + -
172C LEU 3.2 7.4 - - - -
173C LEU* 2.9 35.0 - - + +
174C TYR 2.8 0.6 + - - -
175C TYR* 1.3 70.2 - - - +
177C LEU* 1.3 63.5 + - + +
179C PRO* 2.8 18.6 - - - +
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Residues in contact with LEU 177 (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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135C ILE* 3.6 20.6 - - + -
139C PHE* 5.7 2.5 - - + -
151C LEU* 4.0 12.6 - - + -
154C LEU* 4.4 3.6 - - + -
173C LEU* 2.5 61.6 + - + +
174C TYR* 2.6 15.5 + - + +
176C CYS* 1.3 69.6 - - + +
178C LYS* 1.3 51.2 - - - +
179C PRO 2.7 4.0 - - - -
180C LEU* 2.3 70.4 + - + +
181C CYS* 4.3 2.1 - - - -
188C MET* 5.5 1.6 - - + -
197C ILE* 3.3 34.5 - - + -
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Residues in contact with LYS 178 (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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111C ARG* 5.3 5.4 - - - +
174C TYR* 3.0 49.5 + - + +
175C TYR* 4.1 9.0 - - + +
177C LEU* 1.3 75.4 - - - +
179C PRO* 1.3 67.7 - - + +
180C LEU 3.1 0.4 + - - -
181C CYS* 3.5 26.9 - - - +
188C MET* 3.5 28.2 - - + +
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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