Contacts of the helix formed by residues 169 - 178 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44D TRP* 3.8 29.2 - - + -
45D TYR* 4.9 14.4 - - + -
120D ARG* 5.8 0.4 - - - +
122D PHE* 4.6 17.9 - - + -
155D SER* 5.4 1.1 - - - +
167D ARG* 2.9 15.9 - - - +
168D MET* 1.3 88.1 - - + +
170D GLU* 1.3 67.8 + - - +
171D SER* 3.4 3.4 + - - +
172D LEU* 3.4 10.0 + - - +
173D LEU* 3.5 6.9 + - - +
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Residues in contact with GLU 170 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150D THR* 4.9 1.7 + - - -
151D LEU* 2.9 34.0 - - + +
152D TYR* 2.8 49.9 + - - +
155D SER* 5.0 4.7 - - - +
168D MET 3.3 1.0 + - - -
169D PRO* 1.3 71.5 - - - +
171D SER* 1.3 55.9 + - - +
173D LEU* 2.7 42.1 + - + +
174D TYR* 2.9 7.6 + - - +
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Residues in contact with SER 171 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108D GLN 3.8 19.4 + - - -
110D GLY 5.7 4.3 - - - -
120D ARG* 5.3 2.2 - - - -
122D PHE* 4.1 19.7 - - - -
169D PRO* 3.4 2.7 + - - +
170D GLU* 1.3 77.8 - - - +
172D LEU* 1.3 62.4 + - - +
174D TYR* 3.0 26.6 - - - +
175D TYR* 3.5 12.7 + - - -
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Residues in contact with LEU 172 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D TRP* 4.4 13.9 - - + +
104D LEU* 5.1 12.6 - - + -
122D PHE* 3.2 64.1 - - + +
123D ILE 5.1 5.2 - - - +
124D LEU* 5.7 7.0 - - + -
131D TRP* 4.2 15.7 - - + +
168D MET* 3.9 18.4 - - + -
169D PRO 3.4 4.9 + - - +
170D GLU 3.3 1.0 - - - -
171D SER* 1.3 74.4 - - - +
173D LEU* 1.3 53.6 + - - +
175D TYR* 2.7 21.3 + - + +
176D CYS* 2.6 42.5 + - - -
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Residues in contact with LEU 173 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135D ILE* 4.6 8.1 - - + -
151D LEU* 4.5 10.1 - - + -
154D LEU* 4.5 20.2 - - + -
155D SER* 3.8 19.5 - - - -
165D PHE* 4.9 7.6 - - + +
168D MET* 2.9 49.8 - - + +
169D PRO 3.5 4.2 + - - +
170D GLU* 2.7 23.3 + - + +
172D LEU* 1.3 77.9 - - - +
174D TYR* 1.3 50.9 + - - +
176D CYS* 2.8 4.7 + - - -
177D LEU* 2.6 60.2 + - + +
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Residues in contact with TYR 174 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111D ARG* 5.1 14.8 + - + +
151D LEU* 5.2 3.9 - - + +
170D GLU 2.9 9.4 + - - +
171D SER* 3.0 20.2 - - - +
173D LEU* 1.3 73.5 - - - +
175D TYR* 1.3 75.3 + + - +
177D LEU* 3.5 2.9 + - - +
178D LYS* 2.8 45.0 + - + +
188D MET* 4.0 17.3 - - + +
193D ASN 4.8 12.7 + - - -
194D ASP* 5.2 7.4 - - - -
195D LYS* 4.6 27.6 - - + -
197D ILE* 5.3 2.0 - - - -
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Residues in contact with TYR 175 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104D LEU* 5.0 21.5 - - + -
110D GLY* 3.3 29.4 - - - -
111D ARG* 2.8 48.5 + - + +
122D PHE* 6.1 1.8 - + - -
128D LEU* 5.3 8.1 - - - +
171D SER 3.7 15.0 - - - -
172D LEU* 2.7 29.6 + - + +
174D TYR* 1.3 92.3 - + - +
176D CYS* 1.3 61.3 + - - -
177D LEU 3.0 1.3 - - - -
178D LYS* 3.7 13.8 + - + +
179D PRO* 3.4 13.3 - - - +
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Residues in contact with CYS 176 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128D LEU* 4.2 10.5 - - - +
131D TRP* 3.3 42.0 - - + -
132D ALA* 2.8 34.5 - - - +
135D ILE* 4.3 6.5 - - + -
168D MET* 3.4 24.9 - - - -
172D LEU* 2.6 33.6 + - - -
173D LEU* 2.8 6.0 + - - +
175D TYR* 1.3 73.5 - - - +
177D LEU* 1.3 64.4 + - + +
179D PRO* 2.9 5.6 - - - +
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Residues in contact with LEU 177 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135D ILE* 3.6 39.3 - - + -
151D LEU* 5.7 0.2 - - + -
154D LEU* 5.2 7.0 - - + -
173D LEU* 2.6 48.0 + - + +
174D TYR 3.8 2.5 - - - +
176D CYS* 1.3 79.0 - - + +
178D LYS* 1.3 52.6 + - - +
179D PRO* 2.7 17.8 - - - -
180D LEU* 2.9 47.2 + - + +
181D CYS* 3.8 6.2 + - - -
188D MET* 4.3 2.5 - - + -
197D ILE* 3.4 35.0 - - + -
199D ILE* 5.1 6.3 - - + -
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Residues in contact with LYS 178 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111D ARG* 6.1 2.9 - - - +
174D TYR* 2.8 35.9 + - + +
175D TYR* 4.1 18.6 - - + +
176D CYS 3.6 0.2 - - - -
177D LEU* 1.3 68.7 - - - +
179D PRO* 1.3 65.6 - - + +
181D CYS* 3.9 23.6 - - + +
182D ASP* 4.2 17.9 + - - +
188D MET* 4.9 7.0 - - - -
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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