Contacts of the helix formed by residues 167 - 173 (chain B) in PDB entry 1UIR
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 ASN 167 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160B THR* 6.0 2.2 - - - +
161B ASP 4.6 2.4 + - - -
162B PRO* 4.0 5.7 - - - +
163B VAL* 3.1 33.1 + - - +
164B GLY 3.1 16.0 + - - +
165B GLU 3.1 3.4 - - - -
166B ASP* 1.3 75.4 - - - +
168B PRO* 1.3 67.5 - - - +
169B ALA* 2.9 33.8 + - - +
170B ARG* 2.9 36.4 - - + +
312B TYR* 5.4 1.4 - - - -
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Residues in contact with PRO 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B PHE* 6.2 3.8 - - + -
140B ASP* 5.7 1.2 - - - +
166B ASP 3.0 12.7 - - - +
167B ASN* 1.3 87.5 - - - +
169B ALA* 1.3 60.4 + - - +
170B ARG* 3.0 2.7 + - - -
171B LEU* 3.3 23.3 + - + +
172B LEU* 5.2 1.4 - - - +
312B TYR* 4.6 17.5 - - + +
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Residues in contact with ALA 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159B LEU* 6.3 0.4 - - + -
160B THR* 5.8 4.7 - - + +
162B PRO* 4.2 8.3 - - + -
167B ASN* 2.9 23.3 + - - +
168B PRO* 1.3 75.0 - - + +
170B ARG* 1.3 54.8 + - - +
171B LEU 3.0 3.1 - - - -
172B LEU* 2.7 46.0 + - + +
173B TYR* 3.7 11.7 - - + -
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Residues in contact with ARG 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162B PRO* 3.9 16.9 - - + +
164B GLY 3.7 9.6 - - - +
165B GLU* 2.6 46.5 + - - +
167B ASN 2.9 20.3 + - - +
168B PRO* 3.0 0.9 - - + -
169B ALA* 1.3 78.0 - - - +
171B LEU* 1.3 60.4 + - + +
172B LEU 3.1 0.2 - - - -
173B TYR* 3.2 19.9 + - - +
174B THR* 3.5 13.2 - - - +
293B SER* 4.6 0.9 + - - -
298B PRO* 2.8 52.2 + - + +
299B PHE 3.8 14.0 - - - +
300B TYR* 3.7 28.8 - - + +
310B ALA* 3.1 18.0 + - - +
311B PRO 5.2 1.2 + - - -
312B TYR* 3.8 24.2 - - + +
313B LYS 5.6 0.2 - - - +
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Residues in contact with LEU 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B ASP* 6.1 0.9 - - - +
142B ARG* 3.1 35.1 + - - +
168B PRO* 3.6 14.4 - - + +
169B ALA 3.0 0.6 - - - -
170B ARG* 1.3 79.8 - - + +
172B LEU* 1.3 58.9 + - + +
173B TYR 3.3 2.5 - - - -
174B THR* 3.7 9.5 + - + -
177B PHE* 3.6 9.7 - - - +
295B ASP* 4.1 25.6 - - + +
298B PRO* 4.6 7.2 - - + -
312B TYR* 3.7 48.2 - - + +
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Residues in contact with LEU 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B VAL* 4.9 5.4 - - + -
109B ILE* 6.5 1.6 - - + -
140B ASP* 4.1 16.2 - - - +
141B ALA* 4.5 6.5 - - + +
142B ARG* 4.1 19.3 - - + +
157B ILE* 5.4 1.0 - - - +
159B LEU* 3.8 36.2 - - + +
168B PRO 5.2 1.3 - - - +
169B ALA* 2.7 26.7 + - + +
171B LEU* 1.3 81.6 - - + +
173B TYR* 1.3 66.6 + - + +
174B THR 3.7 0.2 - - - -
177B PHE* 3.1 54.5 - - + -
178B TYR* 4.0 4.5 + - - -
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Residues in contact with TYR 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157B ILE* 5.7 1.5 - - + +
159B LEU* 3.3 36.3 + - + +
160B THR 2.8 30.1 + - - -
161B ASP* 4.1 6.5 + - - -
162B PRO* 3.7 21.8 - - + -
169B ALA* 3.7 15.5 - - + -
170B ARG 3.2 8.3 + - - +
172B LEU* 1.3 85.6 - - - +
174B THR* 1.3 60.8 + - - +
178B TYR* 3.3 27.2 + - - -
193B MET* 4.6 11.6 - - + +
194B GLN* 4.9 7.0 + - - -
195B THR* 5.9 1.6 - - - -
209B VAL* 4.1 17.3 - - + -
212B THR* 3.7 7.6 - - - +
293B SER* 3.2 20.8 - - - -
299B PHE* 3.8 29.8 - + + -
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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