Contacts of the helix formed by residues 158 - 171 (chain B) in PDB entry 5UFL
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 158 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B PHE* 5.0 9.9 - - + -
118B LEU* 4.4 30.1 - - + +
121B ILE* 5.7 6.3 - - + -
146B PHE* 6.4 0.4 - - + -
150B HIS* 3.4 40.6 - - + +
154B SER 6.0 1.1 - - - +
157B GLU* 1.3 76.9 - - - +
159B LYS* 1.3 61.0 + - + +
160B MET 3.4 0.4 - - - -
161B PRO* 3.4 20.4 - - + +
162B CYS* 3.1 26.6 - - + -
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Residues in contact with LYS 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B HIS 3.9 17.0 - - - +
151B ILE* 3.6 24.2 + - - +
152B GLN 5.2 3.0 + - - -
153B SER 4.1 1.1 - - - +
154B SER 3.4 34.7 - - - +
157B GLU* 3.2 4.6 - - - +
158B LEU* 1.3 79.2 - - + +
160B MET* 1.3 56.7 + - - +
162B CYS* 3.3 10.5 - - - -
163B LEU* 3.0 40.6 + - + +
192B THR* 5.6 2.6 - - - +
196B LEU* 3.7 33.7 - - - +
199B HIS* 5.6 4.2 - - - +
204B VAL* 6.0 2.9 - - + -
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Residues in contact with MET 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B GLU* 3.5 33.7 + - - +
159B LYS* 1.3 78.8 - - - +
161B PRO* 1.4 70.1 - - + +
163B LEU* 3.4 4.9 + - - +
164B GLY 3.1 16.8 + - - -
199B HIS* 5.9 0.2 - - + -
201B SER* 3.3 29.2 - - - +
203B THR* 3.8 18.6 - - + -
204B VAL* 3.8 24.1 - - + +
207B PHE* 3.4 26.8 - - + -
249B LEU* 6.2 0.7 - - - -
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Residues in contact with PRO 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B LEU* 3.8 28.0 - - + -
121B ILE* 3.5 22.3 - - + +
122B GLN* 4.6 11.7 - - + +
125B GLN* 3.6 19.0 + - - +
157B GLU 3.5 9.6 - - - +
158B LEU* 3.4 22.0 - - + +
160B MET* 1.4 97.5 - - + +
162B CYS* 1.3 55.7 + - - +
164B GLY 3.3 1.2 + - - -
165B LEU 3.0 22.7 + - - -
207B PHE* 5.4 0.2 - - + -
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Residues in contact with CYS 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B ILE* 3.8 10.9 - - + +
146B PHE* 6.4 0.7 - - + -
147B LEU* 3.4 34.4 - - + +
150B HIS* 4.1 24.7 - - + -
151B ILE* 4.1 13.3 - - - +
158B LEU* 3.1 31.6 - - + -
159B LYS* 3.3 17.9 - - - -
161B PRO* 1.3 74.5 - - - +
163B LEU* 1.3 59.3 + - - +
165B LEU* 4.0 1.1 - - - -
166B LEU* 3.1 28.1 + - - +
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Residues in contact with LEU 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B ILE* 3.8 24.9 - - + -
159B LYS* 3.0 32.9 + - + +
160B MET* 3.5 6.3 - - - +
162B CYS* 1.3 76.8 - - - +
164B GLY* 1.3 58.8 + - - +
166B LEU 3.4 0.7 + - - -
167B ALA* 3.0 29.5 + - - +
193B LEU* 3.9 16.8 - - + -
196B LEU* 4.0 13.0 - - + -
204B VAL* 3.7 35.9 - - + +
207B PHE* 3.8 11.0 - - + -
208B ALA* 4.4 7.6 - - + -
211B ILE* 3.6 30.1 - - + +
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Residues in contact with GLY 164 (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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125B GLN* 3.5 22.4 - - - -
160B MET 3.1 8.1 + - - -
161B PRO 3.3 2.0 + - - -
163B LEU* 1.3 76.8 - - - +
165B LEU* 1.3 62.9 - - - +
167B ALA* 3.6 3.0 + - - +
168B ASN* 3.4 27.5 + - - +
207B PHE* 3.5 23.3 - - - -
253B TYR* 3.6 2.6 + - - -
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Residues in contact with LEU 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B ILE* 3.7 35.7 - - + +
124B LEU* 3.4 37.0 - - + -
125B GLN* 4.1 11.8 - - + +
128B THR* 4.0 11.4 - - + +
143B LEU* 4.4 7.0 - - + -
147B LEU* 4.0 9.0 - - + -
161B PRO 3.0 15.4 + - - +
162B CYS* 4.1 5.2 - - - +
163B LEU 3.3 0.2 - - - -
164B GLY* 1.3 74.8 - - - +
166B LEU* 1.3 64.2 + - - +
168B ASN* 3.1 19.7 + - - +
169B LEU* 3.2 39.4 + - + -
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Residues in contact with LEU 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B ILE* 4.2 29.6 - - + -
147B LEU* 4.2 13.8 - - + +
148B ILE* 4.0 11.9 - - + -
151B ILE* 3.5 27.8 - - + -
162B CYS 3.1 16.0 + - - +
163B LEU 3.4 4.4 + - - +
165B LEU* 1.3 79.6 - - - +
167B ALA* 1.3 61.0 + - - +
169B LEU* 3.3 9.7 + - + +
170B CYS* 3.1 46.3 + - - -
180B ILE* 4.5 5.4 - - + -
189B PHE* 3.6 23.3 - - + -
211B ILE* 4.3 7.9 - - + -
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Residues in contact with ALA 167 (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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163B LEU 3.0 17.0 + - - +
164B GLY* 3.7 9.0 - - - +
165B LEU 3.2 0.4 - - - -
166B LEU* 1.3 76.8 - - - +
168B ASN* 1.3 61.9 + - - +
170B CYS* 3.7 2.5 + - - +
171B ARG* 3.2 26.2 + - - +
207B PHE* 4.0 11.9 - - - +
210B SER* 4.2 16.6 - - - +
211B ILE* 3.7 21.7 - - + +
214B SER* 5.0 1.2 + - - -
253B TYR* 4.4 11.7 - - + -
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Residues in contact with ASN 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B GLN* 3.1 29.7 + - - +
128B THR* 3.4 28.7 + - - +
129B TYR* 3.5 18.1 - - - +
130B ASN 5.4 0.7 - - - +
133B ILE* 3.3 16.4 - - - +
164B GLY 3.4 8.7 + - - -
165B LEU 3.1 7.7 + - - +
167B ALA* 1.3 76.0 - - - +
169B LEU* 1.3 62.9 + - - +
171B ARG* 3.5 18.4 + - - +
253B TYR* 2.7 36.9 + - - -
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Residues in contact with LEU 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B THR* 4.5 7.6 - - + -
133B ILE* 3.6 35.8 - - + +
140B ILE* 4.8 9.9 - - + -
143B LEU* 4.4 11.0 - - + -
144B ILE* 3.7 29.2 - - + -
147B LEU* 3.7 20.6 - - + -
165B LEU* 3.2 35.3 + - + +
166B LEU* 3.3 10.5 + - + +
168B ASN* 1.3 76.6 - - - +
170B CYS* 1.3 56.1 + - - +
173B ASN* 3.2 27.9 + - - +
176B VAL* 3.4 12.0 - - + +
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Residues in contact with CYS 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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166B LEU* 3.1 31.4 + - - +
167B ALA* 4.2 3.8 - - - +
168B ASN 3.4 0.2 - - - -
169B LEU* 1.3 74.6 - - - +
171B ARG* 1.3 58.7 + - - +
172B HIS 3.3 0.2 + - - -
173B ASN 3.6 3.5 + - - +
176B VAL* 4.4 5.2 - - - -
177B GLN* 2.8 38.0 + - - +
180B ILE* 3.4 31.2 - - - -
189B PHE* 6.3 0.2 - - - -
211B ILE* 4.3 16.2 - - - -
214B SER* 3.3 20.0 - - - +
215B LEU* 4.4 11.9 - - + -
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Residues in contact with ARG 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B TYR* 4.8 4.8 - - - -
130B ASN* 3.7 37.8 + - - +
131B VAL 5.3 1.2 - - - +
133B ILE* 4.8 1.0 - - - +
167B ALA 3.2 16.8 + - - +
168B ASN* 3.5 10.9 + - - +
169B LEU 3.4 0.4 - - - -
170B CYS* 1.3 76.1 - - - +
172B HIS* 1.3 93.4 + - + +
173B ASN* 3.1 15.4 + - - -
210B SER* 6.1 4.9 - - - -
214B SER* 4.2 13.7 + - - -
253B TYR* 6.6 0.4 - - - -
256B ASP* 3.7 38.7 + - - +
257B LEU* 5.9 0.9 - - - +
260B ASP* 3.0 29.7 + - - +
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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