Contacts of the helix formed by residues 158 - 166 (chain B) in PDB entry 3UFJ
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 HIS 158 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155B PRO 5.4 0.4 - - - -
156B GLY 3.2 18.9 + - - -
157B ASN* 1.3 72.1 + - - +
159B PHE* 1.3 63.9 + - - +
160B TRP 3.5 1.1 + - - -
161B LYS* 3.5 5.9 + - - -
162B CYS* 2.9 26.4 + - - -
271B SER 4.5 3.1 - - - -
272B SER* 2.8 31.1 + - - +
273B SER 3.2 6.2 + - - -
274B ALA* 3.1 28.6 - - + -
276B CYS 4.9 0.4 + - - -
279B PHE* 3.9 17.5 + - + -
280B PRO 3.9 20.6 - - - -
281B ARG* 4.7 1.5 - - - -
282B ALA* 3.3 34.9 + - + +
285B LYS* 6.3 2.0 - - + -
8D T 5.2 3.1 - - - -
12E G 4.5 2.9 + - - -
13E T 5.0 2.7 - - - -
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Residues in contact with PHE 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B ILE* 4.4 20.6 - - + -
152B TYR* 3.7 16.6 - + + -
157B ASN* 2.4 33.8 + - - +
158B HIS* 1.3 70.2 - - - +
160B TRP* 1.3 98.4 + + + +
162B CYS* 2.9 8.1 + - - +
163B LEU* 2.8 59.1 + - + -
187B ILE* 6.3 0.9 - - + -
189B PHE* 3.3 40.8 - + - -
230B ASN* 6.1 0.4 - - - -
272B SER* 3.8 12.9 - - - -
289B TYR* 3.4 24.0 - + - -
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Residues in contact with TRP 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B HIS 3.2 18.0 + - - -
152B TYR* 2.6 29.9 + - + -
153B PRO 4.4 5.6 - - - -
155B PRO* 6.1 3.4 - - + -
157B ASN 4.6 3.7 + - - -
158B HIS 3.5 0.4 - - - -
159B PHE* 1.3 100.6 - + + +
161B LYS* 1.3 56.3 + - - +
163B LEU* 3.4 13.3 + - + +
164B PHE* 2.8 30.3 + - - +
172B GLN* 3.5 5.0 + - - +
173B LEU* 3.5 39.7 + - + +
174B ASN* 3.8 21.8 - - + -
175B HIS* 3.6 25.2 - + - +
177B ASP 5.0 1.3 - - - -
178B ASP* 3.7 25.6 - - + -
181B LEU* 5.2 5.8 - - + -
189B PHE* 3.7 23.6 - + - -
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Residues in contact with LYS 161 (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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158B HIS* 3.5 10.4 + - - +
159B PHE 3.2 0.2 - - - -
160B TRP* 1.3 76.3 - - - +
162B CYS* 1.3 50.9 + - - +
164B PHE* 3.1 5.0 + - - +
165B MET* 2.7 38.1 + - - +
172B GLN* 3.5 19.6 - - - +
282B ALA* 4.1 15.0 - - + -
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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
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158B HIS* 2.9 25.8 - - - -
159B PHE* 2.9 7.7 + - - +
161B LYS* 1.3 73.2 - - - +
163B LEU* 1.3 57.9 + - - +
165B MET* 4.4 6.1 - - - -
166B SER* 2.7 39.5 + - - -
282B ALA* 3.4 34.3 - - - -
285B LYS* 4.4 9.2 - - - +
286B VAL* 4.9 4.2 - - - +
289B TYR* 3.4 34.1 - - + -
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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
----------------------------------------------------------
136B ILE* 5.8 4.0 - - + -
159B PHE* 2.8 48.8 + - + +
160B TRP* 3.6 23.6 - - + +
162B CYS* 1.3 72.1 - - - +
164B PHE* 1.3 65.5 + - - +
166B SER* 4.6 1.1 - - - -
168B LEU* 3.4 26.6 + - + +
169B SER* 2.9 47.8 + - - +
173B LEU* 5.6 1.3 - - + -
185B TYR* 4.6 8.5 - - + -
187B ILE* 6.0 8.3 - - + -
289B TYR* 4.1 16.0 - - + -
292B LEU* 6.2 1.8 - - + -
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Residues in contact with PHE 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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160B TRP 2.8 11.6 + - - +
161B LYS 3.3 7.2 - - - +
163B LEU* 1.3 75.6 - - - +
165B MET* 1.3 75.8 - - + +
166B SER 2.7 2.9 + - - -
167B GLY* 2.7 16.3 + - - -
169B SER* 2.8 16.1 + - - +
170B GLU 3.8 13.5 - - - -
171B VAL* 3.2 28.7 - - - -
172B GLN* 2.9 42.6 - - + +
173B LEU 4.8 0.2 - - - +
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Residues in contact with MET 165 (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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161B LYS 2.7 18.7 + - - +
162B CYS* 3.9 6.7 - - - +
164B PHE* 1.3 83.1 - - + +
166B SER* 1.3 61.6 + - - +
167B GLY* 3.1 2.1 + - - -
282B ALA 5.6 2.0 - - - +
286B VAL* 4.8 13.9 - - + -
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Residues in contact with SER 166 (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 CYS 2.7 20.3 + - - -
163B LEU 4.1 0.2 - - - -
164B PHE 2.7 5.1 + - - -
165B MET* 1.3 72.7 - - - +
167B GLY* 1.3 56.9 + - - -
168B LEU* 3.3 20.3 - - - +
286B VAL* 4.8 5.3 - - - +
289B TYR* 3.4 33.0 - - - -
290B ILE* 4.1 16.0 - - - +
293B LYS* 5.2 3.5 - - - +
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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
------------------------------------------------------------
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