Contacts of the helix formed by residues 169 - 177 (chain B) in PDB entry 4U2M
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 169 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40B ALA* 3.8 25.2 - - + +
145B LEU* 3.6 26.0 - - + +
148B LEU* 4.0 5.4 - - + +
149B ARG* 3.8 20.2 - - + -
153B ILE 3.0 20.2 + - - -
154B LEU 3.3 26.9 - - - -
155B THR* 3.6 7.8 + - + -
156B ASP* 3.3 6.3 - - - +
157B VAL* 4.6 0.2 - - - -
168B ALA* 1.3 73.0 - - - +
170B LYS* 1.3 65.8 + - - +
171B THR* 4.4 5.8 - - - +
172B VAL* 3.1 23.8 + - + +
173B LEU* 3.2 14.1 + - - +
214B TYR* 2.7 34.4 + - - +
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Residues in contact with LYS 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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23B LEU* 3.7 25.5 - - + +
156B ASP* 2.9 48.0 + - - +
157B VAL* 3.9 12.0 - - + +
168B ALA 4.0 0.6 + - - -
169B HIS* 1.3 70.5 - - - +
171B THR* 1.3 57.8 + - - +
173B LEU* 3.2 5.0 + - - +
174B MET* 2.9 31.7 + - - +
184B PHE* 3.7 38.5 - - + -
190B CYS 2.9 26.3 + - - -
191B ASN* 4.3 3.4 - - - +
192B LEU 3.1 26.2 + - - -
193B SER* 5.2 0.2 - - - +
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Residues in contact with THR 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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14B LEU* 2.9 28.0 - - + -
17B GLN* 2.9 41.8 + - - +
23B LEU* 3.3 17.9 + - - +
38B HIS* 3.0 34.8 - - + +
40B ALA* 6.1 4.3 - - - -
41B VAL* 4.9 3.8 - - + -
156B ASP* 5.1 0.8 + - - -
169B HIS* 3.1 5.6 - - - +
170B LYS* 1.3 77.7 - - - +
172B VAL* 1.3 58.7 + - + +
175B ALA* 3.1 13.5 + - - +
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Residues in contact with VAL 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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10B VAL* 5.3 4.5 - - + -
14B LEU* 4.9 5.6 - - + -
142B LEU* 5.1 4.0 - - + -
145B LEU* 3.8 31.0 - - + -
169B HIS* 3.1 17.0 + - + +
171B THR* 1.3 77.2 - - + +
173B LEU* 1.3 65.6 + - - +
175B ALA* 3.1 15.5 + - - +
176B CYS* 3.2 27.2 + - - -
213B MET* 4.4 9.9 - - + +
214B TYR* 3.8 46.4 - - + +
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Residues in contact with LEU 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 VAL* 4.1 10.1 - - + -
159B ILE* 3.8 34.1 - - + -
168B ALA* 4.0 13.7 - - + -
169B HIS 3.2 10.3 + - - +
170B LYS 3.2 6.7 + - - +
172B VAL* 1.3 75.5 - - - +
174B MET* 1.3 60.9 + - - +
176B CYS* 3.2 1.6 + - - -
177B SER* 3.0 28.8 + - - -
180B PHE* 3.7 28.3 - - + -
184B PHE* 4.0 10.3 - - + -
206B PHE* 5.3 0.9 - - + -
210B LEU* 3.6 21.5 - - + -
213B MET* 3.6 26.2 - - + -
214B TYR* 5.0 2.9 - - + -
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Residues in contact with MET 174 (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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13B GLN* 4.9 3.1 + - - -
17B GLN* 3.7 33.9 - - - +
22B LEU* 4.2 10.5 - - + -
23B LEU* 3.7 16.8 - - + -
170B LYS 2.9 16.8 + - - +
173B LEU* 1.3 76.7 - - - +
175B ALA* 1.3 62.1 + - - +
176B CYS 3.3 0.5 + - - -
177B SER 3.7 10.6 + - - +
180B PHE* 4.1 1.3 - - - +
181B TYR* 3.4 48.3 - - + +
184B PHE* 3.5 33.2 - - + +
185B THR* 3.8 24.7 - - + -
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Residues in contact with ALA 175 (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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10B VAL* 4.3 22.5 - - + +
13B GLN* 3.4 45.1 + - + +
14B LEU* 4.5 2.9 - - + -
17B GLN* 3.7 5.8 - - - +
171B THR 3.1 15.9 + - - +
172B VAL* 3.1 13.9 + - - +
174B MET* 1.3 79.1 - - - +
176B CYS* 1.3 58.9 + - - +
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Residues in contact with CYS 176 (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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6B HIS* 3.8 24.0 - - + -
10B VAL* 3.8 15.7 - - - -
172B VAL* 3.2 21.1 + - - +
174B MET 3.2 0.2 - - - -
175B ALA* 1.3 79.0 - - - +
177B SER* 1.3 56.8 + - - +
213B MET* 3.7 44.2 - - + -
236B GLN 4.8 0.5 - - - +
237B MET* 3.4 25.9 - - + +
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Residues in contact with SER 177 (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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173B LEU 3.0 12.4 + - - +
174B MET 3.7 5.1 - - - +
175B ALA 3.7 1.6 - - - -
176B CYS* 1.3 79.3 - - - +
178B GLY* 1.3 56.9 + - - +
179B LEU* 3.7 2.4 - - - +
180B PHE* 3.1 32.3 + - - -
181B TYR* 2.9 27.9 + - - +
213B MET* 4.2 11.0 - - - -
235B LEU* 2.8 24.0 + - - +
237B MET* 4.2 4.9 - - - -
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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