Contacts of the helix formed by residues 169 - 177 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40D ALA* 3.8 20.8 - - + +
145D LEU* 3.6 25.3 - - + +
148D LEU* 3.9 7.1 - - + +
149D ARG* 3.8 20.4 - - + -
153D ILE 3.0 20.4 + - - -
154D LEU 3.4 26.5 - - - -
155D THR* 3.7 7.7 + - + -
156D ASP* 3.3 5.8 - - - +
157D VAL* 4.7 0.2 - - - -
168D ALA* 1.3 72.9 - - - +
170D LYS* 1.3 66.5 + - - +
171D THR* 4.3 11.7 - - + -
172D VAL* 3.1 23.1 + - + +
173D LEU* 3.2 15.0 + - - +
214D TYR* 2.7 30.7 + - - +
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Residues in contact with LYS 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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23D LEU* 3.6 25.3 - - + +
156D ASP* 2.9 48.6 + - - +
157D VAL* 3.9 12.5 - - + +
168D ALA 4.0 0.6 + - - -
169D HIS* 1.3 70.1 - - - +
171D THR* 1.3 58.9 + - - +
173D LEU* 3.2 5.1 + - - +
174D MET* 2.9 32.1 + - - +
184D PHE* 3.7 38.6 - - + -
190D CYS 2.9 26.3 + - - -
191D ASN* 4.3 3.4 + - - +
192D LEU 3.1 26.2 + - - -
193D SER* 5.2 0.2 - - - +
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Residues in contact with THR 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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14D LEU* 3.1 22.0 - - + +
17D GLN* 2.5 44.0 + - - -
23D LEU* 3.6 14.0 - - - +
38D HIS* 3.5 25.3 - - + -
40D ALA* 4.8 13.7 - - + -
41D VAL* 4.8 4.3 - - + -
145D LEU* 5.6 0.9 - - + -
156D ASP* 5.1 0.6 + - - -
169D HIS* 4.3 13.0 - - + -
170D LYS* 1.3 80.4 - - - +
172D VAL* 1.3 69.1 + - + +
175D ALA* 3.1 8.3 + - - +
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Residues in contact with VAL 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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10D VAL* 5.3 4.3 - - + -
14D LEU* 4.9 3.4 - - + -
142D LEU* 5.2 4.7 - - + -
145D LEU* 3.8 30.5 - - + -
169D HIS* 3.1 16.2 + - + +
171D THR* 1.3 81.0 - - + +
173D LEU* 1.3 65.1 + - - +
175D ALA* 3.1 15.6 + - - +
176D CYS* 3.2 25.7 + - - -
213D MET* 4.4 11.2 - - + +
214D TYR* 3.8 43.7 - - + +
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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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157D VAL* 4.1 10.3 - - + -
159D ILE* 3.8 33.9 - - + -
168D ALA* 4.0 13.9 - - + -
169D HIS 3.2 9.6 + - - +
170D LYS 3.2 6.0 + - - +
172D VAL* 1.3 76.1 - - - +
174D MET* 1.3 62.5 + - - +
176D CYS* 3.1 1.9 + - - +
177D SER* 3.1 29.5 + - - -
180D PHE* 3.8 27.6 - - + -
184D PHE* 4.0 10.8 - - + -
206D PHE* 5.2 0.9 - - + -
210D LEU* 3.6 21.8 - - + -
213D MET* 3.6 26.7 - - + -
214D TYR* 5.0 2.5 - - + -
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Residues in contact with MET 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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13D GLN* 4.8 3.3 + - - -
17D GLN* 3.7 34.3 - - + +
22D LEU* 4.2 10.8 - - + -
23D LEU* 3.7 16.6 - - + -
170D LYS 2.9 16.0 + - - +
173D LEU* 1.3 78.1 - - - +
175D ALA* 1.3 63.3 + - - +
176D CYS 3.3 0.7 + - - -
177D SER 3.7 10.2 + - - +
180D PHE* 4.1 1.3 - - - +
181D TYR* 3.5 47.7 - - + +
184D PHE* 3.5 34.3 - - + +
185D THR* 3.8 24.7 - - + -
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Residues in contact with ALA 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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9D HIS 5.8 0.2 - - - -
10D VAL* 4.3 21.6 - - + +
13D GLN* 3.4 45.1 + - + +
14D LEU* 4.5 3.1 - - + -
17D GLN* 3.6 6.2 - - - +
171D THR 3.1 15.6 + - - +
172D VAL* 3.1 13.2 + - - +
174D MET* 1.3 79.2 - - - +
176D CYS* 1.3 59.2 + - - +
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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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6D HIS* 3.8 29.4 - - + -
10D VAL* 3.8 16.6 - - - -
172D VAL* 3.2 19.6 + - - +
173D LEU 3.1 2.2 + - - +
175D ALA* 1.3 78.5 - - - +
177D SER* 1.3 58.5 + - - +
178D GLY 4.3 0.2 - - - -
212D PHE* 5.9 1.6 - - + -
213D MET* 3.6 40.6 - - + -
236D GLN 4.8 0.7 - - - +
237D MET* 3.4 20.3 - - - +
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Residues in contact with SER 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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173D LEU 3.1 11.7 + - - -
174D MET 3.7 5.2 + - - +
175D ALA 3.7 1.6 - - - -
176D CYS* 1.3 79.0 - - - +
178D GLY* 1.3 58.5 + - - +
179D LEU* 3.2 2.8 + - - +
180D PHE* 3.1 31.3 + - - +
181D TYR* 3.0 28.0 + - - +
213D MET* 4.2 1.1 - - - -
235D LEU* 2.8 22.3 + - - +
237D MET* 3.6 18.6 - - - -
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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