Contacts of the helix formed by residues 164 - 171 (chain H) in PDB entry 5U07
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 164 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52H GLU* 4.3 1.7 + - - +
57H ASP* 2.8 30.5 + - - +
58H LYS 3.1 9.1 + - - -
59H ALA* 3.0 45.2 - - + +
120H PRO* 3.7 21.8 - - + +
163H ARG* 1.3 73.2 - - - +
165H VAL* 1.3 83.8 + - - +
166H SER* 3.3 11.4 + - - +
167H VAL* 3.1 11.8 - - + +
168H ASN* 2.5 35.6 + - - -
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Residues in contact with VAL 165 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51H VAL* 4.6 11.7 - - + -
52H GLU* 6.3 0.7 - - + -
55H LEU* 3.8 16.2 - - + -
57H ASP* 3.1 22.2 + - - +
164H ASN* 1.3 85.1 + - - +
166H SER* 1.3 57.1 + - - +
168H ASN* 3.1 12.4 + - + +
169H LEU* 2.9 33.5 + - + +
246H THR* 5.7 4.3 - - + -
251H THR* 6.5 1.3 - - - -
255H ALA* 4.0 21.3 - - + -
258H GLU* 3.8 19.5 - - - +
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Residues in contact with SER 166 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48H ARG* 4.2 8.9 + - - +
51H VAL* 4.9 6.0 - - - +
52H GLU* 2.5 43.8 + - - +
59H ALA* 4.5 4.7 - - - -
118H TYR* 3.0 18.0 + - - -
164H ASN* 3.2 2.6 + - - -
165H VAL* 1.3 79.7 - - - +
167H VAL* 1.3 56.0 + - - +
169H LEU* 4.5 2.2 - - - -
170H PHE* 2.8 45.1 + - - +
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Residues in contact with VAL 167 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59H ALA* 5.0 1.6 - - + -
118H TYR* 3.3 40.4 - - + +
120H PRO* 5.3 1.1 - - + -
163H ARG* 3.4 19.1 - - + -
164H ASN* 3.1 37.4 + - + +
166H SER* 1.3 74.7 - - - +
168H ASN* 1.3 66.3 + - - +
171H GLY* 2.7 31.8 + - - +
172H ARG* 3.7 30.5 - - + +
182H VAL* 4.2 11.6 - - + +
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Residues in contact with ASN 168 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163H ARG* 3.3 27.5 + - - +
164H ASN 2.5 27.5 + - - -
165H VAL* 3.1 9.9 + - + +
167H VAL* 1.3 82.8 - - - +
169H LEU* 1.3 60.3 + - - +
182H VAL* 5.0 2.7 - - - +
183H ASP 4.4 0.2 - - - +
185H ALA* 3.6 4.7 + - - +
242H LEU* 3.5 10.2 - - + +
245H ASN* 3.1 56.3 + - + +
246H THR* 3.5 32.0 - - + +
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Residues in contact with LEU 169 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51H VAL* 5.2 8.3 - - + -
165H VAL* 2.9 25.3 + - + +
166H SER* 4.0 3.6 - - - +
168H ASN* 1.3 78.9 - - - +
170H PHE* 1.3 69.1 + - + +
185H ALA* 2.7 24.7 + - + -
186H VAL* 3.0 37.4 + - + +
237H VAL* 4.9 2.5 - - + -
242H LEU* 3.5 34.5 - - + -
255H ALA* 4.4 11.7 - - + +
256H VAL* 5.2 0.7 - - + -
259H PHE* 3.7 39.3 - - + -
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Residues in contact with PHE 170 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273D ASN* 5.7 1.9 - - - +
44H LYS* 3.5 47.9 + - + -
47H VAL* 4.1 12.6 - - + -
48H ARG* 3.6 32.1 - - + -
51H VAL* 6.0 2.2 - - + -
61H ARG* 6.1 1.1 - - - +
118H TYR* 4.9 4.9 - - + +
166H SER* 2.8 30.9 + - - +
169H LEU* 1.3 84.9 - - + +
171H GLY* 1.3 66.8 - - - +
184H GLY* 3.4 12.8 + - - -
186H VAL* 4.0 31.7 - - + +
188H PHE* 5.8 2.5 - + + -
259H PHE* 3.9 23.1 - + - -
12K G 4.6 12.1 + - - +
13K U 4.9 6.2 + - - +
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Residues in contact with GLY 171 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61H ARG* 4.4 4.9 + - - -
118H TYR* 4.0 13.7 - - - -
167H VAL* 2.7 28.8 + - - -
170H PHE* 1.3 79.0 - - - +
172H ARG* 1.3 62.1 + - - +
182H VAL 3.1 14.1 - - - -
183H ASP 3.9 0.2 - - - -
184H GLY* 3.4 13.4 - - - -
12K G 4.9 8.4 - - - +
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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