Contacts of the helix formed by residues 164 - 171 (chain G) in PDB entry 5U0A
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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52G GLU* 4.2 2.2 + - - +
57G ASP* 2.7 36.8 + - - +
58G LYS 3.0 9.9 + - - -
59G ALA* 2.9 46.9 - - + +
120G PRO* 3.6 17.5 - - + +
163G ARG* 1.3 74.1 - - - +
165G VAL* 1.3 80.3 + - - +
166G SER* 3.1 10.1 + - - +
167G VAL* 3.1 9.6 + - + +
168G ASN* 2.7 39.1 + - - -
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Residues in contact with VAL 165 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51G VAL* 4.3 17.0 - - + -
52G GLU* 6.3 0.7 - - + -
55G LEU* 3.7 32.3 - - + -
57G ASP* 3.2 20.1 + - - +
164G ASN* 1.3 88.1 + - - +
166G SER* 1.3 57.0 + - - +
168G ASN* 3.2 13.0 + - + +
169G LEU* 2.9 36.9 + - + +
246G THR* 6.2 2.0 - - + -
251G THR* 6.6 0.2 - - - -
255G ALA* 4.2 22.4 - - + -
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Residues in contact with SER 166 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48G ARG* 4.1 11.4 + - - +
51G VAL* 5.0 4.7 - - - +
52G GLU* 2.7 37.2 + - - +
59G ALA* 4.6 0.9 - - - -
118G TYR* 3.2 24.3 + - - -
164G ASN* 3.1 6.2 + - - -
165G VAL* 1.3 78.7 - - - +
167G VAL* 1.3 59.2 + - - +
169G LEU* 4.3 2.0 - - - -
170G PHE* 2.9 44.8 + - - +
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Residues in contact with VAL 167 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59G ALA* 4.6 3.6 - - + -
118G TYR* 3.5 34.3 - - + +
120G PRO* 5.1 1.6 - - + -
163G ARG* 4.2 6.1 - - + -
164G ASN* 3.1 28.0 + - + +
166G SER* 1.3 75.8 - - - +
168G ASN* 1.3 60.4 + - - +
171G GLY* 2.9 26.3 + - - +
172G ARG* 3.5 42.0 - - + +
182G VAL* 3.7 23.3 - - + +
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Residues in contact with ASN 168 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163G ARG* 3.0 36.6 + - - +
164G ASN 2.7 30.2 + - - +
165G VAL* 3.5 13.2 - - + +
167G VAL* 1.3 73.3 - - - +
169G LEU* 1.3 62.1 + - - +
182G VAL* 4.8 0.7 - - - -
183G ASP 4.4 0.3 - - - +
185G ALA* 3.9 3.3 + - - +
242G LEU* 3.5 11.3 - - + +
245G ASN* 2.9 37.4 + - + +
246G THR* 3.5 36.6 - - + +
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Residues in contact with LEU 169 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51G VAL* 5.1 10.3 - - + -
165G VAL* 2.9 26.4 + - + +
166G SER* 4.0 2.5 - - - +
168G ASN* 1.3 79.3 - - - +
170G PHE* 1.3 77.2 + - + +
185G ALA* 2.9 24.0 + - + -
186G VAL* 3.3 34.6 + - + +
237G VAL* 5.1 2.7 - - + -
242G LEU* 3.6 33.7 - - + -
255G ALA* 4.3 11.9 - - + +
259G PHE* 3.9 32.8 - - + -
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Residues in contact with PHE 170 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44G LYS* 3.5 44.8 + - + +
47G VAL* 4.0 24.5 - - + -
48G ARG* 3.7 32.3 - - + -
51G VAL* 6.1 1.6 - - + -
61G ARG* 6.2 1.8 - - - +
118G TYR* 5.2 3.1 - - + +
166G SER* 2.9 23.4 + - - +
169G LEU* 1.3 88.7 - - + +
171G GLY* 1.3 67.8 + - - +
184G GLY* 3.6 11.5 - - - -
186G VAL* 3.9 32.0 - - + +
188G PHE* 4.7 2.5 - + - -
259G PHE* 4.2 11.7 - + - -
273H ASN* 5.9 0.9 - - - +
18K A 4.6 8.3 + - - +
19K G 4.3 11.2 + - - +
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Residues in contact with GLY 171 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61G ARG* 5.1 3.3 + - - -
118G TYR* 4.1 13.0 - - - -
167G VAL* 2.9 23.4 + - - -
169G LEU 3.6 1.2 - - - -
170G PHE* 1.3 85.1 - - - +
172G ARG* 1.3 61.7 + - - +
182G VAL 3.2 17.0 - - - -
184G GLY* 3.6 10.8 - - - -
18K A 4.9 9.7 - - - +
19K G 5.3 0.3 + - - -
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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