Contacts of the helix formed by residues 168 - 177 (chain H) in PDB entry 5XRZ
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 ASP 168 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69G HIS* 3.6 28.5 + - + +
70G ARG* 4.6 6.6 + - - -
186G VAL* 4.2 7.3 - - - +
46H ARG* 3.6 22.3 + - - +
164H ASN 4.6 0.4 + - - -
165H CYS* 2.9 21.2 + - + +
167H LEU* 1.3 75.1 - - - +
169H LYS* 1.3 69.4 + - - +
170H ASP* 3.7 13.5 + - - +
171H TYR* 3.1 21.1 + - + +
172H LEU* 3.0 23.5 + - - +
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Residues in contact with LYS 169 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53G SER* 5.8 0.6 + - - -
65G TYR* 4.3 13.3 + - - -
67G GLU* 4.0 30.2 + - - +
69G HIS* 5.2 0.8 + - - -
167H LEU 3.4 7.4 + - - +
168H ASP* 1.3 73.8 + - - +
170H ASP* 1.3 61.1 + - - +
172H LEU* 3.2 14.6 + - + +
173H ARG* 2.9 34.5 + - + +
26L T 4.6 15.0 - - - +
27L T 5.3 10.5 - - - -
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Residues in contact with ASP 170 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70G ARG* 4.6 11.1 + - - -
183G PRO* 3.5 13.7 - - - +
184G LEU* 3.4 39.7 + - - +
186G VAL* 3.6 14.6 - - + +
168H ASP* 3.3 12.0 + - - +
169H LYS* 1.3 78.2 - - - +
171H TYR* 1.3 57.2 + - - +
173H ARG* 3.3 27.9 + - - +
174H SER* 2.9 32.4 + - - -
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Residues in contact with TYR 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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186G VAL* 3.6 9.4 - - - +
188G LEU* 3.5 27.8 - - + -
46H ARG* 3.5 27.4 - - + +
47H LEU* 2.4 46.0 + - - +
52H ILE* 3.7 10.7 - - + +
165H CYS* 3.1 37.5 - - + -
166H ILE* 4.5 3.6 - - - -
168H ASP* 3.1 25.7 + - + +
170H ASP* 1.3 80.0 - - - +
172H LEU* 1.3 64.3 + - + +
174H SER* 3.4 2.3 + - - -
175H LEU* 2.9 55.1 + - + +
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Residues in contact with LEU 172 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63H VAL* 6.4 0.9 - - + -
64H CYS* 3.7 43.5 - - + +
166H ILE* 4.0 23.8 - - + +
167H LEU* 5.7 1.1 - - - -
168H ASP 3.0 16.7 + - - +
169H LYS* 3.2 15.4 + - + +
171H TYR* 1.3 79.0 - - + +
173H ARG* 1.3 65.3 + - + +
175H LEU* 3.0 19.6 + - + +
176H ASN* 2.9 32.3 + - - +
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Residues in contact with ARG 173 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183G PRO* 3.7 19.7 + - - +
184G LEU 3.6 15.4 + - - -
185G GLU* 5.1 3.0 - - - +
169H LYS* 2.9 19.1 + - + +
170H ASP* 3.3 33.5 + - - +
172H LEU* 1.3 75.4 - - + +
174H SER* 1.3 63.7 + - - +
176H ASN* 3.3 19.1 + - - +
177H LYS* 3.2 49.0 + - - +
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Residues in contact with SER 174 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185G GLU* 4.7 5.4 - - - +
186G VAL* 3.0 39.6 + - - -
188G LEU* 3.4 20.7 - - - +
170H ASP 2.9 18.8 + - - -
171H TYR 3.8 2.0 - - - -
173H ARG* 1.3 75.2 + - - +
175H LEU* 1.3 64.7 + - - +
177H LYS* 3.3 25.5 + - - +
178H LEU* 3.8 8.8 - - - +
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Residues in contact with LEU 175 (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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188G LEU* 3.7 16.2 - - + -
47H LEU 4.5 1.8 - - - +
49H PRO* 3.9 38.8 - - + +
52H ILE* 3.6 27.8 - - + -
64H CYS* 5.8 1.6 - - - -
171H TYR* 2.9 49.7 + - + +
172H LEU* 3.0 19.0 + - + +
174H SER* 1.3 76.0 - - - +
176H ASN* 1.3 66.1 + - - +
177H LYS 3.1 1.0 + - - -
178H LEU* 3.3 20.1 + - + +
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Residues in contact with ASN 176 (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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62H LYS* 4.7 15.6 + - - +
64H CYS* 5.4 7.2 - - - -
172H LEU* 2.9 31.0 + - - +
173H ARG* 3.3 13.3 + - - +
175H LEU* 1.3 77.2 - - - +
177H LYS* 1.3 59.2 + - + +
178H LEU 3.2 10.2 + - - +
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Residues in contact with LYS 177 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185G GLU* 5.1 12.3 + - - +
173H ARG* 3.2 45.9 - - - +
174H SER* 3.3 19.1 + - - +
175H LEU 3.1 1.4 - - - -
176H ASN* 1.3 77.8 - - + +
178H LEU* 1.3 64.1 + - - +
179H PRO* 4.8 0.9 - - - +
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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