Contacts of the helix formed by residues 166 - 176 (chain P) in PDB entry 5A0Q
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 TYR 166 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28P VAL* 6.4 3.6 - - + -
29P ALA* 5.4 12.8 - - + -
161P ALA* 3.6 31.0 - - - +
162P MET* 3.9 6.5 - - - +
163P GLY 3.3 21.1 - - - +
164P LYS 3.3 2.9 - - - -
165P ASN* 1.3 77.6 - - - +
167P VAL* 1.4 81.6 + - + +
168P ASN 3.3 0.2 - - - -
169P GLY 3.5 2.0 - - - +
170P LYS* 2.9 59.4 + - + +
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Residues in contact with VAL 167 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165P ASN* 4.3 9.0 - - - +
166P TYR* 1.4 114.5 - - + +
168P ASN* 1.4 65.4 + - - +
170P LYS* 4.7 2.9 - - - +
171P THR* 2.9 17.7 + - - -
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Residues in contact with ASN 168 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165P ASN* 2.7 34.1 + - - +
167P VAL* 1.4 83.8 + - - +
169P GLY* 1.4 63.0 + - - +
170P LYS 3.3 0.9 - - - -
171P THR* 3.1 19.5 + - - -
172P PHE* 3.0 23.9 + - + -
196P GLU* 4.0 19.5 - - + +
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Residues in contact with GLY 169 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161P ALA* 4.1 11.2 - - - -
165P ASN 3.3 13.2 + - - -
166P TYR 3.1 6.5 + - - -
168P ASN* 1.4 76.4 - - - +
170P LYS* 1.3 58.7 + - - +
172P PHE* 3.5 3.6 + - - -
173P LEU* 3.1 15.1 + - - +
193P THR* 3.1 38.9 - - - +
196P GLU* 5.1 1.1 - - - +
197P SER* 5.3 1.3 - - - -
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Residues in contact with LYS 170 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147P GLN* 4.8 6.9 + - - +
157P TRP* 3.6 37.5 - - + +
160P THR* 3.6 17.9 + - - -
161P ALA* 3.2 36.0 + - + +
166P TYR* 2.9 36.5 + - + +
167P VAL* 4.7 4.0 - - - +
169P GLY* 1.3 72.6 - - - +
171P THR* 1.4 63.9 + - - +
173P LEU* 3.3 9.2 + - - +
174P GLU* 3.2 23.8 + - - +
53Q HIS* 5.3 8.4 - - + -
55Q LEU* 4.5 2.8 - - - +
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Residues in contact with THR 171 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167P VAL 2.9 20.3 + - - -
168P ASN* 3.1 15.5 + - - -
170P LYS* 1.4 73.6 - - - +
172P PHE* 1.3 67.1 + - - +
174P GLU* 3.2 35.0 + - + +
175P LYS* 3.3 31.2 + - + +
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Residues in contact with PHE 172 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168P ASN* 3.0 30.5 + - + -
169P GLY* 3.7 5.6 - - - +
171P THR* 1.3 77.0 - - - +
173P LEU* 1.3 56.3 + - - +
175P LYS* 3.8 15.9 - - - +
176P ARG* 2.7 76.4 + - + +
192P LEU 5.4 3.8 - - - -
193P THR* 3.5 23.6 - - + +
196P GLU* 2.4 62.1 - - + -
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Residues in contact with LEU 173 (chain P).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35P VAL* 3.9 13.0 - - + -
36P GLY 4.6 0.2 - - - +
37P ILE* 3.7 28.0 - - + -
159P ALA* 4.0 17.2 - - + +
160P THR* 3.3 40.2 - - - +
161P ALA* 4.0 3.8 - - + -
169P GLY 3.1 19.4 + - - +
170P LYS* 3.6 8.3 - - - +
171P THR 3.2 0.6 - - - -
172P PHE* 1.3 76.7 - - - +
174P GLU* 1.4 54.5 + - - +
175P LYS 3.6 0.2 - - - -
177P TYR* 3.1 24.7 - - + +
189P THR* 3.7 24.9 - - + +
193P THR* 4.0 9.0 - - + +
55Q LEU* 3.7 11.1 - - + +
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Residues in contact with GLU 174 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170P LYS 3.2 10.0 + - - +
171P THR* 3.2 29.0 - - + +
173P LEU* 1.4 76.4 - - - +
175P LYS* 1.4 60.0 + - + +
177P TYR 3.1 14.2 - - - +
178P ASN* 4.6 6.1 + - - +
53Q HIS* 4.4 15.0 + - - -
54Q LYS* 3.6 45.4 + - - +
55Q LEU* 3.6 24.6 - - + +
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Residues in contact with LYS 175 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171P THR* 3.3 44.3 + - + +
172P PHE* 3.6 17.3 - - - +
174P GLU* 1.4 80.7 - - + +
176P ARG* 1.4 102.2 + - - +
177P TYR* 3.1 3.8 + - - +
178P ASN* 5.6 3.1 + - - -
54Q LYS* 5.5 0.7 - - - +
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Residues in contact with ARG 176 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172P PHE* 2.7 53.1 + - + +
175P LYS* 1.4 113.4 - - - +
177P TYR* 1.3 58.8 + - - +
181P LEU* 6.1 0.3 - - - +
189P THR* 4.0 17.4 + - - +
192P LEU* 6.4 2.9 - - + -
193P THR* 5.1 1.1 - - - +
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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