Contacts of the helix formed by residues 163 - 174 (chain H) in PDB entry 5JKL
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 SER 163 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158H MET 4.4 2.6 + - - -
159H GLY* 3.0 22.8 + - - -
160H ALA* 4.2 1.0 - - - -
161H PRO 3.9 2.9 - - - +
162H GLU* 1.3 73.1 - - - +
164H GLY* 1.3 62.5 + - - +
165H LEU* 3.4 10.4 + - - +
166H ALA* 2.8 35.0 + - - +
167H GLU* 3.3 17.7 + - - +
165J LEU* 5.8 2.3 - - - +
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Residues in contact with GLY 164 (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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161H PRO 4.2 3.0 + - - -
162H GLU 3.4 6.9 + - - -
163H SER* 1.3 71.3 - - - +
165H LEU* 1.3 57.5 + - - +
167H GLU* 3.4 7.1 + - - +
168H TYR* 3.0 29.8 + - - +
157I LYS* 3.4 35.9 + - - +
158I MET* 4.8 0.2 - - - +
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Residues in contact with LEU 165 (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 SER* 3.2 9.1 + - - +
164H GLY* 1.3 72.1 - - - +
166H ALA* 1.3 60.5 + - - +
168H TYR* 3.3 2.1 + - + +
169H LEU* 2.9 58.7 + - + +
157I LYS 3.6 5.5 + - - -
158I MET* 3.9 52.5 - - + +
163I SER* 5.7 3.4 - - - +
165I LEU* 5.0 13.5 - - + -
166I ALA* 5.1 3.6 - - - -
169I LEU* 4.3 14.4 - - + -
165J LEU* 4.9 13.7 - - + -
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Residues in contact with ALA 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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155H LEU* 4.7 1.6 - - + -
158H MET* 3.4 48.7 - - + +
160H ALA* 4.0 11.2 - - + +
163H SER* 2.8 28.1 + - - +
165H LEU* 1.3 77.0 - - - +
167H GLU* 1.3 63.3 + - - +
169H LEU* 3.3 0.6 + - - -
170H PHE* 3.0 21.5 + - - +
165J LEU* 5.2 4.9 - - - -
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Residues in contact with GLU 167 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48H LEU* 4.1 20.3 - - + +
51H PHE* 3.7 7.6 - - + -
95H SER* 3.5 15.1 - - - -
96H GLY* 2.9 26.7 + - - -
97H LEU* 2.9 25.3 + - - +
155H LEU* 4.2 11.2 - - + -
160H ALA* 3.7 22.6 - - + +
161H PRO* 3.9 6.8 - - + +
163H SER 3.3 14.3 + - - +
164H GLY* 3.4 8.0 + - - +
165H LEU 3.3 0.2 - - - -
166H ALA* 1.3 76.2 - - - +
168H TYR* 1.3 63.9 + - - +
170H PHE* 3.4 0.3 + - - +
171H ASP* 2.9 25.3 + - - +
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Residues in contact with TYR 168 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48H LEU* 4.0 11.2 - - + +
164H GLY 3.0 18.3 + - - +
165H LEU 3.6 2.7 - - - +
167H GLU* 1.3 76.1 - - - +
169H LEU* 1.3 82.7 + - + +
171H ASP 3.3 1.2 + - - -
172H LYS* 3.1 61.9 + - + +
154I ASN* 3.4 25.8 - - - +
157I LYS* 6.5 0.2 - - + -
158I MET* 3.4 47.1 - - + -
169I LEU 4.5 2.2 - - - -
170I PHE* 3.5 14.2 - + - -
173I HIS* 3.4 20.2 - - + +
174I THR* 2.6 30.4 + - - -
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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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158H MET* 4.0 9.6 - - + -
165H LEU* 2.9 44.7 + - + +
166H ALA 4.0 2.7 - - - +
168H TYR* 1.3 89.8 - - + +
170H PHE* 1.3 58.7 + - - +
172H LYS* 3.1 1.8 + - + -
173H HIS* 2.8 59.6 + - + +
204H CL 4.0 8.5 - - + -
169I LEU* 4.2 18.6 - - + -
173I HIS* 4.6 4.0 - - + +
165J LEU* 4.3 21.3 - - + -
168J TYR* 4.3 2.0 - - - -
169J LEU* 4.4 16.8 - - + -
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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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51H PHE* 3.6 20.2 - + - -
100H MET* 4.5 2.5 - - + -
151H HIS* 3.6 39.5 - + + -
154H ASN* 3.9 21.5 - - + -
155H LEU* 3.5 26.5 - - + -
158H MET* 3.8 17.4 - - + +
166H ALA 3.0 17.2 + - - +
167H GLU 3.8 1.3 - - - +
169H LEU* 1.3 75.5 - - - +
171H ASP* 1.3 65.6 + - - +
174H THR* 2.9 47.5 + - + -
175H LEU* 3.2 30.7 + - + -
168J TYR* 3.5 11.7 - + - -
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Residues in contact with ASP 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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48H LEU* 3.2 20.0 - - + +
49H LYS* 4.3 2.4 + - - +
50H ASN* 2.9 57.0 + - - +
51H PHE* 3.0 25.6 + - + -
167H GLU 2.9 18.8 + - - +
168H TYR 3.3 5.8 + - - +
170H PHE* 1.3 76.8 - - - +
172H LYS* 1.3 85.4 + - - +
175H LEU* 3.6 5.2 + - - -
176H GLY 3.1 18.9 + - - -
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Residues in contact with LYS 172 (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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47H ALA 5.7 1.0 + - - -
48H LEU* 4.5 3.6 - - - +
49H LYS* 6.5 0.2 - - - -
50H ASN* 4.2 9.6 - - - +
168H TYR* 3.1 58.6 + - + +
169H LEU* 3.1 5.1 + - - +
170H PHE 3.1 0.2 - - - -
171H ASP* 1.3 108.9 + - - +
173H HIS* 1.3 75.2 + - + +
176H GLY* 3.5 19.1 - - - -
154I ASN* 5.0 1.0 + - - -
173I HIS* 4.0 35.2 - - + +
174I THR* 3.9 8.7 - - - -
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Residues in contact with HIS 173 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169H LEU* 2.8 43.0 + - + +
172H LYS* 1.3 79.5 - - + +
174H THR* 1.3 61.7 + - - +
176H GLY 4.7 3.4 - - - +
202H FE 2.2 31.2 - - - -
204H CL 3.2 15.3 - - + -
173I HIS* 3.2 17.4 + + - -
168J TYR* 3.4 15.4 - + + +
169J LEU* 4.5 3.9 - - + +
172J LYS* 4.0 28.9 - - + +
173J HIS* 3.1 16.6 + + - -
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Residues in contact with THR 174 (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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151H HIS* 3.7 21.5 - - + +
154H ASN* 5.8 0.3 - - - -
170H PHE* 2.9 39.3 + - + -
173H HIS* 1.3 78.0 - - - +
175H LEU* 1.3 66.9 + - + +
176H GLY 3.4 5.6 + - - +
168J TYR* 2.7 30.7 + - - -
172J LYS* 3.8 7.7 - - - +
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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