Contacts of the helix formed by residues 163 - 174 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165I LEU* 5.7 2.3 - - - +
158K MET 4.4 3.0 + - - -
159K GLY* 2.9 24.1 + - - -
160K ALA* 4.2 1.4 - - - -
161K PRO 3.9 3.2 - - - +
162K GLU* 1.3 75.5 - - - +
164K GLY* 1.3 60.5 + - - +
165K LEU* 3.5 11.8 + - - +
166K ALA* 3.0 39.6 + - - +
167K GLU* 3.4 12.0 + - - +
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Residues in contact with GLY 164 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157J LYS* 3.5 36.8 + - - +
158J MET* 4.6 1.0 - - - +
48K LEU* 5.8 0.2 - - - +
161K PRO 4.3 3.3 + - - -
162K GLU 3.4 6.9 + - - -
163K SER* 1.3 69.9 - - - +
165K LEU* 1.3 59.9 + - - +
167K GLU* 3.4 8.1 + - - +
168K TYR* 3.0 28.8 + - - +
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Residues in contact with LEU 165 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165I LEU* 4.9 13.2 - - + -
157J LYS 3.6 5.5 + - - -
158J MET* 3.8 51.6 - - + +
163J SER* 5.9 2.0 - - - +
165J LEU* 5.0 13.7 - - + -
166J ALA* 5.2 3.1 - - - -
169J LEU* 4.2 14.6 - - + -
163K SER* 3.2 8.9 + - - +
164K GLY* 1.3 74.0 - - - +
166K ALA* 1.3 65.3 + - - +
168K TYR* 3.3 3.9 + - + +
169K LEU* 2.9 53.4 + - + +
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Residues in contact with ALA 166 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165I LEU* 5.2 4.9 - - - +
155K LEU* 4.8 1.3 - - + -
158K MET* 3.2 52.8 - - + +
160K ALA* 3.8 14.1 - - + +
163K SER* 3.0 24.4 + - - +
165K LEU* 1.3 76.3 - - - +
167K GLU* 1.3 61.9 + - - +
169K LEU* 4.9 0.4 - - - -
170K PHE* 3.0 21.5 + - - +
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Residues in contact with GLU 167 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48K LEU* 4.1 22.3 - - + +
51K PHE* 3.9 4.9 - - + -
95K SER* 3.6 14.1 - - - -
96K GLY* 2.8 28.3 + - - -
97K LEU* 3.0 23.1 + - - +
155K LEU* 4.1 10.5 - - + -
160K ALA* 3.7 22.9 - - + +
161K PRO* 3.9 7.9 - - - +
163K SER 3.4 12.1 + - - +
164K GLY* 3.4 9.9 + - - +
165K LEU 3.3 0.6 - - - -
166K ALA* 1.3 72.3 - - - +
168K TYR* 1.3 66.6 + - - +
170K PHE* 3.4 1.9 + - - +
171K ASP* 2.9 25.1 + - - +
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Residues in contact with TYR 168 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154J ASN* 3.4 26.5 - - - +
158J MET* 3.5 46.7 - - + -
169J LEU 4.4 2.9 - - - -
170J PHE* 3.5 13.5 - + - -
173J HIS* 3.3 21.7 - - + +
174J THR* 2.7 32.5 + - - -
48K LEU* 4.0 10.6 - - + +
164K GLY 3.0 17.3 + - - +
165K LEU 3.5 3.1 - - - +
167K GLU* 1.3 78.2 - - - +
169K LEU* 1.3 82.4 + - + +
171K ASP 3.3 0.2 + - - -
172K LYS* 3.1 56.6 + - + +
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Residues in contact with LEU 169 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204H CL 4.1 8.3 - - + -
165I LEU* 4.2 20.6 - - + -
168I TYR* 4.3 0.9 - - - -
169I LEU* 4.3 16.4 - - + -
169J LEU* 4.3 18.6 - - + -
173J HIS* 4.5 4.3 - - + -
158K MET* 3.9 12.1 - - + -
165K LEU* 2.9 41.3 + - + +
168K TYR* 1.3 97.1 - - + +
170K PHE* 1.3 57.8 + - - +
172K LYS* 3.3 1.0 + - - +
173K HIS* 2.8 60.0 + - + +
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Residues in contact with PHE 170 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168I TYR* 3.6 11.9 - + - -
51K PHE* 3.6 23.3 - + - -
100K MET* 4.4 1.8 - - + -
151K HIS* 3.6 41.1 - + + -
154K ASN* 3.9 21.3 - - + -
155K LEU* 3.7 21.5 - - + -
158K MET* 3.6 18.2 - - + +
166K ALA 3.0 17.3 + - - +
167K GLU 3.7 2.9 - - - +
169K LEU* 1.3 75.3 - - - +
171K ASP* 1.3 65.0 + - - +
174K THR* 3.0 45.2 + - + -
175K LEU* 3.2 32.2 + - + -
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Residues in contact with ASP 171 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48K LEU* 3.3 17.1 - - + -
49K LYS* 4.2 3.9 + - - +
50K ASN* 2.9 57.4 + - - +
51K PHE* 3.0 27.2 + - + -
167K GLU 2.9 17.5 + - - +
168K TYR 3.4 6.1 - - - +
170K PHE* 1.3 76.8 - - - +
172K LYS* 1.3 79.7 + - - +
175K LEU* 3.6 5.0 - - - -
176K GLY 3.0 23.4 + - - -
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Residues in contact with LYS 172 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154J ASN* 5.0 1.0 + - - -
173J HIS* 4.0 34.5 - - + +
174J THR* 3.8 10.1 - - - +
47K ALA 5.7 0.4 + - - -
48K LEU* 4.6 4.4 - - - +
50K ASN* 4.3 8.1 - - - +
168K TYR* 3.1 57.9 + - + +
169K LEU* 3.8 6.1 - - - +
171K ASP* 1.3 106.4 + - - +
173K HIS* 1.3 76.2 + - + +
176K GLY* 3.6 17.8 - - - -
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Residues in contact with HIS 173 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202H FE 2.2 31.1 - - - -
204H CL 3.2 15.9 - - + -
168I TYR* 3.4 13.7 - + - +
169I LEU* 4.5 4.2 - - + +
172I LYS* 3.9 28.5 - - + +
173I HIS* 3.2 17.2 + + - -
173J HIS* 3.1 20.7 + + - -
169K LEU* 2.8 37.8 + - + +
172K LYS* 1.3 81.8 - - + +
174K THR* 1.3 60.8 + - - +
176K GLY 4.7 3.5 - - - +
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Residues in contact with THR 174 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49I LYS* 6.1 2.2 - - - +
168I TYR* 2.7 30.3 + - - -
172I LYS* 3.9 7.4 - - - +
151K HIS* 3.6 30.7 - - + +
154K ASN* 5.7 0.2 - - - -
170K PHE* 3.0 29.8 + - + -
173K HIS* 1.3 80.1 - - - +
175K LEU* 1.3 64.7 + - + +
176K GLY 3.4 4.7 + - - +
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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