Contacts of the helix formed by residues 163 - 174 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165H LEU* 5.7 2.8 - - - +
158I MET 4.3 3.0 + - - -
159I GLY* 3.0 24.9 + - - -
160I ALA* 4.2 0.2 - - - -
161I PRO 3.8 6.6 - - - +
162I GLU* 1.4 74.5 - - - +
164I GLY* 1.3 60.8 + - - +
165I LEU* 3.7 9.5 + - - +
166I ALA* 3.0 38.0 + - - +
167I GLU* 3.4 9.9 + - - +
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Residues in contact with GLY 164 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48I LEU* 5.8 0.2 - - - +
161I PRO 4.2 3.1 + - - -
162I GLU 3.4 6.7 + - - -
163I SER* 1.3 69.6 - - - +
165I LEU* 1.4 65.0 + - - +
167I GLU* 3.4 7.4 + - - +
168I TYR* 3.0 23.6 + - - +
157K LYS* 3.3 39.5 + - - +
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Residues in contact with LEU 165 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165H LEU* 5.0 13.0 - - + -
163I SER* 3.2 7.6 + - - +
164I GLY* 1.4 77.3 - - - +
166I ALA* 1.3 52.4 + - - +
168I TYR* 3.3 3.4 + - + +
169I LEU* 2.8 63.7 + - + +
157K LYS 3.5 5.7 + - - -
158K MET* 3.9 51.1 - - + +
163K SER* 5.7 3.1 - - - +
165K LEU* 4.9 14.4 - - + -
166K ALA* 5.2 3.1 - - - +
169K LEU* 4.2 14.6 - - + -
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Residues in contact with ALA 166 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165H LEU* 5.1 4.9 - - - +
155I LEU* 4.9 1.6 - - + -
158I MET* 3.4 49.5 - - + +
160I ALA* 3.9 12.1 - - + +
163I SER* 3.0 28.5 + - - +
164I GLY 3.3 0.2 - - - -
165I LEU* 1.3 73.9 - - - +
167I GLU* 1.3 65.1 + - - +
169I LEU* 4.9 0.7 - - - -
170I PHE* 3.0 22.5 + - - +
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Residues in contact with GLU 167 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48I LEU* 4.2 19.3 - - + +
51I PHE* 3.8 5.4 - - + -
95I SER* 3.6 14.2 - - - -
96I GLY* 2.9 27.0 + - - -
97I LEU* 2.8 25.1 + - - +
155I LEU* 4.2 11.2 - - + -
160I ALA* 3.6 26.7 - - + +
161I PRO* 3.9 7.0 - - - +
163I SER 3.4 7.5 + - - +
164I GLY* 3.4 9.7 + - - +
165I LEU 3.3 0.6 - - - -
166I ALA* 1.3 78.2 - - - +
168I TYR* 1.3 62.5 + - - +
170I PHE* 3.4 1.9 + - - +
171I ASP* 2.9 25.3 + - - +
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Residues in contact with TYR 168 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48I LEU* 4.0 10.1 - - + +
164I GLY 3.0 17.4 + - - +
165I LEU 3.5 3.4 - - - +
167I GLU* 1.3 76.6 - - - +
169I LEU* 1.3 81.0 + - + +
171I ASP 3.3 1.2 + - - -
172I LYS* 3.1 64.3 + - + +
154K ASN* 3.5 25.1 - - - +
158K MET* 3.5 47.6 - - + -
169K LEU 4.5 2.7 - - - -
170K PHE* 3.6 13.7 - + - -
173K HIS* 3.4 10.7 - - + +
174K THR* 2.7 40.1 + - - -
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Residues in contact with LEU 169 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165H LEU* 4.3 15.7 - - + -
168H TYR* 4.3 2.2 - - - -
169H LEU* 4.2 24.0 - - + -
204H CL 3.9 9.9 - - + -
158I MET* 4.1 8.5 - - + -
165I LEU* 2.8 43.7 + - + +
166I ALA 4.0 2.9 - - - +
168I TYR* 1.3 92.8 - - + +
170I PHE* 1.3 56.7 + - - +
172I LYS* 3.2 0.8 + - - -
173I HIS* 2.8 60.0 + - + +
169K LEU* 4.3 18.6 - - + -
173K HIS* 4.5 4.3 - - - +
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Residues in contact with PHE 170 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168H TYR* 3.5 11.2 - + - -
51I PHE* 3.6 23.3 - + - -
100I MET* 4.4 2.5 - - + -
151I HIS* 3.6 33.0 - + + -
154I ASN* 3.9 21.5 - - + -
155I LEU* 3.6 23.6 - - + -
158I MET* 3.8 18.0 - - + +
166I ALA 3.0 17.9 + - - +
167I GLU 3.8 1.8 - - - +
169I LEU* 1.3 71.9 - - - +
171I ASP* 1.3 60.7 + - - +
174I THR* 2.9 61.3 + - + -
175I LEU* 3.2 29.2 + - + -
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Residues in contact with ASP 171 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48I LEU* 3.2 17.2 - - + +
49I LYS* 4.2 5.7 + - - +
50I ASN* 2.8 51.1 + - - +
51I PHE* 2.9 26.9 + - + -
167I GLU 2.9 18.5 + - - +
168I TYR 3.4 5.4 - - - +
170I PHE* 1.3 77.0 - - - +
172I LYS* 1.3 80.5 + - - +
175I LEU* 3.6 4.9 + - - -
176I GLY 3.0 24.3 + - - -
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Residues in contact with LYS 172 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47I ALA 5.6 0.8 + - - -
48I LEU* 4.5 4.0 - - - +
49I LYS 5.7 0.2 - - - +
50I ASN* 4.3 8.7 - - - +
168I TYR* 3.1 57.3 + - + +
169I LEU 3.8 4.7 - - - +
170I PHE 3.2 0.2 - - - -
171I ASP* 1.3 106.9 + - - +
173I HIS* 1.3 72.0 + - + +
174I THR 3.7 0.2 - - - -
176I GLY* 3.4 21.8 - - - +
154K ASN* 4.9 1.6 + - - -
173K HIS* 3.9 36.6 - - + +
174K THR* 3.9 9.6 - - - +
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Residues in contact with HIS 173 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168H TYR* 3.4 11.2 - + + +
169H LEU* 4.6 4.1 - - + +
172H LYS* 4.0 29.4 - - + +
173H HIS* 3.2 17.5 + + - -
202H FE 2.2 32.1 - - - -
204H CL 3.1 16.6 - - + -
169I LEU* 2.8 46.5 + - + +
172I LYS* 1.3 77.1 - - + +
174I THR* 1.3 61.6 + - - +
176I GLY* 5.3 2.7 - - - -
173K HIS* 3.2 17.2 + + - -
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Residues in contact with THR 174 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168H TYR* 2.6 32.0 + - - -
172H LYS* 3.9 7.2 - - - +
151I HIS* 3.7 20.9 - - + +
154I ASN* 5.7 0.3 - - - -
170I PHE* 2.9 46.5 + - + -
173I HIS* 1.3 74.9 - - - +
175I LEU* 1.3 63.2 + - + +
176I GLY 3.3 4.5 - - - -
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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