Contacts of the strand formed by residues 187 - 191 (chain D) in PDB entry 1JPM
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 LYS 187 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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157D GLN 2.8 7.2 + - - +
158D THR* 3.5 21.4 - - + +
159D LEU 2.9 26.0 + - - -
179D ARG* 4.7 1.6 - - - +
186D VAL* 1.3 76.5 - - - +
188D LEU* 1.3 63.2 + - - +
189D ARG* 4.2 0.9 - - - +
214D GLY 5.7 0.4 - - - -
216D GLU* 4.0 35.9 - - + +
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Residues in contact with LEU 188 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159D LEU* 3.5 18.4 - - + -
161D ILE* 4.2 20.0 - - + -
175D ILE* 3.8 26.2 - - + -
178D ILE* 4.2 15.9 - - + -
179D ARG* 3.4 43.0 - - + +
186D VAL* 3.8 16.8 - - + -
187D LYS* 1.3 83.5 - - - +
189D ARG* 1.3 63.1 + - - +
190D LEU* 5.1 1.8 - - + -
213D LEU 4.5 1.6 - - - +
214D GLY 5.0 0.2 - - - +
215D ILE* 3.9 14.9 - - + +
216D GLU* 2.9 31.3 + - - +
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Residues in contact with ARG 189 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131D GLU 5.3 2.6 + - - -
133D ASP* 2.9 34.8 + - - +
158D THR* 3.6 20.0 + - + +
159D LEU 2.8 10.3 + - - +
160D LYS* 3.2 11.9 - - + +
161D ILE* 2.7 31.9 + - - +
187D LYS* 4.2 0.6 - - - +
188D LEU* 1.3 71.2 - - - +
190D LEU* 1.3 59.2 + - - +
216D GLU* 2.7 34.4 + - - +
217D LEU* 3.9 20.2 - - + -
219D GLU* 5.7 2.5 - - - +
293D MET* 4.0 13.1 - - - -
319D ARG* 3.3 40.9 - - - +
320D PHE 3.2 24.0 + - - +
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Residues in contact with LEU 190 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160D LYS* 5.3 0.7 - - - -
161D ILE* 3.2 34.8 - - + +
163D VAL* 4.2 19.7 - - + -
175D ILE* 3.8 22.2 - - + -
188D LEU* 4.8 3.4 - - + +
189D ARG* 1.3 77.1 - - - +
191D ASP* 1.3 61.7 + - - +
192D ALA 4.1 0.4 - - - -
208D MET* 3.5 37.2 - - + -
215D ILE* 3.7 28.0 - - + -
217D LEU* 2.9 12.8 + - - +
218D VAL* 3.4 9.6 - - + -
219D GLU* 2.8 29.9 + - - +
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Residues in contact with ASP 191 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160D LYS* 4.9 16.6 + - + +
161D ILE 3.0 9.8 + - - +
162D LYS* 3.4 9.6 - - + -
163D VAL* 3.0 22.7 + - - +
190D LEU* 1.3 75.6 - - - +
192D ALA* 1.3 59.7 + - - +
193D ASN* 2.9 45.8 + - - +
219D GLU* 3.0 23.4 - - + +
220D GLN* 5.0 1.4 - - - +
245D GLU* 5.2 0.2 - - - +
1001D MG 2.2 30.7 - - - -
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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