Contacts of the strand formed by residues 186 - 191 (chain D) in PDB entry 5HP1
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 ASP 186 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65D LYS* 4.9 4.5 + - - -
108D VAL* 3.9 18.5 - - + +
109D LEU 3.3 7.7 - - - +
110D ASP* 4.0 11.3 + - - +
111D VAL* 4.4 2.9 - - - -
182D GLN* 3.6 9.4 - - - +
183D TYR 2.9 32.3 + - - +
184D MET 3.3 0.2 - - - -
185D ASP* 1.3 85.1 - - - +
187D LEU* 1.3 59.8 + - - +
188D TYR* 3.6 19.8 + - + -
409D THR* 3.7 15.6 + - - +
410D TRP* 3.4 27.6 + - - -
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Residues in contact with LEU 187 (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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107D THR 3.3 5.5 - - - +
108D VAL* 3.4 1.8 - - - -
109D LEU* 2.7 48.7 + - + +
111D VAL* 4.2 13.2 - - + +
164D MET* 3.6 36.1 - - + -
168D LEU* 4.2 5.4 - - + -
180D ILE* 4.0 18.4 - - + -
181D TYR 3.6 1.3 - - - +
182D GLN* 3.7 31.6 - - + -
186D ASP* 1.3 72.1 - - - +
188D TYR* 1.3 61.3 + - - +
189D VAL* 3.8 2.9 + - + +
205D LEU* 4.0 26.5 - - + -
209D LEU* 4.2 12.1 - - + -
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Residues in contact with TYR 188 (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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100D LEU* 3.8 23.2 - - + +
106D VAL* 4.2 7.0 - - + -
107D THR 3.6 2.5 - - - -
108D VAL* 3.5 29.5 - - + +
179D VAL 3.5 1.2 - - - +
180D ILE* 3.2 4.9 - - - -
181D TYR* 2.6 56.5 + + + +
183D TYR* 3.9 10.9 - - + +
186D ASP* 3.6 34.9 + - + -
187D LEU* 1.3 74.1 - - - +
189D VAL* 1.3 59.6 + - - +
190D GLY 4.0 1.1 + - - -
234D LEU* 4.6 2.5 - - + -
377D THR* 5.0 8.1 + - + -
380D ILE* 3.6 38.0 - - + +
381D VAL* 3.9 28.5 - - + -
410D TRP* 4.0 5.4 + - - -
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Residues in contact with VAL 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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106D VAL* 3.4 2.4 - - - +
107D THR 2.9 36.8 + - - +
109D LEU* 4.4 6.1 - - + -
171D PHE* 5.0 4.9 - - + -
178D ILE* 3.5 27.8 - - + -
179D VAL 3.4 2.7 - - - -
180D ILE* 4.1 14.1 - - + -
187D LEU* 4.3 13.5 - - + +
188D TYR* 1.3 74.4 - - - +
190D GLY* 1.3 57.8 + - - +
198D HIS* 3.5 9.8 + - + -
202D ILE* 3.7 25.8 - - + -
205D LEU* 3.6 29.2 - - + -
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Residues in contact with GLY 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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100D LEU* 4.0 8.3 - - - +
103D LYS* 3.9 11.8 - - - +
105D SER 3.1 10.3 - - - -
106D VAL* 3.7 14.1 - - - -
178D ILE* 3.3 8.8 - - - +
179D VAL 2.9 33.2 + - - -
189D VAL* 1.3 74.3 - - - +
191D SER* 1.3 60.1 + - - -
198D HIS* 4.4 0.7 - - - -
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Residues in contact with SER 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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103D LYS* 3.8 12.4 - - - +
104D LYS* 3.3 2.1 + - - +
105D SER* 2.8 33.0 + - - +
177D ASP 5.4 1.3 - - - -
178D ILE* 4.0 22.2 - - - +
190D GLY* 1.3 76.1 - - - -
192D ASP* 1.3 58.9 + - - +
193D LEU* 3.5 27.7 + - - +
198D HIS* 2.6 30.1 + - - +
201D LYS* 5.9 0.4 - - - +
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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