Contacts of the strand formed by residues 186 - 192 (chain A) in PDB entry 1X6N
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 HIS 186 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159A VAL* 3.9 18.9 - - + +
160A VAL 3.2 2.1 + - - +
161A GLY* 3.1 29.8 - - - -
162A SER 3.2 5.2 + - - -
184A LEU* 3.8 5.4 - - - +
185A THR* 1.3 106.2 + - - +
187A LEU* 1.3 60.0 + - - +
188A LEU* 4.2 12.6 - - + -
266A LEU* 4.1 2.5 - - - -
267A LYS* 3.4 27.9 - - + +
269A LEU* 4.1 14.6 - - + -
358A GLU* 2.8 32.8 + - - -
384A HIS* 3.6 21.7 + + - -
386A PHE* 4.6 7.2 - + + -
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Residues in contact with LEU 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A SER* 3.6 13.0 - - - +
163A TYR 5.0 0.4 - - - -
164A PHE* 4.0 23.1 - - + +
179A ILE* 4.0 18.6 - - + -
184A LEU* 4.2 16.6 - - + -
186A HIS* 1.3 73.0 - - - +
188A LEU* 1.3 65.1 + - - +
256A LEU* 3.6 31.2 - - + -
259A LEU* 3.7 20.9 - - + -
266A LEU* 4.0 17.5 - - + +
267A LYS 2.8 11.5 + - - +
268A ILE* 3.2 10.9 - - + +
269A LEU 2.9 22.7 + - - -
541A ILE* 5.4 2.2 - - + -
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Residues in contact with LEU 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A GLY* 5.1 0.7 - - - -
162A SER 3.0 22.1 + - - +
163A TYR* 3.4 51.9 - - + +
164A PHE* 2.8 30.7 + - - +
186A HIS* 4.4 12.1 - - + -
187A LEU* 1.3 79.9 - - - +
189A TYR* 1.3 60.2 + - - +
268A ILE* 6.0 0.2 - - - -
269A LEU* 3.1 21.5 - - + +
271A SER* 4.7 0.7 - - - -
311A ASP* 3.4 29.6 - - + +
386A PHE* 3.8 26.2 - - + -
537A PHE* 5.8 0.4 - - + -
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Residues in contact with TYR 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A TYR* 5.1 1.1 - - - -
164A PHE* 3.7 19.5 - + + -
166A GLU* 2.5 42.1 + - + +
188A LEU* 1.3 72.0 - - - +
190A GLY* 1.3 56.7 + - - +
191A PHE* 2.6 19.8 + - - -
192A ILE* 4.1 23.3 - - + -
234A ALA* 3.8 6.2 - - - +
252A ASN* 2.9 43.3 + - + +
253A PHE* 3.6 20.4 - + - -
256A LEU* 3.8 20.2 - - + -
268A ILE* 5.7 1.1 - - + -
269A LEU 2.7 15.2 + - - +
270A PRO* 4.1 7.6 - - + -
271A SER* 3.2 20.4 + - - +
307A PHE* 4.2 13.9 - + + -
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Residues in contact with GLY 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A TYR* 5.3 2.0 - - - -
164A PHE 2.4 24.3 + - - +
165A VAL* 3.8 18.1 - - - +
166A GLU* 3.9 17.7 + - - +
188A LEU 3.8 0.2 + - - -
189A TYR* 1.3 71.3 - - - +
191A PHE* 1.3 79.5 + - - +
539A TRP* 5.2 4.0 - - - -
2B NAA 5.9 1.4 - - - +
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Residues in contact with PHE 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A TYR* 5.0 0.2 - + - -
165A VAL* 6.0 0.7 - - + -
166A GLU* 4.9 6.9 - - - +
189A TYR* 2.6 13.3 + - - -
190A GLY* 1.3 79.0 - - - +
192A ILE* 1.3 67.2 + - - +
193A PRO* 3.7 6.8 - - - +
229A HIS* 4.7 6.6 + - - +
271A SER* 2.9 33.4 - - - -
273A GLY 3.2 24.5 - - - +
274A GLY* 3.5 5.6 - - - -
277A LEU* 4.0 13.1 - - + +
313A ASP* 3.1 28.0 - - - -
539A TRP* 3.5 33.9 - + - -
601A AMI 3.6 23.8 - - - -
1B NAA 3.7 20.9 - - - -
2B NAA 4.8 9.0 - - + -
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Residues in contact with ILE 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A GLU* 5.4 0.7 - - - +
189A TYR* 4.1 25.4 - - + -
191A PHE* 1.3 75.6 - - - +
193A PRO* 1.3 71.7 - - + +
226A ILE* 3.7 28.5 - - + -
227A SER 3.1 26.7 - - - +
228A ILE* 4.9 5.4 - - + -
229A HIS 5.9 0.2 - - - +
253A PHE* 4.6 5.2 - - + -
270A PRO* 3.9 26.5 - - + -
271A SER 2.7 10.8 + - - +
272A ILE* 3.5 13.9 - - + +
273A GLY* 3.4 21.0 + - - -
277A LEU* 4.6 0.3 - - - +
300A PHE* 3.8 22.7 - - + -
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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