Contacts of the strand formed by residues 90 - 95 (chain L) in PDB entry 6AHU
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 GLY 90 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86L PHE 3.4 7.6 + - - -
87L ILE* 2.9 17.3 - - - +
88L LYS 3.6 1.8 + - - -
89L LYS* 1.3 78.5 - - - +
91L SER* 1.3 66.7 + - - -
111L PRO 4.7 4.0 - - - +
183L TRP* 3.8 4.7 - - - -
184L HIS 4.4 0.4 - - - -
186L THR* 4.1 19.3 - - - -
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Residues in contact with SER 91 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87L ILE* 5.5 0.2 - - - +
90L GLY* 1.3 76.5 + - - -
92L CYS* 1.3 60.1 + - - +
93L TYR* 4.2 13.3 + - - -
111L PRO* 3.6 35.2 + - - +
182L ALA 4.4 0.2 - - - +
183L TRP* 3.2 17.8 - - - +
184L HIS* 3.5 22.2 + - - +
186L THR* 5.3 0.8 + - - -
286L LEU* 5.9 0.5 - - - +
288L GLU* 4.9 8.6 + - - -
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Residues in contact with CYS 92 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82L PHE* 3.6 29.8 - - - -
86L PHE* 3.8 28.7 + - + -
87L ILE* 4.4 16.4 - - + +
90L GLY 4.2 0.8 - - - -
91L SER* 1.3 73.0 - - - +
93L TYR* 1.3 80.2 + - - +
109L LEU* 3.5 21.2 - - + +
110L LEU 4.1 6.8 - - - +
111L PRO* 5.2 1.0 - - - +
181L LEU* 4.9 3.6 - - - -
182L ALA 3.8 10.1 - - - -
183L TRP* 3.8 2.7 - - + -
193L MET* 4.7 10.1 - - - -
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Residues in contact with TYR 93 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34L GLN 4.8 2.3 + - - -
37L TYR* 3.9 22.7 - + + -
38L TYR* 4.9 3.8 - + + -
91L SER* 4.5 8.5 - - - -
92L CYS* 1.3 84.9 - - - +
94L ALA* 1.3 60.7 + - - +
109L LEU* 4.2 12.1 - - - +
111L PRO* 3.6 43.5 - - + +
180L LEU 4.3 1.8 - - - -
181L LEU* 3.4 18.2 - - - +
182L ALA 3.1 23.5 + - - +
284L PHE* 3.9 22.9 - + + -
285L ILE 5.9 0.2 - - - -
286L LEU* 3.7 23.3 - - + -
287L PRO* 3.6 32.8 - - + +
288L GLU* 3.5 21.0 + - - -
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Residues in contact with ALA 94 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38L TYR* 2.7 26.6 + - - -
77L LEU* 4.5 8.7 - - + -
93L TYR* 1.3 78.1 - - - +
95L LEU* 1.3 57.4 + - - +
107L VAL* 4.4 2.2 - - + -
108L ALA* 3.4 3.8 - - - -
109L LEU* 3.1 37.5 + - + +
115L LEU* 5.9 0.9 - - + -
179L PHE* 3.9 17.5 - - + -
180L LEU 3.9 4.0 - - - -
181L LEU* 3.8 16.2 - - + -
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Residues in contact with LEU 95 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38L TYR* 3.6 33.7 - - + +
94L ALA* 1.3 75.1 - - - +
96L THR* 1.3 76.0 + - - +
97L TYR* 3.2 1.4 + - - -
106L THR* 4.7 2.9 - - + -
107L VAL 3.8 7.6 - - - +
108L ALA* 4.6 0.2 - - + -
179L PHE* 3.3 3.5 - - - -
180L LEU* 2.7 53.5 + - + +
284L PHE* 4.7 1.3 - - + -
317L PHE* 4.0 33.2 - - + -
319L ASP* 4.0 15.0 - - + +
320L SER* 4.8 1.6 - - - +
321L PRO* 3.9 29.2 - - + -
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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