Contacts of the strand formed by residues 85 - 90 (chain L) in PDB entry 6D6U
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 85 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39K GLN* 5.6 2.4 + - - -
42K GLU* 5.8 0.5 - - - +
36L TYR 3.6 0.2 - - - +
37L GLN* 3.4 5.7 - - - -
38L GLN* 2.9 46.9 + - + +
84L ALA* 1.3 77.0 - - - +
86L TYR* 1.3 63.2 + - - +
87L HIS* 4.0 20.8 + - + +
101L THR 3.2 6.7 - - - +
102L LYS* 3.3 39.3 + - - +
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Residues in contact with TYR 86 (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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6L GLN* 2.9 23.4 + - - +
21L LEU* 4.2 24.5 - - + -
35L TRP* 5.0 8.5 - + + -
36L TYR 3.3 9.0 - - - -
37L GLN* 3.7 22.8 + - + -
47L LEU* 3.8 27.8 - - + -
62L PHE* 3.9 15.2 - + - -
73L LEU* 4.5 13.5 - - + -
75L ILE* 4.3 17.2 - - + +
82L ASP* 2.8 30.7 + - - +
84L ALA* 3.9 15.7 - - + -
85L ASP* 1.3 78.7 - - - +
87L HIS* 1.3 61.8 + - - +
100L GLY* 3.7 0.3 - - - -
101L THR* 2.9 21.9 + - - +
103L LEU* 4.5 15.0 - - + -
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Residues in contact with HIS 87 (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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39K GLN* 4.9 2.5 + - - -
43K GLN 4.6 5.2 - - - -
44K GLY* 4.3 13.2 - - - -
45K LEU* 4.6 19.4 + - + +
6L GLN* 4.3 2.5 - - - -
34L SER 3.6 1.9 - - - +
35L TRP* 3.3 7.4 - - - -
36L TYR* 2.8 53.2 + - + +
38L GLN* 3.5 28.1 + - + -
44L PRO* 6.1 0.9 - - + -
85L ASP* 4.0 19.8 + - + +
86L TYR* 1.3 75.0 - - - +
88L CYS* 1.3 59.8 + - - +
89L GLY 4.1 0.2 + - - -
97L PHE* 4.8 16.4 - - + +
98L GLY 4.4 6.0 + - - +
99L ALA 4.1 7.2 + - - -
100L GLY* 3.4 28.6 + - - -
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Residues in contact with CYS 88 (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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4L MET* 4.7 3.6 - - - +
6L GLN* 4.2 24.7 + - - -
23L CYS* 2.0 49.6 - - + -
33L VAL* 4.3 4.7 - - + -
34L SER 3.7 4.9 - - - -
35L TRP* 3.5 27.2 - - + -
87L HIS* 1.3 72.8 - - - +
89L GLY* 1.3 58.9 + - - +
97L PHE* 3.7 1.9 - - - +
98L GLY* 2.8 30.5 + - - -
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Residues in contact with GLY 89 (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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4L MET* 5.3 1.3 - - - -
32L TYR 3.9 1.2 - - - +
33L VAL* 4.6 2.6 - - - +
34L SER* 3.0 42.2 + - - +
87L HIS 4.1 0.2 + - - -
88L CYS* 1.3 75.6 - - - +
90L GLN* 1.3 63.6 + - - -
91L SER* 5.2 0.9 - - - -
96L THR 3.6 11.7 - - - -
97L PHE* 3.8 19.6 - - - -
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Residues in contact with GLN 90 (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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2L ILE* 3.6 20.0 - - + +
4L MET* 3.6 36.1 - - + +
29L VAL* 3.3 34.2 - - + +
32L TYR 3.9 6.5 - - - +
33L VAL* 4.5 6.5 - - + +
89L GLY* 1.3 74.0 - - - -
91L SER* 1.3 58.7 + - - +
92L TYR* 3.1 24.4 + - - +
93L SER 3.6 4.4 + - - +
94L TYR 3.9 9.9 + - - -
95L PRO* 3.3 17.3 - - - +
96L THR* 3.4 31.0 + - - +
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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