Contacts of the strand formed by residues 89 - 96 (chain D) in PDB entry 2Y1T
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 PHE 89 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6D LYS* 4.1 17.7 - - + -
7D TYR 4.1 2.2 - - - -
8D LEU* 3.6 52.0 - - + -
43D PRO* 6.6 0.2 - - + -
45D GLY* 3.8 5.8 - - - +
46D VAL 3.3 26.7 - - - +
47D ALA* 3.7 10.8 - - + -
83D TYR* 2.7 24.9 + - - -
86D ASP 3.6 16.8 - - - -
87D ASN* 3.1 36.0 + - - +
88D ASP* 1.3 78.0 - - - +
90D TRP* 1.3 63.4 - - - +
91D PHE* 3.2 27.6 - - + -
143D DUD 4.1 0.3 - - - +
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Residues in contact with TRP 90 (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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26D LEU* 3.5 29.8 - - + -
43D PRO* 3.9 0.9 - - - +
44D LEU* 3.0 35.1 + - + +
45D GLY 4.1 1.7 + - - -
46D VAL* 2.8 26.4 + - + +
47D ALA* 4.3 1.8 - - - -
48D MET* 3.7 53.7 + - + +
50D LEU* 4.3 5.6 - - + -
56D ALA* 3.6 23.1 - - + -
58D VAL* 3.9 19.5 - - + -
79D ILE* 3.8 34.2 - - + +
83D TYR* 4.0 10.2 - + - -
88D ASP 3.8 8.5 - - - -
89D PHE* 1.3 80.0 - - - +
91D PHE* 1.3 67.1 + - - +
111D PHE* 3.9 17.3 - + - -
143D DUD 3.5 5.4 - - + +
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Residues in contact with PHE 91 (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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41D LEU* 3.2 46.2 - - + -
42D VAL 3.2 6.7 - - - +
43D PRO* 3.6 34.8 - - + -
44D LEU* 3.8 9.5 - - - +
58D VAL* 5.4 3.5 - - - +
83D TYR* 4.5 4.7 - - - -
87D ASN 6.0 0.2 - - - -
89D PHE* 3.2 38.4 - - + -
90D TRP* 1.3 72.9 - - - +
92D PHE* 1.3 59.5 + - - +
93D PRO* 3.7 2.5 - - - +
143D DUD 2.8 38.3 + - + +
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Residues in contact with PHE 92 (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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41D LEU* 4.4 0.7 - - - -
42D VAL* 2.8 36.7 + - + +
44D LEU* 4.1 10.0 - - + +
58D VAL* 4.9 2.0 - - + -
60D PRO* 4.0 13.9 - - + -
64D THR* 4.5 5.8 - - + -
70D VAL* 3.9 15.7 - - + -
71D ILE 4.5 0.7 - - - -
72D GLN* 3.1 49.6 - - + -
91D PHE* 1.3 72.2 - - - +
93D PRO* 1.3 61.6 - - - +
94D ALA* 3.2 35.0 + - + -
108D ILE* 3.8 38.1 - - + -
109D CYS* 3.6 28.9 - - + -
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Residues in contact with PRO 93 (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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39D PHE* 3.8 19.3 - - + -
40D LYS 4.0 2.0 - - - +
41D LEU* 4.0 13.4 - - + -
72D GLN* 3.3 17.8 - - + +
73D THR* 3.1 35.3 + - - +
74D ASN* 3.3 33.0 - - - +
91D PHE 3.7 2.9 - - - +
92D PHE* 1.3 81.9 - - - +
94D ALA* 1.3 57.4 + - - +
143D DUD 3.6 19.5 - - + +
62F SER 5.9 3.4 - - - +
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Residues in contact with ALA 94 (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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34D ILE* 4.1 10.9 - - + +
38D GLU 4.0 0.7 - - - +
39D PHE* 3.3 8.6 - - - -
40D LYS* 2.9 44.0 + - - +
42D VAL* 4.0 10.5 - - + -
70D VAL* 4.0 14.6 - - + -
71D ILE 3.4 4.9 - - - -
73D THR* 4.5 0.2 - - - -
92D PHE* 3.2 25.7 + - + -
93D PRO* 1.3 73.1 - - - +
95D TYR* 1.3 59.3 + - - +
96D ALA 4.2 0.4 + - - -
102D ILE* 5.3 0.4 - - + -
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Residues in contact with TYR 95 (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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37D ASP* 3.2 49.0 + - - +
38D GLU 3.6 10.8 - - - -
39D PHE* 4.3 3.1 - - + -
70D VAL* 3.3 3.4 - - - -
71D ILE* 3.0 41.4 + - + +
73D THR* 3.4 20.1 - - + +
94D ALA* 1.3 72.9 - - - +
96D ALA* 1.3 74.5 + - - +
97D LEU* 3.7 19.7 + - + -
65F TYR* 3.2 32.1 - + - -
97F LEU* 3.6 43.1 + - + +
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Residues in contact with ALA 96 (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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34D ILE* 3.6 32.3 - - + +
35D LYS 3.6 7.9 - - - +
37D ASP* 2.7 33.1 + - - -
38D GLU 2.9 9.3 + - - -
69D GLY 3.6 4.7 - - - -
70D VAL* 3.9 11.4 - - + +
94D ALA 4.2 0.6 - - - -
95D TYR* 1.3 76.1 - - - +
97D LEU* 1.3 58.9 + - - +
98D ARG 3.3 18.6 - - - +
100D THR* 4.2 1.1 - - + -
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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