Contacts of the strand formed by residues 39 - 49 (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 39 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34D ILE* 4.6 2.1 - - - +
38D GLU* 1.3 78.2 - - - +
40D LYS* 1.3 63.1 + - - +
41D LEU* 3.7 32.1 - - + -
73D THR* 3.5 28.7 - - + -
93D PRO* 3.8 26.9 - - + -
94D ALA 3.3 13.5 - - - -
95D TYR* 4.3 4.9 - - + +
65F TYR* 3.8 36.6 - + + +
66F LYS* 6.1 6.3 - - + -
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Residues in contact with LYS 40 (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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30D GLU* 4.3 19.2 + - - -
32D VAL* 3.6 29.4 - - + -
33D ALA 5.7 0.7 - - - +
34D ILE* 4.0 21.1 - - + +
39D PHE* 1.3 83.8 - - - +
41D LEU* 1.3 81.5 + - - +
42D VAL* 3.2 12.4 + - + +
43D PRO* 4.6 2.7 - - - -
92D PHE 3.5 0.2 - - - +
94D ALA 2.9 33.3 + - - +
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Residues in contact with LEU 41 (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* 3.7 19.3 - - + -
40D LYS* 1.3 87.5 - - - +
42D VAL* 1.3 64.1 + - - +
43D PRO* 3.5 4.2 - - - +
91D PHE* 3.2 48.5 - - + +
92D PHE 3.9 0.7 - - - -
93D PRO* 4.0 25.8 - - + -
143D DUD 5.6 2.9 - - + +
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Residues in contact with VAL 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D ALA* 4.1 13.2 - - + -
30D GLU 5.5 0.2 - - - +
32D VAL* 4.4 11.7 - - + -
34D ILE* 4.4 8.5 - - + -
40D LYS* 3.5 26.0 - - + +
41D LEU* 1.3 70.9 - - - +
43D PRO* 1.3 80.8 - - + +
44D LEU* 4.1 0.2 - - - +
91D PHE* 3.2 2.8 - - - -
92D PHE* 2.8 44.1 + - - +
94D ALA* 4.0 14.8 - - + -
102D ILE* 4.4 11.4 - - + -
108D ILE* 3.4 28.5 - - + -
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Residues in contact with PRO 43 (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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8D LEU* 5.6 5.4 - - + -
28D ALA* 3.6 5.7 - - - -
29D ALA* 2.9 35.3 + - + -
30D GLU* 3.9 39.5 - - + +
32D VAL* 4.6 0.9 - - + -
40D LYS* 4.6 4.5 - - - -
41D LEU 3.5 9.4 - - - +
42D VAL* 1.3 90.1 - - + +
44D LEU* 1.3 59.5 + - - +
45D GLY* 3.5 2.9 - - - +
90D TRP 3.9 0.2 - - - +
91D PHE* 3.6 26.5 - - + -
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Residues in contact with LEU 44 (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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12D GLN* 4.2 4.3 - - - +
26D LEU* 3.8 22.2 - - + -
27D ARG* 3.1 37.4 + - - +
29D ALA* 3.9 2.5 - - - -
43D PRO* 1.3 75.7 - - - +
45D GLY* 1.3 63.2 + - - +
46D VAL* 3.4 21.0 + - + +
58D VAL* 5.2 3.1 - - + -
90D TRP* 3.0 26.4 + - + +
91D PHE 3.8 20.0 - - - +
92D PHE* 4.1 7.9 - - + +
108D ILE* 3.9 28.7 - - + -
109D CYS* 3.7 25.8 - - - -
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Residues in contact with GLY 45 (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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7D TYR* 3.4 4.5 - - - -
8D LEU* 2.8 41.7 + - - +
12D GLN* 3.9 11.0 - - - +
29D ALA* 3.6 15.8 - - - +
43D PRO* 3.5 5.6 - - - +
44D LEU* 1.3 78.4 - - - +
46D VAL* 1.3 58.1 + - - +
89D PHE* 3.8 8.3 - - - +
90D TRP 4.1 2.8 + - - -
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Residues in contact with VAL 46 (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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5D ILE* 3.9 17.5 - - + -
6D LYS 3.4 5.2 - - - +
7D TYR* 3.6 31.0 - - + -
15D ILE* 4.4 10.3 - - + -
26D LEU* 4.4 8.7 - - + -
44D LEU* 3.8 18.4 - - + +
45D GLY* 1.3 80.2 - - - +
47D ALA* 1.3 54.4 - - - +
48D MET* 3.8 20.2 - - + -
89D PHE* 3.3 7.8 - - - -
90D TRP* 2.8 46.0 + - + -
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Residues in contact with ALA 47 (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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5D ILE* 3.4 0.5 - - - +
6D LYS* 2.9 36.6 + - + +
46D VAL* 1.3 71.4 - - - +
48D MET* 1.3 67.1 + - - +
85D GLY 3.9 5.6 - - - +
86D ASP 4.7 2.2 - - - +
88D ASP 3.2 29.2 - - - +
89D PHE* 4.0 15.5 - - + -
90D TRP* 4.3 1.3 - - - -
128E LEU* 3.6 19.9 - - + +
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Residues in contact with MET 48 (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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3D ILE* 3.6 24.2 - - + -
4D LYS 3.2 10.3 - - - +
5D ILE* 3.9 21.8 - - + -
26D LEU* 4.2 3.6 - - + -
46D VAL* 3.8 22.0 - - + -
47D ALA* 1.3 81.8 - - - +
49D GLU* 1.4 60.4 - - - +
50D LEU* 3.8 8.5 + - + +
79D ILE* 5.9 0.3 - - - +
83D TYR 3.1 23.2 - - - +
84D LYS* 3.4 5.5 - - - -
88D ASP 4.4 1.2 + - - -
90D TRP* 3.7 52.7 + - + +
111D PHE* 3.8 27.6 - - + -
122E LEU* 4.9 0.4 - - - -
128E LEU* 3.7 6.0 - - - +
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Residues in contact with GLU 49 (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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2D GLN 4.4 0.9 - - - +
3D ILE* 3.5 4.9 - - - -
4D LYS* 2.9 63.0 + - + +
48D MET* 1.4 70.4 - - - +
50D LEU* 1.3 71.7 + - - +
84D LYS* 4.0 38.0 + - + +
128E LEU* 4.3 19.0 - - + +
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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