Contacts of the strand formed by residues 89 - 96 (chain B) in PDB entry 2XN9
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 ALA 89 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38B ARG* 3.6 22.7 - - + +
39B GLN 3.8 6.1 - - - +
40B ASP* 3.7 9.0 - - - +
87B PRO 3.2 3.6 + - - -
88B THR* 1.3 78.5 - - - +
90B PHE* 1.3 63.6 + - - +
91B TYR* 3.6 24.4 - - + -
110B ARG* 3.9 6.8 - - - -
111B LEU 3.0 31.3 + - - +
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Residues in contact with PHE 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A GLN* 4.1 0.2 - - - -
40A GLY* 3.5 35.9 - - - -
41A GLU 3.9 11.2 - - - -
11B LYS 5.7 0.2 - - - -
38B ARG* 3.6 2.8 - - - -
39B GLN* 2.9 64.5 + - + +
89B ALA* 1.3 74.7 - - - +
91B TYR* 1.3 58.9 + - - +
92B LEU* 3.7 26.2 + - + -
107B PRO 3.6 2.7 - - - -
108B GLY* 3.5 18.4 - - - -
109B THR 3.6 27.1 - - - -
110B ARG* 4.1 19.5 - - + -
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Residues in contact with TYR 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B GLN* 3.0 9.0 + - - -
23B LEU* 3.4 29.4 - - + -
36B TRP* 3.9 5.6 - - + -
37B TYR 3.5 4.3 - - - -
38B ARG* 3.8 9.6 + - + -
48B ILE* 3.9 15.9 - - + -
66B TYR* 2.8 43.9 + + - -
78B LEU* 3.7 17.9 - - + -
80B VAL* 4.4 6.3 - - + +
87B PRO* 2.6 31.4 + - - +
89B ALA* 3.6 25.8 - - + -
90B PHE* 1.3 73.7 - - - +
92B LEU* 1.3 61.1 + - - +
108B GLY* 3.3 2.5 - - - -
109B THR 2.9 36.2 + - - +
111B LEU* 4.0 14.4 - - + -
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Residues in contact with LEU 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A GLN* 4.1 1.1 - - - +
41A GLU 4.1 0.2 - - - +
42A GLY* 3.9 11.9 - - - -
43A PRO* 3.7 23.3 - - + -
8B GLN* 3.8 0.4 - - - -
36B TRP* 3.3 6.2 - - - -
37B TYR* 2.6 48.8 + - + +
39B GLN* 3.9 15.3 - - + +
45B LEU* 3.8 28.7 - - + -
90B PHE* 3.7 15.4 + - + +
91B TYR* 1.3 74.6 - - - +
93B CYS* 1.3 58.9 + - - +
105B PHE* 4.0 13.2 - - + -
106B GLY 3.5 24.2 - - - +
108B GLY* 3.6 18.8 - - - +
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Residues in contact with CYS 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B ILE* 4.4 2.7 - - + -
8B GLN* 3.0 19.4 + - + +
25B CYS* 2.0 54.7 - - + -
34B MET* 3.8 13.9 - - - -
35B TYR 3.2 12.1 - - - -
36B TRP* 4.1 11.2 - - + -
76B PHE* 4.9 1.1 - - - -
92B LEU* 1.3 73.0 - - - +
94B ALA* 1.3 66.7 + - - +
105B PHE* 3.5 4.7 - - - -
106B GLY 2.9 25.4 + - - -
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Residues in contact with ALA 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B ILE* 5.3 2.5 - - - -
34B MET* 3.1 5.7 - - - +
35B TYR* 2.8 35.3 + - + -
37B TYR* 4.2 4.0 - - + -
93B CYS* 1.3 78.9 - - - +
95B SER* 1.3 63.1 + - - +
103B GLN* 3.5 29.6 - - + +
104B TYR 3.1 15.9 - - - +
105B PHE* 3.8 16.2 - - + -
106B GLY 4.8 0.4 - - - +
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Residues in contact with SER 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B ILE* 4.0 6.1 - - - +
27B GLN* 4.1 20.3 - - - -
29B LEU* 3.7 14.0 - - - +
31B HIS* 2.7 30.7 + - - +
33B ALA 3.1 14.8 - - - -
34B MET* 4.2 2.7 - - - -
35B TYR* 4.2 3.1 - - - -
94B ALA* 1.3 75.6 - - - +
96B SER* 1.3 62.4 + - - +
103B GLN* 3.7 0.9 - - - -
104B TYR* 3.0 32.4 + - - +
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Residues in contact with SER 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B HIS* 3.3 22.6 - - - +
32B ASP 3.9 1.2 + - - -
33B ALA* 3.1 24.4 + - - +
35B TYR* 2.8 27.3 + - - -
95B SER* 1.3 75.8 - - - +
97B SER* 1.3 64.2 + - - +
100B SER 5.1 0.9 - - - -
101B TYR 5.1 1.8 - - - -
102B GLU 3.2 22.9 - - - -
103B GLN* 4.1 9.5 - - - +
104B TYR* 4.7 0.2 - - - -
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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