Contacts of the strand formed by residues 86 - 96 (chain B) in PDB entry 5IXG
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 GLN 86 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B THR* 3.5 26.2 - - + +
57B THR 3.2 8.3 - - - +
58B ASP* 3.1 25.5 + - - +
59B ILE* 4.2 6.5 - - - +
84B PHE* 3.2 12.7 - - - +
85B PRO* 1.3 93.6 - - + +
87B ALA* 1.3 61.0 + - - +
88B ASN* 6.1 0.2 - - + -
108B THR* 4.4 3.5 - - - +
109B LEU* 5.1 0.2 - - - -
110B HIS 5.0 5.4 + - - -
111B GLY 5.7 0.5 + - - -
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Residues in contact with ALA 87 (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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56B THR* 3.3 5.9 - - - +
57B THR* 2.9 33.2 + - - +
59B ILE* 4.4 2.2 - - + +
86B GLN* 1.3 74.5 - - - +
88B ASN* 1.3 60.3 + - - +
107B LEU* 4.4 4.5 - - + -
108B THR 3.2 13.5 - - - +
109B LEU* 4.0 12.8 - - + -
201B OTP 4.0 41.1 - - + +
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Residues in contact with ASN 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B ASP* 3.1 22.6 + - - -
55B VAL 3.0 19.0 + - - -
56B THR* 3.1 17.5 + - + +
86B GLN* 6.1 0.2 - - + -
87B ALA* 1.3 75.3 - - - +
89B TYR* 1.3 61.5 + - - +
90B LYS* 2.7 33.3 + - - +
106B ASN 3.8 1.2 - - - +
107B LEU* 3.5 3.7 - - - -
108B THR* 2.8 49.5 + - - -
201B OTP 4.6 0.4 - - - -
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Residues in contact with TYR 89 (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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53B VAL* 4.4 8.7 - - + -
54B ASP* 3.4 3.1 - - - -
55B VAL* 2.8 53.6 + - + +
88B ASN* 1.3 74.8 - - - +
90B LYS* 1.3 74.4 + - - +
91B GLY 4.1 0.4 - - - -
103B VAL* 3.1 39.1 + - + +
105B GLY 3.4 6.1 + - - -
106B ASN 3.4 24.9 - - - -
107B LEU* 3.9 9.4 - - + -
116B LEU* 2.9 49.0 + - + -
118B LEU* 3.7 24.7 - - + +
201B OTP 3.9 14.8 - - + +
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Residues in contact with LYS 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B VAL 3.2 9.0 - - - +
54B ASP* 3.5 23.7 + - + +
88B ASN* 2.7 37.8 + - - +
89B TYR* 1.3 79.7 - - - +
91B GLY* 1.3 58.2 + - - +
105B GLY* 3.2 1.4 - - - -
106B ASN* 2.9 33.9 + - + +
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Residues in contact with GLY 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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52B THR* 3.2 9.1 - - - -
53B VAL 3.0 30.2 + - - +
89B TYR* 4.1 2.8 - - - -
90B LYS* 1.3 76.0 - - - +
92B THR* 1.3 63.0 + - - -
103B VAL* 3.6 13.9 - - - -
104B VAL 3.3 12.1 - - - -
105B GLY* 3.7 3.6 - - - -
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Residues in contact with THR 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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50B THR* 4.1 10.5 - - - +
51B GLY 3.5 11.9 - - - +
52B THR* 4.4 8.6 - - + +
91B GLY* 1.3 74.8 + - - -
93B ILE* 1.3 72.7 + - - +
94B LYS* 3.6 26.3 + - + +
103B VAL* 3.3 3.0 - - - +
104B VAL 2.9 33.8 + - - -
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Residues in contact with ILE 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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42B VAL* 4.2 7.4 - - + -
43B THR 4.0 1.8 - - - +
44B LEU* 3.9 18.6 - - + -
49B LYS 4.3 1.6 - - - +
50B THR* 3.9 9.7 + - - -
51B GLY* 2.8 32.5 + - - +
52B THR* 3.8 18.2 - - - +
53B VAL* 3.9 27.1 - - + -
92B THR* 1.3 77.7 - - - +
94B LYS* 1.3 67.6 + - - +
95B PHE* 4.0 11.8 - - + -
100B PRO* 3.7 29.6 - - + -
102B SER 3.4 8.7 - - - +
103B VAL* 4.2 7.4 - - + -
120B ILE* 4.6 3.6 - - + -
201B OTP 4.6 9.2 - - + -
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Residues in contact with LYS 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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49B LYS 5.3 0.7 - - - -
92B THR* 3.9 32.5 - - - +
93B ILE* 1.3 77.8 - - - +
95B PHE* 1.3 65.6 + - - +
100B PRO* 3.5 3.6 - - - +
101B VAL* 2.8 26.2 + - + -
102B SER* 2.9 30.8 + - - +
104B VAL* 4.1 24.9 - - + -
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Residues in contact with PHE 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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44B LEU* 3.8 19.1 - - + -
46B ARG* 4.0 32.5 - - + -
49B LYS* 3.4 40.6 + - + -
50B THR 3.4 26.9 - - - -
93B ILE* 4.0 15.5 - - + -
94B LYS* 1.3 82.1 - - - +
96B ASP* 1.3 63.8 + - - +
97B GLY 4.1 6.5 - - - +
98B ASP 3.7 16.8 - - - -
99B LYS 3.3 19.3 - - - -
100B PRO* 3.8 16.8 - - + -
101B VAL* 3.9 2.8 - - - +
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Residues in contact with ASP 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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95B PHE* 1.3 74.6 - - - +
97B GLY* 1.3 63.4 + - - +
98B ASP 3.6 0.9 + - - -
99B LYS* 3.0 16.8 + - - +
101B VAL* 3.5 28.7 - - + +
145C SER* 5.4 2.0 - - - -
159C PHE 4.4 0.5 - - - +
160C LYS* 3.4 25.9 + - + +
161C MET* 2.8 34.4 + - - +
162C LYS* 3.0 35.3 + - - +
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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