Contacts of the strand formed by residues 87 - 94 (chain B) in PDB entry 5IXC
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 VAL 87 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B LEU* 3.6 4.6 - - - +
52B SER* 2.9 46.3 + - - +
85B LYS* 4.6 17.7 - - + -
86B ASN* 1.3 76.8 - - - +
88B LEU* 1.3 63.3 + - - +
89B GLU* 3.7 2.5 + - + +
108B LEU* 4.1 33.0 - - + -
109B TYR 3.6 9.9 - - - +
110B ASP* 4.7 10.8 - - + +
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Residues in contact with LEU 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B LEU* 5.1 1.1 - - + -
26B VAL* 4.2 14.6 - - + -
49B LEU* 4.5 4.7 - - + -
50B GLN 3.4 26.9 - - - +
51B LEU* 4.0 11.6 - - + +
78B PHE* 4.1 22.2 - - + -
86B ASN 4.1 0.8 + - - -
87B VAL* 1.3 73.6 - - - +
89B GLU* 1.3 60.7 + - - +
90B LEU* 3.7 24.9 + - + +
107B VAL 3.7 1.0 - - - +
108B LEU* 3.5 2.6 - - - -
109B TYR* 2.8 45.7 + - + +
111B ILE* 4.0 14.1 - - + +
138B PHE* 3.7 31.9 - - + -
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Residues in contact with GLU 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B ILE* 3.6 2.7 - - - +
49B LEU* 3.5 2.1 - - - -
50B GLN* 2.7 73.2 + - + +
52B SER 6.2 0.2 - - - +
87B VAL* 3.7 2.9 + - + +
88B LEU* 1.3 71.9 - - - +
90B LEU* 1.3 64.3 + - - +
91B SER* 3.7 19.1 + - - -
93B TYR* 5.1 4.2 + - - -
106B LYS* 3.4 29.2 + - + +
107B VAL 3.5 4.0 - - - +
108B LEU* 3.5 25.6 - - + -
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Residues in contact with LEU 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B VAL* 5.5 0.2 - - + -
28B VAL* 6.0 0.2 - - + -
47B VAL* 4.5 4.5 - - + -
48B ILE 3.3 3.1 - - - +
49B LEU* 3.4 26.5 - - + -
88B LEU* 3.7 30.7 - - + +
89B GLU* 1.3 75.1 - - - +
91B SER* 1.3 60.7 - - - +
105B PHE* 4.6 1.4 - - - -
106B LYS* 3.8 0.5 - - - -
107B VAL* 2.9 67.1 + - + +
109B TYR* 5.6 2.0 - - + -
124B PHE* 4.3 10.3 - - + -
134B LEU* 3.3 29.2 - - + -
136B VAL* 4.3 18.4 - - + -
138B PHE* 4.6 7.9 - - + -
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Residues in contact with SER 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B TYR 3.9 0.2 - - - +
47B VAL* 3.3 5.6 - - - +
48B ILE* 2.8 40.5 + - - +
89B GLU* 3.7 21.1 + - - -
90B LEU* 1.3 75.6 - - - +
92B ILE* 1.3 65.9 + - - +
93B TYR* 3.3 20.1 + - - -
103B ILE* 3.5 16.4 - - - -
105B PHE* 3.2 13.0 - - - -
106B LYS* 4.2 5.4 - - - -
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Residues in contact with ILE 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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31B ALA* 4.0 16.2 - - + -
34B LEU* 3.9 32.3 - - + -
45B PRO* 4.0 9.9 - - + -
46B TYR 3.3 10.3 - - - +
47B VAL* 4.2 13.5 - - + -
72B TRP* 4.6 2.5 - - + -
91B SER* 1.3 76.9 - - - +
93B TYR* 1.3 62.2 - - - +
103B ILE* 3.7 2.3 - - - -
104B CYS* 2.8 43.0 + - - -
105B PHE* 2.9 47.4 + - + +
133B GLU 5.1 0.2 - - - +
134B LEU* 4.0 14.6 - - + -
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Residues in contact with TYR 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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45B PRO* 3.1 7.6 - - - +
46B TYR* 2.9 57.1 + + + +
48B ILE* 3.7 28.6 - - + +
89B GLU* 5.1 3.6 + - - -
91B SER* 3.3 26.7 + - - -
92B ILE* 1.3 77.5 - - - +
94B ASP* 1.3 59.9 + - - +
95B GLU 3.8 0.9 + - - -
101B ASP* 3.7 23.3 - - + -
102B ASP 3.4 3.8 - - - +
103B ILE* 3.5 40.9 - - + +
104B CYS* 4.3 3.8 - - - -
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Residues in contact with ASP 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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35B ARG 5.3 0.2 - - - +
36B TRP 4.9 0.5 - - - -
37B ALA* 3.5 29.2 + - - +
42B GLU 4.7 0.9 - - - +
43B ALA* 3.6 17.6 - - + +
44B ASP* 3.0 30.4 + - - +
45B PRO* 4.6 0.9 - - - -
93B TYR* 1.3 71.3 - - - +
95B GLU* 1.3 70.4 + - - +
96B ASP* 3.6 3.6 + - - +
101B ASP* 3.6 20.4 - - - +
102B ASP* 2.9 23.6 + - + +
104B CYS* 4.3 8.0 - - + -
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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