Contacts of the strand formed by residues 106 - 116 (chain B) in PDB entry 4MSP
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 LEU 106 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36B TYR 3.5 3.8 - - - +
37B LEU* 4.0 10.5 - - + -
44B PHE* 4.0 9.4 - - + -
66B LEU* 3.9 28.5 - - + -
84B LEU 3.6 1.0 - - - +
85B ILE* 3.4 3.6 - - - +
86B ILE* 2.7 44.2 + - + +
91B GLY* 4.1 13.2 - - - -
92B TYR* 3.9 20.2 - - + +
100B ILE* 3.7 28.3 - - + -
104B SER* 3.8 14.4 - - - +
105B THR* 1.3 80.9 - - - +
107B ILE* 1.3 63.5 + - - +
108B PHE* 3.8 17.0 - - + -
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Residues in contact with ILE 107 (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 GLY* 3.5 1.4 - - - -
36B TYR* 2.8 53.3 + - + +
37B LEU 5.2 0.9 - - - +
38B GLU* 3.9 40.8 - - + +
41B GLY* 6.5 0.4 - - - -
83B LYS* 3.9 31.4 - - + -
84B LEU 3.3 7.6 - - - +
85B ILE* 4.4 12.3 - - + -
106B LEU* 1.3 78.9 - - - +
108B PHE* 1.3 66.0 + - - +
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Residues in contact with PHE 108 (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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33B TYR* 3.7 32.8 - + - -
34B GLU 3.3 7.2 - - - -
35B GLY* 3.8 2.0 - - - -
36B TYR* 5.6 0.4 - - - -
44B PHE* 3.6 27.6 - + - -
66B LEU* 3.8 22.2 - - + -
69B TRP* 3.5 37.2 - + - -
82B ARG 3.6 0.4 - - - +
83B LYS* 3.1 10.7 - - - +
84B LEU* 2.9 34.3 + - + +
86B ILE* 3.7 16.6 - - + -
92B TYR* 5.6 0.9 - + - -
106B LEU* 3.8 22.7 - - + -
107B ILE* 1.3 79.2 - - - +
109B ASN* 1.3 59.0 + - - +
110B ILE* 3.8 18.4 - - + -
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Residues in contact with ASN 109 (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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13B LEU* 3.5 25.9 - - - +
33B TYR* 3.1 4.9 - - - -
34B GLU* 2.9 56.4 + - + +
36B TYR* 4.9 6.9 - - + -
81B LYS* 5.0 5.4 - - - +
82B ARG 3.7 2.1 - - - +
83B LYS* 4.7 1.3 - - + +
108B PHE* 1.3 71.7 - - - +
110B ILE* 1.3 63.3 + - - +
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Residues in contact with ILE 110 (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 VAL* 3.9 25.1 - - + -
32B HIS 3.5 8.3 - - - +
33B TYR* 3.7 13.7 - - + -
69B TRP* 3.7 30.7 - - + -
73B LEU* 3.9 24.5 - - + -
76B MET* 3.7 6.9 - - + +
81B LYS* 3.2 6.5 - - - -
82B ARG 2.8 41.2 + - - +
84B LEU* 3.7 26.5 - - + -
108B PHE* 3.8 12.6 - - + -
109B ASN* 1.3 80.9 + - - +
111B ASP* 1.3 63.9 + - - +
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Residues in contact with ASP 111 (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 VAL* 3.2 7.8 - - - -
32B HIS* 2.9 41.3 + - + +
48B HIS* 6.2 0.6 - - + -
79B GLY* 4.5 3.5 - - - -
80B GLU 3.5 10.0 - - - +
81B LYS* 3.6 35.6 + - + +
110B ILE* 1.3 74.4 - - - +
112B LEU* 1.3 66.8 + - - +
113B LEU* 3.4 18.9 - - + +
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Residues in contact with LEU 112 (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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23B THR* 3.8 15.9 - - + -
29B MET* 3.7 26.2 - - + -
30B LEU 3.6 10.3 - - - +
31B VAL* 4.0 3.4 - - + -
76B MET* 3.7 36.2 - - + +
77B CYS 3.4 31.6 - - - +
78B VAL* 4.1 4.3 - - - -
79B GLY* 2.8 31.4 + - - -
80B GLU 3.0 8.5 + - - +
111B ASP* 1.3 73.9 + - - +
113B LEU* 1.3 58.8 + - - +
114B GLU 3.4 26.2 - - - +
115B ILE* 3.8 7.9 - - + -
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Residues in contact with LEU 113 (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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30B LEU* 2.8 26.2 + - + +
32B HIS* 3.9 25.8 - - + +
55B PRO* 3.8 31.6 - - + -
78B VAL* 3.3 19.0 - - - +
111B ASP* 3.4 36.3 - - + +
112B LEU* 1.3 76.7 - - - +
114B GLU* 1.3 61.1 + - - +
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Residues in contact with GLU 114 (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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28B LEU 3.7 0.2 - - - +
29B MET* 3.5 1.0 - - - -
30B LEU* 2.9 45.3 + - + +
57B TRP* 4.1 4.9 - - + -
78B VAL* 3.7 8.0 - - + +
112B LEU* 3.4 8.0 - - - +
113B LEU* 1.3 82.2 - - - +
115B ILE* 1.3 75.1 + - - +
116B ARG* 2.7 47.6 + - + +
204B PGO 4.9 6.4 + - - -
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Residues in contact with ILE 115 (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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21B ARG* 3.7 51.0 + - + +
23B THR* 3.6 24.9 - - + +
27B ASP* 3.7 32.5 - - + +
28B LEU 3.4 4.7 - - - +
29B MET* 5.3 0.2 - - + -
76B MET 3.7 13.2 - - - +
78B VAL* 3.9 16.0 - - + +
112B LEU* 3.8 18.4 - - + -
114B GLU* 1.3 83.3 - - - +
116B ARG* 1.3 70.2 + - - +
204B PGO 3.6 10.2 + - - -
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Residues in contact with ARG 116 (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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21B ARG* 4.1 4.5 - - - +
27B ASP* 3.5 2.4 - - - -
28B LEU* 2.7 49.8 + - + +
57B TRP* 3.4 22.7 - - + -
114B GLU* 2.7 36.3 + - - +
115B ILE* 1.3 79.5 - - - +
117B ASN* 1.3 63.1 + - - +
204B PGO 4.0 21.2 + - - +
207B PGO 3.5 35.7 + - - +
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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