Contacts of the strand formed by residues 63 - 70 (chain B) in PDB entry 1MS4
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 ILE 63 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B ASP* 3.8 24.0 - - + +
52B ALA 3.4 8.7 - - - +
53B ARG* 3.7 33.2 - - + +
54B TYR* 4.4 0.4 - - - -
59B ASP 3.5 26.0 - - - +
61B SER* 3.1 17.0 + - - +
62B LEU* 1.3 76.5 - - - +
64B ASP* 1.3 70.3 + - - +
85B ASN* 2.6 23.8 + - - +
92B SER 3.2 4.8 + - - -
93B ARG* 3.6 15.3 - - + -
94B VAL 3.3 30.3 + - - +
95B VAL* 4.5 6.7 - - + -
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Residues in contact with ASP 64 (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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20B PHE* 5.1 0.2 - - - -
52B ALA* 2.7 36.5 + - - +
54B TYR* 2.6 35.4 + - + +
63B ILE* 1.3 79.0 - - - +
65B THR* 1.3 57.6 + - - +
81B ILE* 4.0 17.6 - - + +
83B ILE 3.4 7.4 - - - +
84B LYS* 3.8 7.2 - - - -
85B ASN* 2.9 28.4 + - - +
87B ARG* 2.9 30.6 + - - -
94B VAL* 3.9 3.4 - - - -
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Residues in contact with THR 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B ILE* 3.6 26.0 - - + -
50B ALA 3.3 14.1 - - - +
51B ASP* 4.8 1.2 + - - +
64B ASP* 1.3 71.2 - - - +
66B VAL* 1.3 58.9 + - - +
81B ILE* 3.6 5.3 - - - +
82B ALA* 2.8 32.7 + - + -
83B ILE* 2.9 27.8 + - - +
94B VAL* 3.7 16.8 + - - +
97B PRO* 3.8 15.7 - - + +
108B VAL* 4.6 6.1 - - + -
110B VAL* 3.8 16.1 - - - +
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Residues in contact with VAL 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B PHE* 3.8 25.6 - - + -
18B VAL* 3.7 23.1 - - + -
34B PHE* 3.9 19.3 - - + -
48B ALA 3.8 0.6 - - - +
49B ILE* 3.0 6.4 - - - +
50B ALA* 2.6 55.2 + - + +
52B ALA* 4.0 16.2 - - + -
64B ASP 3.6 1.2 + - - -
65B THR* 1.3 74.1 - - - +
67B ALA* 1.3 70.5 + - - +
79B THR* 4.2 6.3 - - + -
80B GLN 3.4 15.3 - - - +
81B ILE* 4.0 3.6 - - + -
82B ALA* 4.8 0.2 - - - -
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Residues in contact with ALA 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B VAL* 4.5 7.2 - - + -
48B ALA 3.2 5.4 - - - +
49B ILE* 3.9 16.6 - - + -
65B THR 4.2 0.6 + - - -
66B VAL* 1.3 75.9 - - - +
68B LYS* 1.3 62.6 + - - +
69B TYR 4.4 0.2 + - - -
78B GLU 3.9 0.5 - - - +
79B THR* 3.6 1.4 - - - -
80B GLN* 2.9 58.2 + - + +
82B ALA* 4.3 4.7 - - + +
151B ILE* 5.7 0.2 - - + -
153B TRP* 4.1 14.1 - - + -
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Residues in contact with LYS 68 (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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10B LEU* 3.7 35.1 + - + -
11B PHE* 3.4 46.2 - - + +
16B SER* 4.9 10.3 + - - -
17B LYS 4.8 4.2 + - - -
18B VAL* 6.0 0.7 - - - -
34B PHE* 5.8 1.1 - - - -
47B VAL* 3.5 3.4 - - - +
48B ALA* 2.7 35.4 + - - +
66B VAL* 5.4 0.9 - - - -
67B ALA* 1.3 78.7 - - - +
69B TYR* 1.3 59.1 + - - +
77B TRP* 3.6 19.9 - - + +
78B GLU 3.0 9.4 - - - +
79B THR* 2.4 46.4 + - + +
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Residues in contact with TYR 69 (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 VAL* 4.3 5.4 - - + -
46B MET 3.1 13.5 - - - +
47B VAL* 4.2 5.4 - - + -
68B LYS* 1.3 75.9 - - - +
70B SER* 1.3 60.5 + - - +
71B VAL* 5.3 1.8 - - + -
77B TRP* 3.4 6.1 - - - -
78B GLU* 3.0 71.4 + - + +
79B THR 5.2 0.4 - - - -
80B GLN* 3.7 29.0 + - - -
149B ALA* 3.3 45.2 + - + -
150B SER* 4.1 6.7 - - - -
151B ILE* 3.7 34.7 + - + -
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Residues in contact with SER 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B GLY 4.5 0.2 - - - +
45B VAL* 3.6 3.0 - - - -
46B MET* 2.8 43.2 + - - +
69B TYR* 1.3 73.6 - - - +
71B VAL* 1.3 61.4 + - - +
72B ASP* 2.4 34.0 + - - -
73B ASP 4.9 0.7 + - - -
74B GLY* 3.1 17.7 + - - -
76B THR 2.9 15.8 + - - -
77B TRP* 3.7 17.7 - - - -
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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