Contacts of the strand formed by residues 63 - 70 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A ASP* 3.7 25.1 - - + +
52A ALA 3.4 9.2 - - - +
53A ARG* 3.7 33.2 - - + +
54A TYR* 4.3 0.7 - - - -
59A ASP 3.6 23.3 - - - +
61A SER* 3.1 17.9 + - - +
62A LEU* 1.3 77.1 - - - +
64A ASP* 1.3 71.1 + - - +
85A ASN* 2.6 33.3 + - - +
92A SER 3.2 4.0 + - - -
93A ARG* 3.8 15.7 - - + -
94A VAL 3.4 21.3 + - - +
95A VAL* 4.5 6.3 - - + -
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Residues in contact with ASP 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A ASP* 3.8 0.3 - - - -
52A ALA* 2.9 31.0 + - + +
54A TYR* 2.6 37.0 + - + +
63A ILE* 1.3 77.3 - - - +
65A THR* 1.3 60.1 + - - +
81A ILE* 4.0 16.8 - - + +
83A ILE 3.5 5.8 - - - +
84A LYS* 3.7 8.1 - - - -
85A ASN* 2.9 28.9 + - - +
87A ARG* 2.7 33.4 + - - -
94A VAL* 3.9 4.0 - - - -
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Residues in contact with THR 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A ILE* 3.8 25.1 - - + -
50A ALA 3.3 11.9 - - - +
51A ASP* 4.8 1.5 + - - +
64A ASP* 1.3 72.0 - - - +
66A VAL* 1.3 61.7 + - - +
81A ILE* 3.7 4.9 - - - +
82A ALA* 2.9 28.1 + - + -
83A ILE* 2.8 29.9 + - - +
94A VAL* 3.7 17.3 + - - +
97A PRO* 3.9 15.5 - - + +
108A VAL* 4.7 7.4 - - + -
110A VAL* 3.8 12.8 - - - +
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Residues in contact with VAL 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A PHE* 3.8 24.2 - - + -
18A VAL* 3.6 24.2 - - + -
34A PHE* 4.1 10.1 - - + -
49A ILE* 3.1 6.8 - - - +
50A ALA* 2.6 49.0 + - + +
52A ALA* 4.0 17.0 - - + -
64A ASP 3.7 1.0 + - - -
65A THR* 1.3 76.1 - - - +
67A ALA* 1.3 77.3 + - - +
68A LYS* 5.8 0.2 - - - -
79A THR* 4.1 7.4 - - + -
80A GLN 3.2 15.3 - - - +
81A ILE* 3.9 9.2 - - + -
82A ALA* 4.6 0.4 - - - -
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Residues in contact with ALA 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A VAL* 4.7 4.9 - - + -
48A ALA 3.0 9.0 - - - +
49A ILE* 3.8 15.0 - - + -
66A VAL* 1.3 79.2 - - - +
68A LYS* 1.3 66.0 + - - +
78A GLU 3.9 0.2 - - - +
79A THR* 3.6 1.7 - - - -
80A GLN* 3.0 56.1 + - + +
82A ALA* 4.3 3.8 - - + +
151A ILE* 5.5 0.4 - - + -
153A TRP* 4.1 13.5 - - + -
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Residues in contact with LYS 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A LEU* 3.6 40.5 + - + +
11A PHE* 3.5 38.8 - - + +
16A SER* 4.9 10.3 - - - -
17A LYS 4.9 3.2 + - - -
18A VAL* 6.1 0.9 - - - -
34A PHE* 6.1 0.9 - - - -
47A VAL* 3.5 1.7 - - - +
48A ALA 2.8 32.0 + - - +
66A VAL* 5.8 0.4 - - - -
67A ALA* 1.3 78.9 - - - +
69A TYR* 1.3 63.2 + - - +
77A TRP* 3.5 23.8 + - + +
78A GLU 3.0 7.6 - - - +
79A THR* 2.3 43.8 + - + +
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Residues in contact with TYR 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A VAL* 4.3 4.5 - - + -
46A MET 3.2 14.1 - - - +
47A VAL* 4.1 4.7 - - + -
67A ALA* 5.8 0.2 - - + -
68A LYS* 1.3 76.1 - - - +
70A SER* 1.3 60.8 - - - +
71A VAL* 5.3 1.1 - - + -
77A TRP* 3.3 6.3 - - - -
78A GLU* 2.8 73.3 + - + +
79A THR 5.2 0.4 - - - -
80A GLN* 3.7 25.1 + - + -
149A ALA* 3.3 46.3 + - + -
150A SER* 3.9 9.0 + - - -
151A ILE* 3.5 34.2 + - + -
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Residues in contact with SER 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A GLY 4.5 0.5 - - - +
45A VAL* 3.6 2.7 - - - -
46A MET* 2.7 40.6 + - - +
69A TYR* 1.3 73.8 - - - +
71A VAL* 1.3 62.4 + - - +
72A ASP* 2.4 32.2 + - - -
73A ASP 4.8 0.9 + - - -
74A GLY* 3.2 16.9 + - - -
76A THR 2.9 17.5 - - - -
77A TRP* 3.7 16.4 - - - -
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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