Contacts of the strand formed by residues 90 - 99 (chain A) in PDB entry 3MWZ
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 90 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A VAL* 4.5 20.8 - - + +
65A LYS* 3.9 32.1 + - + +
66A VAL 3.4 5.8 - - - +
67A ALA* 4.2 11.6 - - + +
85A ASN 5.4 1.4 + - - -
86A ALA* 4.3 18.6 + - - +
88A ALA 3.3 12.0 + - - +
89A ALA* 1.3 74.1 - - - +
91A ARG* 1.3 63.8 + - - +
115A ALA* 3.5 17.5 - - - +
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Residues in contact with ARG 91 (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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31A TRP* 3.4 24.9 - - - -
42A ASP* 2.6 37.4 + - - -
65A LYS* 3.5 11.6 - - - +
66A VAL* 2.9 50.3 + - - +
67A ALA* 4.7 4.0 - - - +
68A GLU 5.0 0.6 - - - +
89A ALA 4.9 4.4 + - - -
90A GLN* 1.3 77.1 - - - +
92A THR* 1.3 60.5 + - - +
93A CYS* 3.7 8.7 + - - -
112A CYS* 3.4 20.0 - - - +
113A ALA 3.2 24.2 - - - +
114A ALA* 4.3 2.0 - - - +
115A ALA* 4.1 17.0 - - - +
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Residues in contact with THR 92 (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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48A MSE 3.7 20.1 - - + +
63A THR* 3.8 18.4 - - + -
64A LEU 3.3 4.5 - - - +
65A LYS* 2.8 29.0 + - - +
91A ARG* 1.3 72.9 - - - +
93A CYS* 1.3 65.8 + - - +
94A THR* 4.8 3.4 - - - +
111A GLU 4.2 0.2 - - - +
112A CYS* 3.6 0.9 - - - -
113A ALA* 2.8 40.8 + - + +
114A ALA 5.4 0.2 + - - -
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Residues in contact with CYS 93 (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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62A LEU 3.7 0.5 - - - +
63A THR* 3.6 2.6 - - - +
64A LEU* 2.8 35.7 + - + +
66A VAL* 3.8 30.7 - - + -
91A ARG* 3.8 7.9 - - - -
92A THR* 1.3 75.9 - - - +
94A THR* 1.3 64.0 + - - +
110A PHE* 3.8 18.6 - - + -
111A GLU 3.2 5.4 - - - +
112A CYS* 2.1 47.3 - - - -
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Residues in contact with THR 94 (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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61A ARG* 3.9 31.0 - - + -
62A LEU 3.4 6.3 - - - +
63A THR* 4.2 18.4 + - - +
92A THR* 4.8 3.6 - - - +
93A CYS* 1.3 75.9 + - - +
95A THR* 1.3 64.4 + - - +
96A VAL* 5.5 2.0 - - + -
109A SER* 4.5 2.1 + - - -
110A PHE* 3.6 1.4 + - - -
111A GLU* 2.8 41.9 + - - +
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Residues in contact with THR 95 (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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27A ALA* 3.9 16.8 - - + +
60A TYR 3.4 0.9 - - - +
61A ARG* 3.3 3.5 - - - +
62A LEU* 2.8 60.0 + - + +
64A LEU* 4.1 17.0 - - + -
94A THR* 1.3 75.6 - - - +
96A VAL* 1.3 64.5 + - - +
97A ILE* 4.1 4.2 - - + +
107A ILE* 3.7 9.4 - - - +
109A SER 2.8 16.9 + - - -
110A PHE* 3.4 25.1 - - + -
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Residues in contact with VAL 96 (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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9A TYR* 3.7 17.0 - - - +
59A ASN* 3.7 36.3 - - + +
60A TYR 3.3 4.3 - - - +
61A ARG* 4.0 17.9 - - + -
94A THR* 5.5 2.0 - - + -
95A THR* 1.3 75.0 - - - +
97A ILE* 1.3 58.8 + - - +
107A ILE* 3.7 1.2 - - - -
108A ASN* 2.8 45.8 + - + +
109A SER* 3.0 27.9 + - - +
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Residues in contact with ILE 97 (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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23A MSE 3.6 49.4 - - + +
26A TYR* 4.3 7.9 - - + -
27A ALA* 3.9 14.6 - - + -
58A THR 3.6 1.2 - - - +
59A ASN* 3.4 2.4 - - - -
60A TYR* 2.8 44.0 + - + +
62A LEU* 3.9 18.6 - - + -
95A THR* 4.1 11.9 - - + +
96A VAL* 1.3 75.4 - - - +
98A TYR* 1.3 61.5 + - - +
105A LYS* 4.1 30.3 - - + -
106A SER 3.3 15.5 - - - +
107A ILE* 4.7 2.9 - - + -
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Residues in contact with TYR 98 (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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1A MSE 3.3 49.0 + - - +
2A GLU* 3.8 25.1 + - - -
3A LEU* 3.9 10.5 - - + -
57A GLY* 4.3 12.9 + - - -
58A THR 3.6 6.5 - - - -
59A ASN* 3.5 20.6 - - - +
96A VAL 4.0 2.2 + - - -
97A ILE* 1.3 72.1 - - - +
99A ARG* 1.3 67.3 + - - +
100A ASN* 3.4 36.3 - - + +
101A MSE 4.9 0.2 + - - -
104A GLU 3.7 1.8 - - - +
105A LYS* 3.3 2.0 - - - -
106A SER* 2.9 37.9 + - - +
108A ASN* 4.5 7.9 - - + -
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Residues in contact with ARG 99 (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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19A GLU* 2.8 44.2 + - - -
23A MSE 3.8 10.3 - - - -
57A GLY* 3.1 0.7 - - - -
58A THR* 2.8 42.6 + - - +
60A TYR* 2.9 41.7 + - + -
97A ILE* 3.9 1.7 + - + -
98A TYR* 1.3 76.0 - - - +
100A ASN* 1.3 74.9 + - - +
103A GLY* 3.5 31.8 + - - -
104A GLU 3.3 3.4 - - - +
105A LYS* 4.2 23.3 - - + +
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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