Contacts of the strand formed by residues 82 - 94 (chain A) in PDB entry 1MM5
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 TRP 82 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74A ALA* 4.9 12.3 - - + -
75A PHE 3.2 4.5 - - - +
76A LYS* 4.7 14.0 - - + +
80A ASN* 4.2 21.2 + - - -
81A LYS* 1.3 87.5 - - - +
83A GLU* 1.3 61.5 + - - +
84A PRO* 3.2 12.4 - - + +
114A ALA 4.9 0.5 - - - +
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Residues in contact with GLU 83 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73A MET* 3.6 1.0 - - - +
74A ALA* 3.3 18.0 - - - -
75A PHE* 2.9 28.5 + - + +
77A ASP* 4.8 6.7 - - - +
81A LYS* 3.2 29.0 - - + +
82A TRP* 1.3 71.1 - - - +
84A PRO* 1.3 66.3 - - - +
85A ILE* 3.7 10.0 + - + +
113A THR* 2.8 29.2 - - + +
114A ALA 3.1 7.3 - - - +
115A ARG* 2.9 40.7 + - - +
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Residues in contact with PRO 84 (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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73A MET 3.3 9.0 - - - +
74A ALA* 4.5 4.2 - - + -
82A TRP* 3.2 13.7 - - + +
83A GLU* 1.3 83.5 - - - +
85A ILE* 1.3 69.8 + - - +
112A VAL 3.2 9.8 - - - +
114A ALA* 3.3 43.5 + - + +
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Residues in contact with ILE 85 (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 TYR* 5.8 0.2 - - - +
71A TYR* 3.4 7.8 - - + +
72A ALA* 3.2 25.3 - - - -
73A MET* 3.0 44.2 + - + -
83A GLU* 3.7 9.0 - - + +
84A PRO* 1.3 87.5 - - - +
86A ALA* 1.3 66.9 + - - +
87A GLY 5.1 0.2 - - - +
111A GLY* 4.6 8.5 - - - -
112A VAL 3.4 12.3 - - - +
113A THR* 3.3 34.3 - - + +
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Residues in contact with ALA 86 (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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70A LEU* 6.1 2.0 - - + -
71A TYR* 3.2 9.6 - - - +
72A ALA* 6.0 0.4 - - + -
85A ILE* 1.3 79.2 - - - +
87A GLY* 1.3 61.4 + - - +
88A TYR* 5.5 0.2 - - - +
110A ALA 3.2 2.9 - - - +
111A GLY* 3.2 3.2 - - - -
112A VAL* 2.8 50.7 + - + +
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Residues in contact with GLY 87 (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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69A GLY 3.6 5.6 - - - -
70A LEU* 2.9 31.0 - - - +
71A TYR* 3.3 37.4 + - - +
86A ALA* 1.3 73.6 - - - +
88A TYR* 1.3 61.9 + - - +
109A THR* 3.7 1.6 - - - -
110A ALA 3.2 8.7 - - - -
111A GLY* 4.0 1.1 - - - -
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Residues in contact with TYR 88 (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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68A HIS* 3.7 27.7 + + - -
69A GLY 3.3 4.5 - - - -
70A LEU* 3.7 26.7 - - + -
86A ALA 5.5 0.2 - - - +
87A GLY* 1.3 73.7 - - - +
89A GLY* 1.3 64.8 + - - +
109A THR* 3.2 6.5 - - - +
110A ALA* 3.1 30.0 + - + +
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Residues in contact with GLY 89 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68A HIS* 4.0 11.6 + - - -
69A GLY 3.3 27.5 + - - -
88A TYR* 1.3 83.1 - - - +
90A TRP* 1.3 67.0 + - - +
91A GLU* 4.8 2.2 - - - -
108A PHE 3.4 14.6 - - - -
109A THR* 3.8 3.2 - - - +
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Residues in contact with TRP 90 (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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66A ASN* 3.7 25.6 - - - +
67A TRP 3.7 4.7 - - - -
68A HIS* 6.1 1.6 - - + +
89A GLY* 1.3 76.8 - - - +
91A GLU* 1.3 69.6 + - - +
92A SER* 4.5 15.9 - - - -
106A LEU 5.9 0.2 - - - -
107A GLY* 3.5 3.1 - - - -
108A PHE* 3.1 55.2 + + - +
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Residues in contact with GLU 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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59A SER* 5.4 1.2 + - - -
66A ASN* 4.1 3.7 - - - +
67A TRP* 2.8 61.2 + - + +
69A GLY* 3.4 22.5 + - - -
71A TYR* 4.0 9.3 + - - -
89A GLY 4.8 0.5 - - - -
90A TRP* 1.3 85.8 - - - +
92A SER* 1.3 64.4 + - - +
93A THR* 6.1 0.7 - - - -
106A LEU* 3.7 10.1 - - - +
107A GLY* 3.5 18.2 - - - +
108A PHE 4.1 1.1 - - - +
109A THR* 3.0 21.4 + - - +
129A LEU* 5.1 5.8 - - - +
130A ALA* 5.6 1.9 - - - -
131A SER* 3.8 17.2 + - - -
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Residues in contact with SER 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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65A GLY 4.4 12.4 + - - -
66A ASN* 5.6 0.5 + - - -
90A TRP* 4.5 15.8 - - - -
91A GLU* 1.3 73.0 + - - +
93A THR* 1.3 61.1 + - - +
94A TRP* 4.0 1.7 + - - -
105A GLY* 3.3 19.6 - - - -
106A LEU 2.8 18.3 + - - -
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Residues in contact with THR 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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65A GLY 5.8 0.2 + - - -
67A TRP* 3.1 54.5 - - + -
91A GLU* 3.9 2.1 + - - -
92A SER* 1.3 72.5 - - - +
94A TRP* 1.3 67.3 + - - +
95A ARG* 3.9 20.9 + - + +
103A HIS* 3.4 32.1 + - - +
104A LEU 3.9 7.9 + - - -
105A GLY* 4.1 3.6 - - - -
131A SER* 5.5 5.8 - - - -
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Residues in contact with TRP 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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92A SER* 4.0 2.3 + - - +
93A THR* 1.3 80.9 + - - +
95A ARG* 1.3 95.8 + - - +
96A PRO* 4.3 0.7 - - - +
103A HIS* 3.8 5.5 - - - -
104A LEU* 2.9 38.0 + - + +
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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