Contacts of the strand formed by residues 62 - 69 (chain G) in PDB entry 1M06
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 GLY 62 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26G PRO* 4.2 0.4 - - - -
27G ALA 3.1 16.8 - - - -
28G ALA* 4.1 2.9 - - - -
29G PRO* 5.2 2.7 - - - -
61G ASP* 1.3 79.4 + - - +
63G SER* 1.3 65.3 + - - -
158G SER* 3.1 1.7 - - - -
159G SER 2.9 35.3 + - - +
162G TRP* 3.0 12.0 + - - -
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Residues in contact with SER 63 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26G PRO* 3.7 6.3 - - - +
27G ALA* 2.8 34.8 + - - +
29G PRO* 5.3 5.2 - - - +
33G ILE* 3.6 18.2 - - - +
34G PRO* 4.4 2.1 - - - +
62G GLY* 1.3 71.7 - - - -
64G PHE* 1.3 61.1 + - - +
156G ILE* 3.6 17.9 - - - +
157G CYS 3.0 14.4 - - - -
158G SER* 2.8 29.9 + - - -
162G TRP* 4.4 0.7 - - - +
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Residues in contact with PHE 64 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24G VAL* 3.9 18.6 - - + -
26G PRO* 4.8 3.1 - - + -
33G ILE* 3.8 1.1 - - - -
34G PRO* 3.8 17.3 - - + +
36G ILE* 3.2 33.0 - - + -
50G LEU* 4.1 21.1 - - + -
54G MET* 3.6 31.0 - - + -
63G SER* 1.3 75.8 - - - +
65G ILE* 1.3 66.6 + - - +
66G VAL* 4.7 7.6 - - + -
87G LEU* 4.5 7.4 - - + -
89G PHE* 4.7 2.7 - + - -
155G VAL 4.3 0.2 - - - +
156G ILE* 3.5 2.4 - - - +
157G CYS* 2.9 72.6 + - + -
162G TRP* 3.7 8.1 - + - -
171G ILE* 5.8 0.9 - - + -
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Residues in contact with ILE 65 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33G ILE* 3.3 25.4 - - + -
34G PRO 2.9 13.4 + - - +
35G VAL* 3.4 8.2 - - + +
36G ILE* 3.1 31.0 + - - +
64G PHE* 1.3 78.0 - - - +
66G VAL* 1.3 80.2 + - - +
67G ALA* 4.0 13.5 - - + +
100G VAL* 4.3 21.8 - - + -
102G PHE* 4.5 6.3 - - + -
112G ILE* 3.9 23.1 - - + -
117G VAL* 4.4 11.2 - - + -
155G VAL 3.7 6.5 - - - +
156G ILE* 3.8 21.1 - - + -
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Residues in contact with VAL 66 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36G ILE* 4.4 18.4 - - + -
37G ASN* 3.6 8.7 - - - +
46G ALA* 6.2 0.7 - - + -
48G VAL* 3.4 41.7 - - + -
50G LEU* 5.5 0.7 - - + -
64G PHE* 4.7 8.1 - - + -
65G ILE* 1.3 77.2 - - - +
67G ALA* 1.3 63.1 + - - +
154G GLY* 3.2 2.9 - - - -
155G VAL* 3.0 31.0 + - + +
171G ILE* 3.7 41.3 - - + +
173G THR* 5.1 6.6 - - + +
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Residues in contact with ALA 67 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35G VAL* 3.9 21.3 - - + +
37G ASN* 3.1 15.1 + - - +
40G SER* 3.1 18.7 + - - +
41G ILE* 3.9 8.5 - - - +
46G ALA* 5.2 0.3 - - - +
65G ILE* 4.0 3.7 + - + +
66G VAL* 1.3 78.6 - - - +
68G MET* 1.3 65.4 + - - +
102G PHE* 3.9 26.2 - - + -
152G PHE* 4.7 5.8 - - + -
153G VAL 3.5 9.4 - - - +
154G GLY* 4.1 0.2 - - - -
173G THR* 5.7 0.4 - - - -
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Residues in contact with MET 68 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40G SER* 4.2 2.0 - - - -
41G ILE* 3.7 12.6 - - + +
44G GLU* 2.6 46.3 - - - +
45G ARG 2.9 12.3 - - - +
46G ALA* 1.8 64.6 - - + +
67G ALA* 1.3 78.4 - - - +
69G LYS* 1.3 58.7 + - - +
152G PHE* 3.6 5.3 - - - -
153G VAL 2.7 37.6 + - - +
173G THR* 2.8 40.4 - - + +
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Residues in contact with LYS 69 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40G SER* 4.9 1.1 + - - +
41G ILE 3.4 7.2 + - - +
42G THR* 2.7 53.3 + - + +
44G GLU* 3.0 8.6 - - - +
68G MET* 1.3 73.7 - - - +
70G VAL* 1.3 71.8 + - - +
71G ASP* 6.0 0.7 - - - +
72G THR* 6.3 0.4 - - - -
107G GLU* 3.6 34.4 + - - +
150G ASN* 3.8 21.1 + - + +
151G VAL 3.7 11.0 - - - +
152G PHE* 3.8 25.1 - - + -
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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