Contacts of the strand formed by residues 75 - 81 (chain M) in PDB entry 2ZJP
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 GLU 75 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9H ASP* 5.1 4.4 - - - +
76H ARG* 2.6 45.9 + - - +
91H PHE* 4.6 3.6 - - - +
92H ASP* 4.8 2.0 + - + +
93H ARG* 3.7 44.9 + - - +
95H ALA* 4.4 3.5 - - - +
111H PHE 5.9 0.2 - - - +
112H GLY* 5.9 0.2 - - - -
113H PRO* 4.1 13.9 - - + -
71M ILE* 4.2 5.4 - - - +
72M SER 2.8 23.8 + - - +
73M PHE 2.3 22.5 + - - +
74M GLY* 1.3 77.7 - - - +
76M GLY* 1.3 66.9 + - - +
77M VAL* 3.2 10.6 - - + +
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Residues in contact with GLY 76 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91H PHE* 3.5 2.4 - - - +
92H ASP* 3.0 35.7 + - - +
69M ARG* 4.0 21.5 - - - -
70M LYS 3.4 7.4 - - - -
71M ILE* 4.3 7.6 - - - +
75M GLU* 1.3 69.8 - - - +
77M VAL* 1.3 71.1 + - - +
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Residues in contact with VAL 77 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89H ILE* 4.2 15.0 - - + -
90H ARG 3.8 10.8 - - - +
91H PHE* 3.9 20.0 - - + -
92H ASP* 4.1 1.0 + - - -
113H PRO* 4.3 3.4 - - + -
134H LEU* 3.9 31.9 - - + -
50M PHE* 4.2 11.2 - - + -
69M ARG* 3.4 3.2 - - - +
70M LYS* 2.5 48.2 + - + +
72M SER* 5.0 2.9 - - - +
75M GLU 3.2 13.0 - - - +
76M GLY* 1.3 80.2 - - - +
78M GLU* 1.3 73.3 + - - +
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Residues in contact with GLU 78 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89H ILE* 4.0 3.8 - - - +
90H ARG* 2.6 56.0 + - + +
92H ASP* 4.8 2.3 - - - +
50M PHE* 4.5 0.2 - - - -
55M ILE* 3.6 11.3 - - + +
67M THR* 3.7 5.8 - - + +
68M VAL 3.4 6.7 - - - -
69M ARG* 3.6 33.2 + - + +
77M VAL* 1.3 84.4 - - - +
79M ARG* 1.3 80.5 + - - +
108M ARG* 2.8 48.1 + - - -
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Residues in contact with ARG 79 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83H ARG* 2.7 33.8 - - - +
87H SER* 3.7 14.8 + - - -
88H THR* 3.0 24.9 + - - -
89H ILE* 3.3 25.0 - - - +
90H ARG* 5.5 0.6 - - - +
134H LEU 4.5 14.8 + - - -
36M ASP* 4.7 8.3 + - - -
48M GLN* 4.6 6.9 - - - +
50M PHE* 3.3 44.2 - - + -
66M PHE 3.1 1.7 - - - +
67M THR* 2.9 30.9 - - - +
68M VAL* 3.3 13.1 + - + +
78M GLU* 1.3 92.2 - - - +
80M VAL* 1.3 60.8 + - - +
81M PHE* 3.4 38.9 - - + -
87M LEU* 5.6 1.2 - - - +
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Residues in contact with VAL 80 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86H GLY 5.1 5.6 - - - +
87H SER* 3.4 12.0 - - - -
88H THR* 3.1 51.9 + - + +
90H ARG* 4.3 5.4 - - - +
65M SER* 4.4 11.7 - - - +
66M PHE 3.4 3.6 - - - +
67M THR* 3.9 12.6 - - - +
79M ARG* 1.3 75.3 - - - +
81M PHE* 1.3 65.7 + - - +
82M PRO* 5.2 1.8 - - + -
2663X U 3.7 44.2 - - - +
2664X G 4.1 8.3 - - - +
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Residues in contact with PHE 81 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85H ASP* 5.5 0.7 - - - -
87H SER* 4.7 5.6 - - - -
34M ARG* 2.9 53.4 - - + +
36M ASP* 4.2 16.8 - - + -
50M PHE* 4.4 10.3 - - + -
65M SER* 2.9 12.6 - - - -
66M PHE* 2.4 58.1 + + + +
68M VAL* 4.0 17.9 - - + -
79M ARG* 3.4 57.7 - - + -
80M VAL* 1.3 76.3 - - - +
82M PRO* 1.3 59.6 - - + +
83M PHE 3.8 0.2 - - - -
85M SER* 4.9 1.1 - - - -
87M LEU* 5.1 2.7 - - + -
88M VAL* 3.9 9.9 - - + -
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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