Contacts of the strand formed by residues 65 - 72 (chain M) in PDB entry 2ZJR
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 SER 65 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56M ALA 3.7 0.2 - - - +
57M ILE* 2.9 28.6 - - - +
58M ASN* 2.9 21.5 + - - +
63M ARG 4.0 4.9 + - - -
64M LYS* 1.3 79.2 - - - +
66M PHE* 1.3 62.1 + - - +
67M THR* 5.5 0.5 + - - -
80M VAL* 4.5 10.0 - - - +
81M PHE 2.9 24.9 - - - -
82M PRO* 3.9 4.0 - - - -
83M PHE* 3.4 10.6 - - - -
2663X U 3.9 17.0 + - - -
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Residues in contact with PHE 66 (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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24M LEU* 4.5 5.6 - - + -
27M PHE* 4.0 30.1 - + + -
32M THR* 4.9 2.7 - - + -
34M ARG* 2.7 60.1 - - + -
54M VAL* 4.2 6.7 - - + -
56M ALA 3.0 10.1 - - - +
57M ILE* 4.6 4.5 - - + -
58M ASN* 6.3 0.2 - - - +
65M SER* 1.3 77.8 - - - +
67M THR* 1.3 62.9 + - - +
68M VAL* 3.9 28.7 + - + -
79M ARG 3.9 0.5 - - - +
80M VAL* 3.7 1.1 - - - -
81M PHE* 2.8 50.7 + + + +
83M PHE* 3.9 15.9 - + + -
91M VAL* 4.3 11.2 - - + -
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Residues in contact with THR 67 (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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90H ARG* 4.4 9.6 + - - +
54M VAL* 3.7 1.3 - - - +
55M ILE* 2.8 55.7 + - + +
56M ALA* 2.9 23.1 + - + +
58M ASN* 4.7 7.8 + - - -
65M SER* 5.5 0.9 + - - -
66M PHE* 1.3 73.1 - - - +
68M VAL* 1.3 68.0 + - - +
78M GLU* 3.9 13.9 - - + +
79M ARG 3.2 10.8 - - - +
80M VAL* 3.3 19.3 - - + +
105M TYR* 6.1 1.6 - - + -
2664X G 4.9 1.6 + - - -
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Residues in contact with VAL 68 (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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32M THR* 4.7 5.2 - - - -
34M ARG* 5.6 1.6 - - + -
50M PHE* 3.4 32.2 - - + +
52M GLY 3.4 18.4 - - - +
53M VAL 3.2 4.7 - - - +
54M VAL* 3.3 33.0 - - + -
66M PHE* 3.9 13.9 - - + -
67M THR* 1.3 74.9 - - - +
69M ARG* 1.3 59.4 + - - +
78M GLU* 3.3 2.1 - - - -
79M ARG* 2.8 39.4 + - + +
81M PHE* 4.2 19.7 - - + -
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Residues in contact with ARG 69 (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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92H ASP* 2.5 49.5 + - - -
52M GLY* 3.6 2.9 - - - -
53M VAL* 2.9 32.3 + - + +
55M ILE* 3.8 23.6 - - + -
67M THR 4.1 0.8 + - - -
68M VAL* 1.3 72.9 - - - +
70M LYS* 1.3 64.7 + - - +
71M ILE* 4.3 16.3 - - + +
76M GLY* 3.3 20.0 - - - -
77M VAL 3.4 5.4 - - - -
78M GLU* 3.4 35.2 + - + +
107M LEU* 4.4 20.4 + - + +
108M ARG* 4.5 20.0 + - - +
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Residues in contact with LYS 70 (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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132H GLU* 5.2 6.5 + - - -
134H LEU* 6.0 1.5 - - - +
49M ALA 3.7 20.8 + - - -
50M PHE* 3.2 39.6 - - + +
51M GLU* 3.3 31.4 + - - +
52M GLY* 4.7 1.3 - - - -
69M ARG* 1.3 78.2 - - - +
71M ILE* 1.3 69.8 + - - +
72M SER* 4.1 20.0 - - - +
77M VAL* 2.4 50.1 + - - +
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Residues in contact with ILE 71 (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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69M ARG* 4.3 16.2 - - + +
70M LYS* 1.3 82.5 - - - +
72M SER* 1.3 61.1 + - - +
73M PHE 4.0 0.5 + - - -
74M GLY* 4.3 10.8 - - - +
75M GLU 3.6 19.7 - - - +
76M GLY* 3.8 14.6 - - - -
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Residues in contact with SER 72 (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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113H PRO* 3.2 13.7 - - - +
132H GLU* 2.8 26.9 + - - -
134H LEU* 3.9 17.4 - - - +
70M LYS* 3.8 21.6 + - - +
71M ILE* 1.3 74.3 - - - +
73M PHE* 1.3 81.4 + - - +
74M GLY 3.2 1.1 - - - -
75M GLU 3.0 14.3 + - - +
77M VAL* 4.7 1.8 - - - -
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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