Contacts of the helix formed by residues 70 - 75 (chain S) in PDB entry 1J5E
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 LYS 70 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1319A A 3.2 14.3 + - - -
1320A C 3.0 50.4 + - + +
3S ARG* 6.5 1.3 - - - +
5S LEU* 3.2 30.8 - - - +
36S ARG 3.2 11.8 - - - +
37S ARG 4.2 11.9 - - - +
38S SER 3.4 10.8 - - - +
39S THR* 3.4 29.4 - - + +
68S GLY 4.6 2.5 - - - +
69S HIS* 1.3 82.0 - - - +
71S LEU* 1.3 52.7 - - - +
72S GLY* 2.2 25.3 + - - -
73S GLU* 2.8 22.9 + - - +
74S PHE* 4.3 0.2 - - - -
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Residues in contact with LEU 71 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15S LEU* 4.0 13.7 - - + -
35S SER 3.6 9.0 - - - +
36S ARG* 4.4 5.2 - - - -
38S SER* 2.9 37.5 - - - +
39S THR 4.6 2.2 - - - +
40S ILE* 3.6 30.3 - - + +
44S MET* 4.5 4.9 - - - -
49S ILE* 4.0 28.5 - - + +
51S VAL* 4.0 27.9 - - + +
60S VAL* 5.9 5.8 - - + -
62S ILE* 5.9 3.8 - - + -
70S LYS* 1.3 66.4 - - - +
72S GLY* 1.3 55.1 + - - +
73S GLU 3.0 1.1 - - - -
74S PHE* 2.6 44.7 + - - +
75S ALA 3.6 2.3 + - - -
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Residues in contact with GLY 72 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1320A C 3.1 25.5 - - - +
87M TYR* 5.3 1.6 - - - +
36S ARG* 3.6 28.9 + - - +
51S VAL* 4.4 2.5 - - - -
70S LYS 2.2 16.8 + - - -
71S LEU* 1.3 71.3 - - - +
73S GLU* 1.3 53.8 + - - -
74S PHE 2.8 5.9 + - - -
75S ALA 2.9 21.5 + - - +
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Residues in contact with GLU 73 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1320A C 3.0 40.7 + - - +
85M GLY 3.3 0.7 - - - +
86M CYS* 3.3 12.8 - - - -
87M TYR* 2.7 38.8 + - + +
88M ARG* 5.0 0.9 - - - +
3S ARG* 2.7 45.9 + - - -
69S HIS* 3.3 11.9 + - - -
70S LYS* 2.8 32.4 + - - +
71S LEU 2.9 1.0 + - - -
72S GLY* 1.3 74.3 - - - +
74S PHE* 1.3 70.7 + - + +
75S ALA 3.6 0.4 - - - -
76S PRO 5.7 0.2 - - - -
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Residues in contact with PHE 74 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84M ILE* 4.0 8.7 - - + -
85M GLY* 4.0 17.4 - - - +
86M CYS* 3.8 25.8 - - - -
40S ILE* 4.0 8.3 - - + -
58S VAL* 4.7 1.9 - - - +
60S VAL* 3.5 35.2 - - + +
66S MET* 3.7 35.0 - - + -
69S HIS* 3.2 43.3 - + + -
71S LEU* 2.6 32.4 + - - +
73S GLU* 1.3 90.5 - - + +
75S ALA* 1.3 57.3 + - - +
76S PRO* 3.7 8.9 - - - +
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Residues in contact with ALA 75 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36S ARG* 2.5 41.0 + - - +
51S VAL* 3.6 23.3 - - + -
52S TYR 4.8 0.2 - - - +
53S ASN* 4.1 3.6 - - - +
58S VAL* 3.5 26.5 - - + -
71S LEU 4.4 0.2 - - - +
72S GLY 2.9 8.4 + - - +
73S GLU 3.6 0.4 - - - -
74S PHE* 1.3 80.4 - - - +
76S PRO* 1.3 67.6 - - - +
77S THR* 3.6 0.9 + - - -
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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