Contacts of the helix formed by residues 50 - 55 (chain A) in PDB entry 3NT7
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 PHE 50 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A PRO* 4.4 12.6 - - + -
13A ILE* 3.7 46.0 - - + -
14A THR 4.4 4.0 - - - +
26A LEU* 3.9 20.2 - - + -
30A TYR* 3.6 42.6 - + - -
47A ASP 5.4 1.0 + - - -
48A LYS 3.2 0.4 - - - -
49A PHE* 1.3 88.9 - + + +
51A ILE* 1.3 58.3 + - - +
52A GLN* 3.1 4.0 - - - -
53A LEU* 2.8 45.6 + - + +
54A LYS 4.2 0.7 + - - -
123A LEU* 3.8 16.6 - - + -
137A TRP* 3.8 22.7 - + - -
140A ILE* 5.1 0.2 - - + -
144A LEU* 5.4 0.9 - - + -
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Residues in contact with ILE 51 (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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47A ASP 3.7 23.3 - - - +
48A LYS* 3.4 27.5 + - + +
49A PHE 3.5 0.6 - - - -
50A PHE* 1.3 76.6 - - - +
52A GLN* 1.3 67.0 + - - +
54A LYS* 3.2 50.4 + - - +
55A GLN* 5.7 0.2 - - - +
75A THR 4.3 2.7 - - - +
76A GLY* 3.5 29.6 + - - +
77A VAL* 3.9 17.5 - - + -
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Residues in contact with GLN 52 (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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19A TRP* 4.1 6.9 + - - -
49A PHE 5.1 1.1 + - - +
50A PHE 3.0 1.8 + - - -
51A ILE* 1.3 78.9 + - - +
53A LEU* 1.3 57.6 + - + +
54A LYS 3.0 5.8 - - - -
55A GLN* 3.0 41.0 + - - +
76A GLY 3.5 7.0 + - - +
77A VAL* 3.8 20.8 - - - +
78A PRO* 3.2 33.4 - - + +
111A ASN* 3.0 30.2 + - - +
117A ILE* 4.2 4.1 - - + +
118A PRO* 3.4 18.7 - - - +
119A TRP* 3.6 22.2 - - + -
123A LEU* 6.5 0.7 - - + -
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Residues in contact with LEU 53 (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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13A ILE* 3.9 13.5 - - + -
14A THR 4.0 8.5 - - - +
15A TYR* 4.1 6.5 - - + -
16A HIS 2.9 23.2 + - - -
19A TRP* 3.0 51.1 + - + +
23A MET* 4.0 21.3 - - + -
26A LEU* 5.0 5.4 - - + -
50A PHE* 2.8 47.1 + - + +
52A GLN* 1.3 76.1 - - - +
54A LYS* 1.3 57.2 + - - +
55A GLN 3.2 0.9 - - - -
119A TRP* 3.9 16.2 - - + -
123A LEU* 5.7 0.7 - - + -
144A LEU* 4.4 9.6 - - + -
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Residues in contact with LYS 54 (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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1A MET* 3.3 31.4 - - + +
14A THR* 4.1 37.1 - - + +
16A HIS* 3.7 8.4 - - - +
51A ILE* 3.3 44.3 - - - +
52A GLN 3.0 0.4 - - - -
53A LEU* 1.3 78.1 - - - +
55A GLN* 1.3 62.5 + - - +
56A PRO* 3.7 5.2 - - - +
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Residues in contact with GLN 55 (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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16A HIS* 3.7 2.0 - - - +
19A TRP* 2.8 32.1 + - - -
52A GLN* 3.0 38.3 + - - +
54A LYS* 1.3 80.2 + - + +
56A PRO* 1.4 77.6 - - - +
60A LYS* 2.8 30.4 + - - +
111A ASN* 3.8 29.8 + - - +
117A ILE* 4.2 12.8 - - + -
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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