Contacts of the strand formed by residues 56 - 63 (chain A) in PDB entry 1N6P
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 ALA 56 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52A THR* 4.4 4.7 - - + +
54A GLY 3.3 4.4 + - - +
55A ALA* 1.3 74.3 - - - +
57A PHE* 1.3 61.1 + - - +
58A LEU* 4.0 14.4 - - + -
73A ILE 3.6 0.3 - - - +
74A TRP* 3.5 6.3 - - - -
75A ASP* 2.8 46.7 + - + +
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Residues in contact with PHE 57 (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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55A ALA 4.3 0.4 + - - -
56A ALA* 1.3 74.8 - - - +
58A LEU* 1.3 68.1 + - - +
59A THR* 3.4 21.3 - - + -
72A GLU* 3.4 46.4 - - + -
73A ILE 3.3 16.8 - - - -
74A TRP* 3.6 44.2 - + + -
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Residues in contact with LEU 58 (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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37A VAL* 3.8 28.9 - - + -
38A LEU* 4.2 24.7 - - + -
41A VAL* 4.0 27.1 - - + -
42A LYS* 4.4 10.8 - - - +
56A ALA* 4.0 17.3 - - + +
57A PHE* 1.3 91.8 - - - +
59A THR* 1.3 66.8 + - - +
73A ILE* 2.8 38.1 + - - +
75A ASP* 4.5 7.6 - - + +
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Residues in contact with THR 59 (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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41A VAL* 3.3 18.3 - - - +
57A PHE* 3.4 19.3 - - + -
58A LEU* 1.3 83.1 - - - +
60A GLN* 1.3 66.1 + - - +
70A LYS* 4.3 14.5 - - - +
71A PHE 3.2 9.4 - - - +
72A GLU* 3.1 27.4 - - - +
73A ILE* 5.0 0.4 - - - -
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Residues in contact with GLN 60 (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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40A PHE* 3.1 59.0 + - + +
41A VAL* 3.4 27.0 + - + -
59A THR* 1.3 78.2 - - - +
61A THR* 1.3 87.4 + - - +
62A VAL* 4.8 0.4 - - + -
69A VAL 3.9 0.3 - - - +
70A LYS* 3.6 1.2 - - - -
71A PHE* 2.7 37.0 + - - +
73A ILE* 4.8 1.5 - - + +
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Residues in contact with THR 61 (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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60A GLN* 1.3 93.4 + - - +
62A VAL* 1.3 72.4 + - - +
68A THR* 3.2 34.8 - - + -
69A VAL 3.2 10.3 - - - +
70A LYS* 3.9 17.2 - - + +
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Residues in contact with VAL 62 (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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40A PHE* 3.5 36.6 - - + -
60A GLN* 4.8 0.7 - - + -
61A THR* 1.3 82.2 - - - +
63A CYS* 1.3 60.6 + - - +
64A LEU* 4.0 2.9 + - + -
68A THR* 3.7 4.2 - - - +
69A VAL* 2.8 54.1 + - + +
71A PHE* 4.3 7.4 - - + -
171A ASN* 4.8 2.9 - - - +
174A PHE* 5.4 0.4 - - + -
175A MET* 3.4 31.6 - - + -
178A ALA* 4.2 13.7 - - + -
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Residues in contact with CYS 63 (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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62A VAL* 1.3 75.0 - - - +
64A LEU* 1.3 72.1 + - - +
67A THR 3.9 5.2 - - - -
68A THR* 4.9 8.5 - - - +
175A MET* 3.6 16.9 - - - +
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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