Contacts of the strand formed by residues 62 - 67 (chain T) in PDB entry 2NX5
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 62 (chain T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36T GLN* 4.3 8.1 - - - -
46T LEU* 3.9 31.6 - - + -
55T GLU 4.3 0.2 - - - +
56T GLU* 3.6 1.4 - - - +
57T LYS* 2.7 44.6 + - + +
58T GLY 3.1 1.1 - - - -
61T ARG* 1.3 114.5 - - + +
63T SER* 1.3 58.6 + - - +
64T SER 4.4 0.2 + - - -
75T LEU* 4.3 12.3 - - + -
76T LEU 3.5 3.6 - - - -
77T LEU* 3.5 30.7 - - + -
84T ASP* 3.9 21.5 - - - -
88T TYR* 4.2 12.1 - + - -
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Residues in contact with SER 63 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54T LEU* 4.5 15.9 - - - +
55T GLU 3.3 5.8 - - - -
56T GLU* 3.3 33.1 + - - +
61T ARG 5.6 0.2 - - - -
62T PHE* 1.3 71.7 - - - +
64T SER* 1.3 60.0 + - - +
74T TYR* 3.7 1.0 - - - +
75T LEU* 3.4 6.9 - - - +
76T LEU* 2.6 66.3 + - - +
78T LYS* 4.8 4.3 + - - +
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Residues in contact with SER 64 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34T TRP* 3.4 14.0 + - - -
47T SER* 2.9 26.9 + - - -
49T ASN* 2.8 34.6 + - - +
53T GLY 3.8 1.2 - - - +
54T LEU* 3.5 3.4 - - - -
55T GLU* 2.6 45.5 + - - +
63T SER* 1.3 73.7 - - - +
65T PHE* 1.3 62.0 + - - +
74T TYR 3.5 2.9 - - - -
75T LEU* 4.7 2.9 - - - +
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Residues in contact with PHE 65 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D ASP* 3.9 17.9 - - + -
53D GLY 4.1 4.7 - - - -
65D PHE* 3.5 34.8 - + - -
66D LEU 3.9 2.5 - - - -
67D SER* 3.7 21.1 - - - -
49T ASN* 4.6 2.4 - - - +
53T GLY 3.4 14.8 - - - -
54T LEU* 4.0 9.4 - - + -
64T SER* 1.3 75.9 + - - +
66T LEU* 1.3 59.1 + - - +
67T SER* 3.6 20.6 - - - -
72T TYR* 3.8 17.9 - + - -
73T SER* 2.6 32.9 + - - -
74T TYR* 3.0 58.7 + + + +
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Residues in contact with LEU 66 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65D PHE* 3.4 10.2 - - - -
24T TYR* 3.3 30.5 - - + +
29T PHE* 4.0 7.0 - - + -
32T LEU* 4.7 3.4 - - + -
49T ASN* 3.6 17.5 - - + +
50T VAL* 3.5 44.4 - - - +
51T LEU 3.8 13.0 - - - +
52T ASP* 3.5 3.4 - - - +
53T GLY 3.1 27.5 + - - +
65T PHE* 1.3 77.8 - - - +
67T SER* 1.3 60.8 + - - +
68T ARG* 3.7 18.6 - - + -
72T TYR 3.6 13.0 - - - +
73T SER* 4.3 9.0 - - - +
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Residues in contact with SER 67 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65D PHE* 4.0 12.6 - - - -
67D SER* 4.7 2.8 - - - -
72D TYR* 4.2 12.1 - - - -
24T TYR* 4.6 0.2 - - - -
52T ASP* 3.4 4.7 - - - -
65T PHE* 3.6 22.2 - - - -
66T LEU* 1.3 74.5 - - - +
68T ARG* 1.3 58.7 + - - +
69T SER 3.4 0.6 + - - -
70T LYS* 3.4 15.9 + - - +
71T GLY 3.0 7.3 + - - -
72T TYR* 2.8 43.9 + - - -
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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