Contacts of the strand formed by residues 60 - 68 (chain E) in PDB entry 4QRR
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 THR 60 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56E TYR* 3.4 6.9 - - - -
57E PHE 2.9 38.6 + - - +
58E SER* 3.1 8.1 + - - +
59E GLU* 1.3 83.8 - - + +
61E GLN* 1.4 65.1 + - - +
66E ARG* 3.4 5.0 + - - +
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Residues in contact with GLN 61 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54E PHE* 3.4 26.4 - - + +
55E GLU 3.4 9.6 - - - +
56E TYR* 2.8 41.3 + - + +
60E THR* 1.4 73.0 - - - +
66E ARG* 1.3 59.0 + - - +
67E ASN 3.4 18.1 - - - +
68E LYS* 3.4 27.8 - - - +
77E SER* 5.7 1.2 - - - +
78E GLY 4.9 1.0 - - - +
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Residues in contact with ARG 66 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A GLN* 4.2 18.0 + - - +
76A GLU* 5.0 5.5 - - - +
115D THR 4.7 1.4 - - - +
117D TYR* 3.3 56.1 - - + -
55E GLU* 3.1 28.4 + - - +
57E PHE* 3.4 46.3 - - + +
60E THR* 3.4 8.3 + - - +
61E GLN* 1.3 72.6 - - - +
67E ASN* 1.4 60.5 + - - +
109E GLU 2.7 29.7 + - - -
110E GLY* 3.7 8.7 + - - -
8P HIS* 3.8 13.7 + - - -
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Residues in contact with ASN 67 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114D GLY* 5.6 1.9 - - - -
115D THR 3.7 12.1 - - - +
116D SER* 3.8 9.9 - - - +
117D TYR* 3.2 42.5 + - + +
119D LYS* 3.9 8.5 - - - +
52E PHE* 3.4 17.3 - - - -
54E PHE* 3.4 0.2 - - - -
55E GLU* 2.8 31.8 + - + -
61E GLN* 3.4 12.7 - - - +
66E ARG* 1.4 81.3 - - - +
68E LYS* 1.3 72.6 + - - +
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Residues in contact with LYS 68 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52E PHE* 3.8 7.0 - - - -
53E LEU 3.8 10.8 - - - +
54E PHE* 4.1 5.6 - - + +
61E GLN* 3.4 29.8 - - - +
67E ASN* 1.3 82.7 + - - +
69E GLY* 1.3 87.9 + - - +
70E ASN* 4.2 2.0 - - - +
71E PHE* 2.9 29.7 + - - +
72E PRO 5.4 0.2 - - - -
76E PHE 6.0 2.0 - - - +
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Residues in contact with GLY 69 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52E PHE* 3.7 21.7 - - - -
53E LEU 2.7 21.6 + - - -
68E LYS* 1.3 94.7 + - - +
70E ASN* 1.3 71.2 + - - -
71E PHE 3.5 2.7 - - - -
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Residues in contact with ASN 70 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51E GLN* 6.3 1.1 - - - +
52E PHE 4.4 0.8 + - - -
68E LYS* 4.2 2.0 - - - +
69E GLY* 1.3 80.6 + - - -
71E PHE* 1.3 67.6 + - - +
72E PRO* 3.9 3.8 - - - +
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Residues in contact with PHE 71 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43E GLN* 3.7 35.2 - - + -
48E GLN* 5.4 3.1 - - - -
51E GLN* 3.7 41.7 - - + -
52E PHE 3.3 27.8 - - - -
53E LEU* 3.7 24.0 - - + +
54E PHE* 6.1 0.7 - - + -
68E LYS* 2.9 21.6 + - - +
69E GLY 3.5 2.6 - - - -
70E ASN* 1.3 82.1 - - - +
72E PRO* 1.4 71.9 - - + +
76E PHE* 3.7 34.5 - + + +
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Residues in contact with PRO 72 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70E ASN 4.2 3.6 - - - +
71E PHE* 1.4 94.9 - - + +
74E GLY* 1.3 65.5 + - - +
75E ARG* 3.1 25.8 + - - +
76E PHE* 3.1 33.4 + - + +
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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