Contacts of the strand formed by residues 62 - 70 (chain F) in PDB entry 4NQD
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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10C LEU* 3.9 22.0 - - + -
91C THR* 6.0 0.4 - - + -
93C GLN* 3.5 22.2 - - - -
29F GLY 3.0 23.4 + - - -
30F PHE* 2.8 43.4 + - + -
31F HIS* 3.4 24.7 - + - -
32F PRO 4.0 0.2 - - - -
33F SER* 3.5 32.3 - - - -
54F LEU* 3.7 23.6 - - + -
55F SER 3.3 14.4 - - - +
56F PHE* 3.4 35.4 - + - -
57F SER* 5.1 0.2 - - - -
60F TRP 3.9 0.7 - - - -
61F SER* 1.3 75.1 - - - +
63F TYR* 1.3 62.3 + - - +
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Residues in contact with TYR 63 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C ARG* 5.6 2.9 + - - -
27C TYR* 4.3 13.2 - - - -
30C SER* 4.6 13.0 + - - -
26F TYR* 3.3 33.9 - + + +
27F VAL 3.1 7.2 - - - +
28F SER* 3.6 23.1 - - - -
29F GLY 4.8 0.2 - - - +
30F PHE* 4.0 0.9 - - - -
52F SER* 5.9 0.4 - - - -
54F LEU* 4.1 0.3 - - - +
55F SER* 2.9 65.6 + - - -
56F PHE 3.8 15.1 + - - -
57F SER* 3.3 25.6 - - - +
62F PHE* 1.3 75.6 - - - +
64F LEU* 1.3 65.5 + - - +
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Residues in contact with LEU 64 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25F CYS 3.7 0.9 - - - +
26F TYR* 3.5 8.9 - - - -
27F VAL* 2.8 37.7 + - + +
30F PHE* 3.9 11.0 - - + -
35F ILE* 3.5 32.3 - - + -
37F VAL* 5.3 0.9 - - + -
51F HIS* 4.8 3.6 - - + -
52F SER* 3.1 32.1 - - - +
53F ASP 3.7 1.3 - - - -
54F LEU* 3.7 29.4 - - + +
63F TYR* 1.3 77.9 - - - +
65F LEU* 1.3 59.3 + - - +
66F TYR* 4.1 28.3 - - + +
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Residues in contact with LEU 65 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232C PRO* 4.2 17.0 - - + +
234C GLY* 4.2 25.6 - - - -
10F TYR* 3.5 24.9 - - - +
24F ASN* 3.7 26.5 - - + +
25F CYS 3.5 11.9 - - - +
26F TYR* 4.3 10.1 - - + -
51F HIS* 3.2 3.8 - - - -
52F SER* 2.9 42.8 + - - +
64F LEU* 1.3 72.2 - - - +
66F TYR* 1.3 62.2 + - - +
67F TYR* 3.8 23.6 - - + -
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Residues in contact with TYR 66 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23F LEU 3.9 0.5 - - - +
24F ASN* 3.5 1.6 - - - -
25F CYS* 2.7 49.3 + - + +
27F VAL* 5.2 0.7 - - + -
35F ILE* 5.2 5.4 + - - +
37F VAL* 3.6 64.9 + - + +
39F LEU* 4.1 5.9 - - + +
49F VAL* 3.6 26.9 - - + -
50F GLU 3.4 2.9 - - - -
51F HIS* 3.3 45.7 + + + -
64F LEU* 4.2 27.5 - - + +
65F LEU* 1.3 74.0 - - - +
67F TYR* 1.4 57.7 + - - +
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Residues in contact with TYR 67 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234C GLY* 5.5 4.5 - - - -
12F ARG* 4.4 8.7 - - - -
22F PHE* 4.0 26.9 - + + -
23F LEU 3.2 7.0 - - - +
24F ASN* 3.2 24.9 - - - +
39F LEU* 3.8 3.3 - - - +
49F VAL* 3.7 2.4 - - - -
50F GLU* 2.8 79.5 + - + +
51F HIS* 3.9 15.7 + - - -
52F SER* 4.2 3.3 - - - -
65F LEU* 3.8 26.7 - - + -
66F TYR* 1.4 71.0 - - - +
68F THR* 1.4 63.0 + - - +
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Residues in contact with THR 68 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22F PHE* 3.2 10.5 - - - -
23F LEU* 2.9 37.0 + - - +
39F LEU* 3.3 18.5 - - - +
46F ILE* 3.7 32.2 - - + +
48F LYS* 3.2 28.5 - - + +
49F VAL* 3.7 6.7 - - + -
50F GLU* 5.6 2.0 - - - -
67F TYR* 1.4 73.1 - - - +
69F GLU* 1.3 69.3 + - - +
70F PHE* 4.2 3.0 - - - +
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Residues in contact with GLU 69 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20F SER* 5.1 11.9 + - - -
21F ASN 3.4 14.1 - - - +
22F PHE* 3.5 35.6 - - + -
68F THR* 1.3 80.2 - - - +
70F PHE* 1.3 64.1 + - - +
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Residues in contact with PHE 70 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11F SER* 4.5 2.0 - - - -
20F SER* 4.7 0.7 - - - -
21F ASN* 2.8 57.3 + - + +
22F PHE 3.5 9.6 - - - -
23F LEU* 3.3 43.7 - - + -
68F THR* 4.4 4.3 - - - +
69F GLU* 1.3 78.1 - - - +
71F THR* 1.3 61.6 + - - +
72F PRO* 3.7 19.0 - - + +
78F TYR* 3.6 39.3 - + + +
95F TRP* 3.6 44.2 - + - -
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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