Contacts of the strand formed by residues 21 - 32 (chain F) in PDB entry 6NQN
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 HIS 21 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17F ALA* 3.3 3.9 - - - -
18F VAL* 3.0 30.8 + - + +
19F ASN* 4.0 15.4 + - + -
20F GLY* 1.3 79.5 + - - +
22F PRO* 1.3 72.5 - - - +
23F PHE* 3.7 5.7 - - - -
51F PRO* 5.0 22.2 - - + +
52F PHE* 5.1 2.0 - - + -
132F MET* 6.0 4.7 - - + -
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Residues in contact with PRO 22 (chain F).
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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16F GLY 3.1 11.9 - - - +
17F ALA* 3.8 6.0 - - + -
20F GLY 3.1 12.5 - - - +
21F HIS* 1.3 91.9 - - + +
23F PHE* 1.3 62.4 + - - +
46F GLU* 6.0 0.2 - - - -
47F GLY* 3.7 14.7 - - - +
119F ARG* 6.2 0.2 - - - +
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Residues in contact with PHE 23 (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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14F MET* 3.6 27.8 - - + -
15F GLU* 3.8 1.0 - - - +
16F GLY* 2.9 39.0 + - - +
17F ALA* 3.3 27.1 - - - -
18F VAL* 4.0 2.5 - - + -
21F HIS 3.7 11.4 - - - +
22F PRO* 1.3 75.2 - - - +
24F ALA* 1.3 65.2 + - - +
25F ILE* 3.9 21.8 - - + -
46F GLU* 3.3 22.0 - - - +
47F GLY* 4.2 2.0 - - - +
50F LEU* 3.7 20.4 - - + -
52F PHE* 3.7 18.4 - + - -
57F LEU* 3.7 24.2 - - + -
120F PHE* 3.9 9.9 - + - -
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Residues in contact with ALA 24 (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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13F ARG* 3.6 31.0 - - - +
14F MET 3.3 10.3 - - - +
15F GLU* 4.4 5.2 - - + -
23F PHE* 1.3 77.3 - - - +
25F ILE* 1.3 60.9 + - - +
44F VAL* 3.6 0.3 - - - -
45F LYS* 2.8 31.1 + - + -
46F GLU* 3.0 33.0 + - + +
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Residues in contact with ILE 25 (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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12F LEU* 4.2 1.0 - - - +
13F ARG* 3.4 2.5 - - - +
14F MET* 2.7 40.5 + - + +
23F PHE* 3.9 18.6 - - + -
24F ALA* 1.3 80.3 - - - +
26F GLU* 1.3 67.1 + - - +
42F LEU* 3.4 30.7 - - + -
43F LYS 3.5 13.0 - - - +
44F VAL* 3.6 26.9 - - + -
45F LYS 4.3 0.2 - - - +
50F LEU* 4.0 2.9 - - + -
54F TYR* 3.9 10.5 - - - +
57F LEU* 3.7 30.5 - - + -
61F PHE* 3.5 12.1 - - + -
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Residues in contact with GLU 26 (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 LYS* 5.5 5.7 + - - -
12F LEU* 3.4 15.0 - - - +
13F ARG* 2.9 41.5 + - + +
25F ILE* 1.3 80.7 - - - +
27F GLY* 1.3 57.8 + - - +
41F ASP 4.0 0.3 - - - +
42F LEU* 3.4 1.9 - - - -
43F LYS* 2.7 39.5 + - - +
45F LYS* 3.4 32.5 + - + -
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Residues in contact with GLY 27 (chain F).
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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10F ILE* 5.2 0.4 - - - -
11F LYS* 3.5 2.8 - - - +
12F LEU* 3.0 49.5 + - - +
26F GLU* 1.3 76.1 - - - +
28F VAL* 1.3 70.6 + - - +
40F MET* 5.6 1.1 - - - -
41F ASP 3.2 11.0 - - - -
42F LEU* 4.1 6.3 - - - -
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Residues in contact with VAL 28 (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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10F ILE* 3.2 10.5 - - - +
11F LYS* 4.5 21.1 - - + -
27F GLY* 1.3 80.4 - - - +
29F GLY* 1.3 59.2 + - - +
40F MET* 3.3 4.4 - - - +
41F ASP* 2.8 41.5 + - + +
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Residues in contact with GLY 29 (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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9F LYS* 3.4 9.2 - - - +
10F ILE* 2.8 38.9 + - - +
28F VAL* 1.3 77.5 - - - +
30F LEU* 1.3 66.8 + - - +
39F SER 3.2 14.1 - - - -
40F MET* 3.7 5.6 - - - -
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Residues in contact with LEU 30 (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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7F ASP* 6.5 0.9 - - + -
8F MET 3.2 13.2 - - - +
9F LYS* 4.1 8.5 - - + +
10F ILE* 4.3 7.9 - - - +
29F GLY* 1.3 79.5 - - - +
31F GLY* 1.3 60.0 + - - +
38F GLN* 3.4 1.7 - - - +
39F SER* 2.9 48.2 + - - +
40F MET* 6.0 0.2 - - - -
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Residues in contact with GLY 31 (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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7F ASP* 3.7 5.0 - - - +
8F MET 2.9 32.2 + - - +
30F LEU* 1.3 79.1 - - - +
32F LYS* 1.3 66.7 + - - +
33F PRO* 3.7 1.0 - - - +
37F LYS 3.2 12.6 - - - -
38F GLN* 3.8 2.5 - - - -
68F PHE* 3.5 16.9 - - - -
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Residues in contact with LYS 32 (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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6F PRO* 3.3 12.9 - - - +
7F ASP* 2.5 39.7 + - - +
31F GLY* 1.3 74.3 - - - -
33F PRO* 1.3 69.0 - - - +
34F PHE 3.2 2.2 - - - +
35F GLU* 3.1 49.1 + - + +
36F GLY 3.1 9.7 + - - -
37F LYS* 2.8 20.2 + - + +
68F PHE* 3.7 0.6 - - - -
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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