Contacts of the strand formed by residues 32 - 40 (chain F) in PDB entry 4NL3
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 GLN 32 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24F THR* 3.7 22.4 - - + +
25F VAL 3.3 11.2 - - - +
26F PHE* 3.7 29.2 - - + -
27F LEU* 4.4 1.1 - - - +
30F GLY 3.7 6.3 + - - +
31F PHE* 1.3 83.9 - - - +
33F LEU* 1.3 74.5 + - - +
34F ARG 5.7 0.2 - - - +
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Residues in contact with LEU 33 (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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63E THR* 4.3 10.8 - - + +
24F THR* 4.6 3.1 - - - -
25F VAL* 2.6 48.5 + - + +
27F LEU* 4.4 15.2 - - + +
31F PHE* 5.6 3.4 - - + -
32F GLN* 1.3 81.0 - - - +
34F ARG* 1.3 57.9 + - - +
35F GLY 4.1 0.2 - - - -
47F LEU* 4.2 13.9 - - + -
49F VAL* 4.2 21.5 - - + -
54F GLN* 3.7 36.3 - - + +
56F VAL* 4.1 17.3 - - + -
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Residues in contact with ARG 34 (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 LEU* 3.5 31.2 - - + +
23F ALA 3.7 3.6 - - - -
24F THR* 3.4 29.0 + - + +
33F LEU* 1.3 74.0 - - - +
35F GLY* 1.3 58.7 + - - +
49F VAL* 3.3 26.7 - - + +
50F GLU* 4.7 4.0 + - - +
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Residues in contact with GLY 35 (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 LEU* 3.4 7.0 - - - +
23F ALA* 3.0 36.4 + - - +
25F VAL* 5.7 0.6 - - - +
33F LEU 4.0 1.2 + - - -
34F ARG* 1.3 76.1 - - - +
36F ARG* 1.3 65.3 + - - -
37F VAL* 5.8 0.2 - - - +
47F LEU* 5.1 7.6 - - - +
48F ASP 3.2 16.6 - - - -
49F VAL* 4.4 3.4 - - - -
50F GLU 5.4 0.2 - - - -
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Residues in contact with ARG 36 (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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16F LEU 5.7 0.2 - - - +
20F LYS* 2.9 39.6 + - - +
21F ILE 3.6 17.3 - - - +
22F LEU* 3.8 36.0 - - - +
35F GLY* 1.3 76.8 - - - +
37F VAL* 1.3 67.3 + - - +
38F VAL* 3.3 0.6 + - + -
47F LEU* 3.5 5.1 - - - -
48F ASP* 2.8 52.7 + - + +
67F GLN* 5.2 1.8 + - - -
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Residues in contact with VAL 37 (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 LEU* 3.7 23.1 - - + +
16F LEU* 4.0 29.8 + - + +
17F ARG* 3.4 38.5 - - + +
20F LYS* 6.0 0.3 - - - -
21F ILE 4.7 3.3 + - - +
23F ALA* 5.7 4.5 - - + -
35F GLY 5.8 0.2 - - - +
36F ARG* 1.3 74.0 - - - +
38F VAL* 1.3 62.4 + - - +
39F SER 4.1 18.2 - - - +
40F PHE* 4.7 4.7 - - + -
45F VAL* 4.3 12.3 - - + -
46F LEU 3.9 3.1 - - - -
47F LEU* 5.0 3.4 - - + +
64F PHE* 4.5 16.4 - - + -
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Residues in contact with VAL 38 (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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72E LEU* 3.6 31.9 - - + -
17F ARG* 3.3 21.8 + - - +
36F ARG 4.9 0.2 - - - -
37F VAL* 1.3 74.2 - - - +
39F SER* 1.3 62.5 + - - +
46F LEU* 2.9 26.1 + - + +
47F LEU 4.1 2.7 - - - +
48F ASP* 3.7 36.6 - - + +
53F GLN* 5.9 4.3 - - + +
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Residues in contact with SER 39 (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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8E LEU* 3.6 28.8 - - - +
72E LEU* 5.4 5.2 - - - -
17F ARG* 4.4 4.3 - - - +
37F VAL* 3.7 2.5 - - - +
38F VAL* 1.3 87.9 - - - +
40F PHE* 1.3 81.5 + - - +
45F VAL* 3.6 3.6 - - - +
46F LEU* 2.8 29.1 + - - +
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Residues in contact with PHE 40 (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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8E LEU* 4.1 8.9 - - - +
10F ASP* 3.5 41.7 - - + -
13F LEU* 3.6 34.5 - - + -
14F ASN* 3.6 35.0 - - + -
17F ARG* 4.6 5.6 - - - -
37F VAL* 4.7 3.8 - - + -
39F SER* 1.3 87.9 + - - +
41F ASP* 1.3 69.4 + - - +
44F THR 3.4 13.9 - - - +
45F VAL* 4.2 14.4 - - + -
58F LYS* 4.5 3.1 - - - -
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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