Contacts of the strand formed by residues 44 - 49 (chain D) 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 THR 44 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D PHE* 3.4 1.7 - - - -
41D ASP* 2.6 63.1 + - - +
43D PHE* 1.3 80.1 - - - +
45D VAL* 1.3 67.5 + - - +
55D LEU* 3.8 20.2 - - + -
56D VAL 3.3 6.5 - - - +
57D PHE* 3.6 32.1 - - + -
58D LYS* 4.4 0.7 - - - +
8H LEU* 3.1 13.2 - - - +
9H GLN* 3.4 20.2 - - + +
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Residues in contact with VAL 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A PHE* 5.7 0.2 - - + -
13D LEU* 4.2 10.5 - - + -
37D VAL* 4.0 19.7 - - + -
39D SER 3.6 11.2 - - - +
40D PHE* 4.1 10.8 - - + -
44D THR* 1.3 80.7 - - - +
46D LEU* 1.3 65.7 + - - +
47D LEU* 3.6 9.8 + - + +
54D GLN 3.3 3.1 - - - +
55D LEU* 4.2 2.5 - - - -
56D VAL* 2.7 37.5 + - + +
58D LYS* 4.1 22.2 - - + -
61D ILE* 4.1 17.3 - - + -
64D PHE* 4.4 15.7 - - + -
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Residues in contact with LEU 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D VAL* 3.8 2.8 - - - -
38D VAL* 2.8 49.0 + - + -
39D SER* 2.8 23.0 + - - +
45D VAL* 1.3 71.7 - - - +
47D LEU* 1.3 64.9 + - - +
53D GLN* 4.1 19.3 - - + +
54D GLN 3.6 22.4 - - - +
55D LEU* 4.2 4.3 - - + +
8H LEU* 4.1 28.0 - - + +
12H TYR* 3.5 36.3 - - + -
72H LEU* 4.4 12.1 - - + -
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Residues in contact with LEU 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D ALA* 6.5 0.2 - - + -
25D VAL* 3.8 33.7 - - + -
33D LEU* 4.4 18.4 - - + +
35D GLY 4.6 5.4 - - - +
36D ARG 3.5 26.2 - - - +
37D VAL* 4.0 17.5 - - + +
38D VAL* 4.1 4.2 - - - +
45D VAL* 4.5 11.9 - - + +
46D LEU* 1.3 77.9 - - - +
48D ASP* 1.3 59.7 + - - +
49D VAL* 3.7 8.7 - - + -
52D LYS 3.4 0.3 - - - +
53D GLN* 3.3 8.1 - - - +
54D GLN* 2.9 43.2 + - + +
56D VAL* 4.1 18.8 - - + -
61D ILE* 6.1 0.7 - - + -
64D PHE* 4.9 1.1 - - + -
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Residues in contact with ASP 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35D GLY* 3.1 4.2 - - - -
36D ARG* 2.6 51.9 + - + +
38D VAL* 3.7 16.6 - - + +
47D LEU* 1.3 70.4 - - - +
49D VAL* 1.3 59.9 + - - +
50D GLU 3.7 1.9 + - - -
51D GLY* 3.2 39.4 + - - +
52D LYS 3.5 2.4 - - - +
53D GLN* 4.9 2.7 - - + +
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Residues in contact with VAL 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D LEU* 3.9 17.7 - - + -
34D ARG 3.6 23.3 - - - +
35D GLY* 4.6 1.8 - - - -
47D LEU* 4.2 13.5 - - + -
48D ASP* 1.3 73.0 - - - +
50D GLU* 1.3 76.3 + - + +
51D GLY 3.3 0.2 - - - -
52D LYS* 2.7 30.6 + - - +
54D GLN* 3.6 26.7 - - + +
1I MET* 3.7 36.6 - - + +
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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