Contacts of the strand formed by residues 35 - 40 (chain L) in PDB entry 4R2G
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 LYS 35 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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280A ASN* 3.3 31.7 + - - +
281A ALA* 4.2 9.7 - - - +
455A THR* 3.6 24.0 + - - +
456A ARG 3.2 27.9 + - - -
457A ASP* 4.4 8.5 + - - +
469A ARG* 6.4 0.2 - - - +
27L HIS* 3.4 32.3 - - + +
29L LYS* 3.8 13.2 - - + -
33L GLN 3.5 0.4 + - - -
34L ILE* 1.3 72.6 - - - +
36L ILE* 1.3 60.2 + - - +
47L GLY* 3.2 29.6 - - - -
48L PRO* 3.6 15.1 - - + +
49L SER* 3.5 10.3 + - - -
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Residues in contact with ILE 36 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28L TRP* 2.7 23.5 + - + +
29L LYS* 3.5 19.5 - - - +
30L ASN* 3.8 15.7 - - + +
35L LYS* 1.3 72.9 - - - +
37L LEU* 1.3 60.5 + - - +
46L LYS* 3.8 3.5 - - - +
47L GLY* 2.9 23.9 + - - +
49L SER* 3.8 23.2 + - - +
51L LEU* 3.7 22.2 - - + -
52L ASN* 5.8 1.2 - - - -
55L ALA* 4.0 11.9 - - + +
69L LEU* 3.6 25.4 - - + -
82L TYR* 3.7 26.7 - - + -
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Residues in contact with LEU 37 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26L PHE* 4.1 5.1 - - + -
27L HIS* 3.5 7.7 + - - -
28L TRP* 2.8 35.4 + - + +
35L LYS 3.9 0.4 - - - -
36L ILE* 1.3 82.3 - - + +
38L GLY* 1.3 59.6 + - - +
44L LEU* 3.5 19.5 - - + -
45L THR 3.3 22.0 - - - +
46L LYS* 4.0 17.5 - - + -
47L GLY 4.4 1.6 - - - +
55L ALA* 4.6 3.6 - - + +
56L ASP* 3.3 40.6 - - - +
57L SER* 3.9 13.0 - - - -
68L PRO 4.2 6.7 - - - +
69L LEU* 4.0 23.1 - - + -
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Residues in contact with GLY 38 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26L PHE* 3.7 24.6 - - - -
27L HIS* 4.0 7.2 + - - -
37L LEU* 1.3 76.2 - - - +
39L ASN* 1.3 62.5 + - - +
44L LEU* 3.2 14.9 - - - +
45L THR* 2.9 35.4 + - - -
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Residues in contact with ASN 39 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23L SER* 4.2 5.1 + - - -
24L ILE 4.0 14.3 + - - -
25L GLN* 3.2 14.5 - - - +
26L PHE* 3.0 48.1 + - + +
27L HIS* 4.9 2.7 - - - -
38L GLY* 1.3 74.6 - - - +
40L GLN* 1.3 76.7 + - - +
41L GLY* 3.1 25.1 + - - +
43L PHE 3.1 15.5 - - - +
45L THR* 3.4 7.0 + - - -
62L TRP* 3.7 15.9 - - + -
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Residues in contact with GLN 40 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A ALA 4.8 8.3 + - - -
283A THR* 3.4 25.2 + - - -
455A THR* 5.3 5.2 - - - +
472A GLY* 3.2 33.5 - - - +
473A GLY 3.4 4.9 - - - +
474A ASP* 3.3 24.0 + - - +
477A ASP* 3.8 5.9 - - - +
25L GLN* 3.4 27.2 + - - +
27L HIS* 6.4 0.4 - - - -
39L ASN* 1.3 83.6 + - - +
41L GLY* 1.3 63.5 + - - +
42L SER 3.2 3.3 + - - -
43L PHE* 3.1 18.3 + - + +
45L THR* 3.9 17.0 - - + +
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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