Contacts of the strand formed by residues 48 - 55 (chain C) in PDB entry 3DC1
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 48 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46C PHE 3.5 2.6 - - - +
47C PRO* 1.3 84.9 - - + +
49C LYS* 1.3 65.1 + - - +
68C MET* 3.6 11.1 - - - +
72C LEU* 3.4 40.7 - - + +
53D ILE* 3.7 27.8 - - + -
54D THR 3.3 6.1 - - - -
55D VAL* 4.3 9.6 - - + -
61D ILE* 3.7 24.5 - - + -
265D ILE* 3.6 26.0 - - + -
269D LEU* 4.1 13.7 - - + -
302D MET* 4.0 26.7 - - + -
303D ILE* 4.3 2.7 - - + -
306D LEU* 3.6 28.7 - - + -
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Residues in contact with LYS 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C PRO 4.9 0.4 + - - -
44C ASN* 3.3 26.7 + - - +
46C PHE 3.0 28.4 + - - -
47C PRO* 3.6 10.1 - - - +
48C PHE* 1.3 73.9 + - - +
50C THR* 1.4 69.9 + - + +
65C GLU* 3.5 20.0 - - + +
68C MET* 3.1 22.7 - - - +
69C LYS* 5.6 7.4 - - + +
54D THR* 2.7 21.0 + - - +
55D VAL 4.6 0.4 - - - -
56D GLU* 3.4 47.1 + - + +
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Residues in contact with THR 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C LYS* 1.4 85.7 - - + +
51C ALA* 1.3 63.5 + - - +
52C VAL* 5.5 4.4 - - - +
63C PHE 3.3 15.5 - - - +
64C GLY* 4.6 1.1 - - - -
65C GLU* 3.8 26.0 - - - +
68C MET* 3.5 6.1 - - - +
52D VAL* 5.2 1.6 + - - +
53D ILE* 3.1 7.1 - - - +
54D THR* 2.8 55.4 + - - +
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Residues in contact with ALA 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C THR* 1.3 77.2 - - - +
52C VAL* 1.3 66.5 + - - +
53C ILE* 4.2 8.7 - - + -
61C ILE 4.4 0.4 - - - -
62C GLN* 3.3 4.9 - - - +
63C PHE* 2.8 36.8 + - + +
68C MET* 3.4 18.5 - - + +
298C PHE* 4.3 11.7 - - + -
52D VAL 3.0 5.6 - - - -
53D ILE* 3.6 19.5 - - + -
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Residues in contact with VAL 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C THR* 5.5 4.9 - - - +
51C ALA* 1.3 79.2 - - - +
53C ILE* 1.3 64.2 + - - +
54C THR* 4.2 8.7 - - + +
60C THR* 3.7 22.4 - - + -
61C ILE 3.6 3.1 - - - -
62C GLN* 4.4 19.3 - - - +
50D THR* 3.6 0.7 + - - +
51D ALA* 3.2 3.8 - - - -
52D VAL* 2.7 59.0 + - + +
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Residues in contact with ILE 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C ALA* 4.4 10.8 - - + -
52C VAL* 1.3 80.0 - - - +
54C THR* 1.3 64.2 + - - +
55C VAL* 4.4 0.2 - - - +
60C THR* 3.4 2.9 - - - +
61C ILE* 2.6 57.4 + - + +
63C PHE* 4.8 3.1 - - + -
298C PHE* 4.1 17.5 - - + -
302C MET* 3.7 37.0 - - + -
48D PHE* 3.7 39.9 - - + -
50D THR 3.1 8.1 - - - +
51D ALA* 4.1 12.8 - - + -
68D MET* 4.3 4.7 - - + -
298D PHE* 5.0 1.8 - - + -
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Residues in contact with THR 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C VAL* 4.9 8.7 - - + -
53C ILE* 1.3 72.6 - - - +
55C VAL* 1.3 61.3 + - - +
60C THR* 4.5 17.5 - - + +
48D PHE* 3.4 3.3 - - - -
49D LYS* 2.7 42.1 + - - +
50D THR* 2.7 44.5 + - - +
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Residues in contact with VAL 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C ILE 3.7 2.6 + - - +
54C THR* 1.3 79.9 - - - +
56C GLU* 1.3 74.6 - - - +
57C ASN 3.8 1.3 + - - -
58C GLY* 3.4 26.1 - - - +
59C LYS 3.8 17.5 - - - +
60C THR* 4.5 5.1 + - - +
61C ILE* 3.9 30.5 - - + -
306C LEU* 3.9 16.2 - - + -
310C TRP* 4.6 1.1 - - + -
47D PRO* 3.2 19.5 - - + +
48D PHE* 4.0 15.9 - - + -
49D LYS* 4.7 1.3 - - - -
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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