Contacts of the strand formed by residues 42 - 47 (chain C) in PDB entry 3S52
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 VAL 42 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116B GLN* 4.1 28.5 - - + +
117B PRO* 3.5 34.1 - - + -
120B LYS* 4.8 1.3 - - - +
22C VAL* 3.1 8.5 - - - +
23C GLY* 2.7 50.9 + - - +
24C SER* 4.6 12.6 - - - +
38C SER* 3.4 22.9 - - - +
40C GLU 4.3 0.2 - - - +
41C PRO* 1.3 70.0 - - - +
43C LEU* 1.3 58.6 + - - +
44C PHE* 5.5 0.4 - - + -
118C TRP* 4.6 9.6 - - + -
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Residues in contact with LEU 43 (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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117B PRO* 3.2 19.5 - - - +
119B GLU* 4.0 9.8 + - - +
120B LYS* 3.8 27.7 + - + +
20C VAL* 5.0 0.9 - - + -
21C CYS 3.2 11.4 - - - +
22C VAL* 4.4 2.0 - - + -
41C PRO* 3.6 25.2 + - + +
42C VAL* 1.3 82.9 - - - +
44C PHE* 1.3 64.7 + - - +
171C LEU* 4.5 0.4 - - + -
174C TYR* 3.6 23.3 - - + -
175C MSE 3.8 37.2 - - + -
178C PHE* 4.6 2.7 - - + -
179C PHE* 3.9 26.2 - - + -
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Residues in contact with PHE 44 (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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117B PRO* 3.9 10.3 - - + -
119B GLU* 3.4 22.7 - - - +
20C VAL* 3.7 1.6 - - - +
21C CYS* 2.8 64.1 + - + +
22C VAL 4.0 3.4 - - - -
23C GLY* 3.9 20.6 - - - -
42C VAL 4.8 0.4 - - - -
43C LEU* 1.3 78.8 - - - +
45C ILE* 1.3 74.6 + - - +
46C LYS* 4.2 2.7 - - + -
72C GLU* 5.5 0.7 - - - -
101C ASP* 3.6 24.2 - - - -
118C TRP* 4.3 17.9 - + + -
122C LYS* 3.6 40.6 - - + -
219C SO4 4.1 11.4 - - - -
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Residues in contact with ILE 45 (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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45B ILE* 6.1 0.7 - - - +
47B PRO* 4.4 17.7 - - + -
119B GLU* 2.9 31.4 + - + +
123B ALA* 4.2 7.9 - - + -
18C LYS* 4.0 22.4 - - + -
19C VAL 3.3 13.7 - - - +
20C VAL* 4.3 12.3 - - + -
44C PHE* 1.3 84.6 - - - +
46C LYS* 1.3 79.5 + - - +
47C PRO* 4.4 1.1 - - + +
119C GLU* 4.9 2.4 - - - +
122C LYS* 5.6 0.7 - - - +
123C ALA* 4.2 11.6 - - - +
179C PHE* 3.9 38.6 - - + -
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Residues in contact with LYS 46 (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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18C LYS* 3.6 0.7 - - - -
19C VAL* 2.8 42.1 + - + +
21C CYS* 4.2 15.9 - - - -
44C PHE* 4.2 11.4 - - + -
45C ILE* 1.3 83.8 - - - +
47C PRO* 1.3 70.5 - - + +
50C ALA* 3.8 9.9 - - + -
101C ASP* 2.5 40.0 + - - +
102C LEU 3.4 7.5 + - - -
122C LYS 2.8 32.0 + - - +
123C ALA* 4.6 0.2 - - - -
127C SER* 3.1 27.2 + - - +
128C CYS* 3.9 19.7 - - + -
188C LEU* 4.5 2.0 - - - -
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Residues in contact with PRO 47 (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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17B ASN* 5.1 1.3 - - - +
18B LYS* 3.6 33.4 - - + -
45B ILE* 4.4 14.4 - - + -
179B PHE* 5.4 0.4 - - + -
17C ASN 4.2 4.9 - - - +
18C LYS* 4.7 3.6 - - + -
19C VAL* 4.9 0.3 - - - +
45C ILE* 4.4 1.8 - - + +
46C LYS* 1.3 91.7 - - + +
48C GLU* 1.3 61.1 + - - +
49C THR* 3.4 18.8 - - - +
50C ALA* 2.9 24.9 + - + +
51C LEU* 4.1 4.6 + - - +
123C ALA* 3.6 31.6 - - + +
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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