Contacts of the strand formed by residues 46 - 55 (chain C) in PDB entry 3R8K
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 ALA 46 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23C PRO* 6.2 0.2 - - + -
44C GLY 3.3 8.4 + - - +
45C PRO* 1.3 77.0 - - - +
47C LYS* 1.3 63.9 + - - +
48C TRP* 4.0 9.4 - - - +
110C TYR* 3.9 25.4 - - + +
116C GLN* 3.7 10.8 - - - +
131C ASP* 4.9 1.6 - - - -
132C ARG* 2.9 37.9 + - + +
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Residues in contact with LYS 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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46C ALA* 1.3 76.6 - - - +
48C TRP* 1.3 63.7 + - - +
110C TYR* 4.3 0.2 - - - -
111C ILE* 3.3 18.5 + - + +
116C GLN* 2.5 65.3 + - - +
117C PHE* 3.5 11.5 + - - +
119C PRO* 3.4 32.1 - - + -
129C ILE* 3.7 13.7 - - + -
130C GLU 3.2 9.2 - - - +
131C ASP* 4.2 26.1 + - - +
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Residues in contact with TRP 48 (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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23C PRO* 3.5 29.4 - - + +
43C TYR* 5.7 2.7 - + - -
46C ALA* 3.7 19.0 - - - +
47C LYS* 1.3 81.5 - - - +
49C VAL* 1.3 56.8 + - - +
50C SER* 3.9 12.3 - - - +
88C PRO* 3.3 25.1 - - + -
90C THR* 3.5 26.9 - - + -
108C SER* 3.5 14.6 - - - -
109C LEU 3.2 11.4 - - - +
110C TYR* 3.2 42.5 - + + -
111C ILE* 4.1 3.8 - - - -
129C ILE* 3.5 3.7 - - - +
130C GLU* 2.5 44.8 + - - +
132C ARG* 3.0 40.8 - - + +
193C TRP* 5.3 4.9 - + - -
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Residues in contact with VAL 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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48C TRP* 1.3 69.8 - - - +
50C SER* 1.3 63.9 + - - +
69C LEU* 3.6 12.4 - - + +
72C TYR* 4.2 28.7 - - + -
73C ILE* 6.0 1.3 - - + -
108C SER* 3.0 3.8 - - - -
109C LEU* 2.7 65.0 + - + +
110C TYR 5.7 0.2 - - - -
111C ILE* 3.9 22.9 - - + +
127C VAL* 3.4 29.8 - - + -
128C PHE 3.3 9.0 - - - +
129C ILE* 4.5 4.5 - - + +
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Residues in contact with SER 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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48C TRP 3.7 1.4 + - - -
49C VAL* 1.3 79.5 + - - +
51C THR* 1.3 61.7 + - - +
69C LEU* 4.0 3.8 - - - -
106C THR* 3.6 6.7 - - - -
107C ILE 3.1 7.2 - - - -
108C SER* 2.9 24.6 + - - -
128C PHE* 2.8 66.2 + - - -
130C GLU* 3.0 20.2 + - - +
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Residues in contact with THR 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 SER* 1.3 75.8 - - - +
52C SER* 1.3 71.2 + - - +
53C VAL* 4.9 1.7 - - + +
65C GLY* 3.7 29.4 - - - +
68C LYS* 3.8 23.8 + - + +
69C LEU* 3.4 23.6 - - + -
105C ILE 3.7 1.2 - - - +
106C THR* 3.3 4.3 - - - -
107C ILE* 2.9 32.9 + - + +
126C ASP* 3.6 16.7 + - - +
127C VAL* 4.3 4.5 - - - -
128C PHE* 3.9 1.1 - - - -
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Residues in contact with SER 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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51C THR* 1.3 78.5 + - - +
53C VAL* 1.3 69.0 + - - +
68C LYS* 5.0 3.8 + - - -
104C THR* 4.4 14.3 - - - +
105C ILE 3.7 3.8 - - - -
106C THR* 3.1 18.8 + - - +
126C ASP* 4.4 5.7 + - - +
128C PHE* 3.9 17.2 - - - -
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Residues in contact with VAL 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 THR* 4.7 4.3 - - - +
52C SER* 1.3 82.4 - - - +
54C GLU* 1.3 73.4 + - - +
55C SER* 3.6 4.6 + - - -
61C ALA* 4.2 29.4 - - + +
64C THR* 4.5 19.7 - - + +
65C GLY* 5.0 1.1 - - - +
68C LYS* 5.6 1.3 - - - +
104C THR* 3.4 2.1 - - - -
105C ILE* 2.8 40.2 + - - +
107C ILE* 4.1 15.9 - - + -
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Residues in contact with GLU 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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53C VAL* 1.3 77.9 - - - +
55C SER* 1.3 60.1 + - - +
102C GLU* 3.1 32.5 - - + +
103C SER 4.2 3.8 - - - -
104C THR* 3.4 27.8 + - + +
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Residues in contact with SER 55 (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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53C VAL* 3.6 6.9 + - - -
54C GLU* 1.3 74.6 - - - +
56C MET* 1.3 65.8 + - - +
57C ASP* 2.9 25.9 + - - +
60C SER* 3.9 4.7 + - - -
61C ALA* 3.6 26.1 - - - +
102C GLU* 3.1 13.1 - - - +
103C SER* 2.7 40.8 + - - +
105C ILE* 4.3 8.3 - - - -
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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