Contacts of the strand formed by residues 39 - 47 (chain C) in PDB entry 1U1C
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 ASP 39 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38C MET* 1.3 77.3 - - - +
40C LYS* 1.3 82.7 + - - +
55C ALA* 3.7 0.5 - - - -
56C GLU* 2.7 51.6 + - + +
57C LEU* 4.7 2.9 - - - +
58C ASP 4.6 8.7 + - - -
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Residues in contact with LYS 40 (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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39C ASP* 1.3 91.4 - - - +
41C PRO* 1.3 70.0 - - - +
42C VAL* 3.7 9.9 + - + +
54C ARG* 3.4 12.1 + - - +
55C ALA* 3.6 4.9 - - - -
56C GLU* 4.1 28.4 + - + +
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Residues in contact with PRO 41 (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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35C ALA* 3.4 28.5 - - + +
36C ALA* 4.1 14.4 - - + +
38C MET 4.2 6.1 - - - +
39C ASP 3.7 0.9 - - - -
40C LYS* 1.3 87.1 - - - +
42C VAL* 1.3 64.2 + - - +
53C TRP* 3.6 25.0 - - + -
54C ARG 3.5 6.3 - - - +
55C ALA* 4.6 0.9 - - - -
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Residues in contact with VAL 42 (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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40C LYS* 4.2 11.9 - - + +
41C PRO* 1.3 79.7 - - - +
43C LYS* 1.3 75.1 + - - +
44C LEU* 3.6 2.6 + - + +
53C TRP* 3.4 5.9 - - - -
54C ARG* 2.7 76.4 + - - +
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Residues in contact with LYS 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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42C VAL* 1.3 83.8 - - - +
44C LEU* 1.3 64.4 + - - +
45C ALA 4.5 5.6 - - - +
46C SER* 3.5 25.7 + - - +
51C THR* 4.0 18.2 - - - -
52C THR 4.0 2.2 - - - +
53C TRP* 3.5 47.8 - - + +
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Residues in contact with LEU 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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10C GLY 5.0 0.7 - - - +
11C LEU* 3.7 23.1 - - + -
15C ASP* 3.8 35.9 - - + +
16C LEU* 5.3 1.6 - - + -
42C VAL* 4.3 3.1 - - + +
43C LYS* 1.3 80.0 - - - +
45C ALA* 1.3 61.4 + - - +
52C THR* 2.9 19.0 + - + +
54C ARG* 3.5 54.7 - - + +
63C ILE* 4.1 14.6 - - + -
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Residues in contact with ALA 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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9C LEU 3.4 24.2 - - - +
10C GLY 3.6 16.2 - - - +
11C LEU* 3.8 6.9 - - + +
43C LYS* 4.0 6.2 - - - +
44C LEU* 1.3 81.8 - - - +
46C SER* 1.3 63.7 + - - +
47C HIS* 4.0 11.2 - - + +
50C PHE 4.3 1.3 - - - -
51C THR* 3.5 2.8 - - - +
52C THR* 2.9 28.4 + - - +
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Residues in contact with SER 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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43C LYS* 3.5 23.8 + - - +
45C ALA* 1.3 76.5 - - - +
47C HIS* 1.3 74.3 + - - +
48C ARG 5.5 2.1 + - - -
50C PHE 3.5 4.7 - - - -
51C THR* 2.9 22.8 + - - +
29D ASP* 5.2 3.9 - - - +
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Residues in contact with HIS 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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8C HIS 3.5 19.3 - - - +
9C LEU 3.6 14.8 + - - -
10C GLY* 4.0 18.8 - - - -
45C ALA* 4.0 13.3 - - + +
46C SER* 1.3 82.7 + - - +
48C ARG* 1.3 66.1 + - + +
49C GLU 3.0 0.5 + - - -
50C PHE* 2.8 43.3 + - - +
29D ASP* 4.7 2.0 - - - -
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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