Contacts of the strand formed by residues 35 - 41 (chain C) in PDB entry 1PYB
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 LEU 35 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25C ALA* 5.0 2.7 - - + -
33C LYS* 3.1 6.7 + - - -
34C LEU* 1.3 83.5 - - + +
36C LYS* 1.3 61.2 + - - +
37C LEU* 2.8 19.8 + - + +
48C VAL 3.4 0.3 - - - +
49C VAL* 4.3 1.0 - - - +
50C ALA* 2.8 35.8 + - + +
51C GLY 2.9 25.4 - - - +
52C ILE* 3.4 30.3 - - + +
56C TYR 4.4 3.6 - - - +
58C PRO* 4.1 27.4 - - + -
61C LEU* 3.8 27.6 - - + -
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Residues in contact with LYS 36 (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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25C ALA* 3.3 3.7 - - - +
26C GLU* 2.9 63.1 + - + +
27C ARG 5.6 0.2 - - - -
28C VAL* 3.7 28.9 - - + +
34C LEU* 3.3 8.2 + - - +
35C LEU* 1.3 67.5 - - - +
37C LEU* 1.3 63.0 + - - +
38C THR* 3.6 1.9 + - - +
47C THR* 5.8 2.7 - - - -
48C VAL 3.6 8.3 - - - +
49C VAL* 3.8 30.3 - - + +
81C GLU* 3.4 27.8 + - + +
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Residues in contact with LEU 37 (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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22C VAL* 3.6 36.8 - - + -
24C SER 3.6 2.2 - - - -
25C ALA* 4.0 16.2 - - + -
35C LEU* 2.8 17.9 + - + +
36C LYS* 1.3 70.3 - - - +
38C THR* 1.3 62.2 + - - +
39C LEU* 3.3 11.7 + - + +
47C THR* 3.6 1.3 - - - -
48C VAL* 2.9 35.7 + - - +
50C ALA* 3.8 15.5 - - + -
52C ILE* 6.0 1.3 - - + -
61C LEU* 3.6 34.8 - - + -
66C ILE* 4.5 8.3 - - + -
86C ILE* 3.8 24.5 - - + -
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Residues in contact with THR 38 (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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21C LYS 3.6 0.3 - - - +
22C VAL* 3.6 0.8 - - - +
23C LEU* 2.9 35.1 + - - +
24C SER* 2.6 53.7 + - - +
26C GLU* 4.6 12.1 - - + +
36C LYS 4.5 4.7 - - - +
37C LEU* 1.3 69.6 - - - +
39C LEU* 1.3 64.5 + - - +
46C ARG 3.9 4.5 - - - -
47C THR* 3.8 22.0 - - + -
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Residues in contact with LEU 39 (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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20C ALA* 4.3 9.6 - - + +
21C LYS 3.5 5.6 - - - +
22C VAL* 3.8 26.7 - - + -
23C LEU* 5.2 1.1 - - - -
37C LEU* 3.3 9.2 + - + +
38C THR* 1.3 72.4 - - - +
40C SER* 1.3 59.8 + - - +
41C LEU* 3.6 9.0 + - + +
45C GLU* 3.6 2.9 - - - +
46C ARG* 2.8 47.5 + - + +
48C VAL* 3.7 29.8 - - + -
66C ILE* 5.2 1.6 - - + -
68C ILE* 3.5 45.3 - - + -
83C GLN 5.2 1.8 - - - +
86C ILE* 4.1 11.2 - - + -
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Residues in contact with SER 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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20C ALA* 3.6 12.4 - - - +
21C LYS* 2.8 29.4 + - - +
23C LEU* 3.8 31.0 - - - +
38C THR 3.7 0.4 + - - -
39C LEU* 1.3 71.6 - - - +
41C LEU* 1.3 58.9 + - - +
42C GLY 2.9 11.1 + - - -
44C GLU 3.7 3.8 - - - -
45C GLU* 4.7 6.5 - - - +
106C GLU* 3.0 26.7 + - - +
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Residues in contact with LEU 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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18C ARG* 3.8 33.4 - - + +
19C VAL 3.8 5.8 - - - +
20C ALA* 3.5 23.1 - - + -
39C LEU* 3.6 10.2 + - + +
40C SER* 1.3 68.1 - - - +
42C GLY* 1.3 58.0 + - - +
43C ASP 2.9 9.9 + - - -
44C GLU* 2.7 33.2 + - + +
46C ARG* 3.5 45.1 - - + +
68C ILE* 5.4 7.0 - - + +
70C ALA* 4.3 12.3 - - + -
83C GLN 5.1 2.2 - - - +
107C GLY* 4.2 11.0 - - - +
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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