Contacts of the strand formed by residues 39 - 45 (chain C) in PDB entry 1YF9
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 GLU 39 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34C SER* 2.5 36.5 + - - +
35C ASP* 5.0 3.1 - - - +
36C THR* 3.1 12.2 + - - +
37C VAL 3.3 1.8 + - - -
38C ALA* 1.3 83.8 - - + +
40C PHE* 1.3 69.7 + - - +
41C TRP* 4.0 18.9 - - + -
60C HIS* 2.7 38.0 + - + +
61C VAL 3.4 5.6 - - - +
62C GLN* 4.4 11.3 + - + +
168C TYR* 5.5 2.4 - - - -
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Residues in contact with PHE 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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21C TYR* 3.5 37.5 - + + -
24C LEU* 3.5 30.7 - - + -
31C VAL* 3.9 11.9 - - + -
32C TYR 3.5 13.2 - - - +
33C PRO* 4.2 4.0 - - + -
34C SER 4.4 0.2 - - - +
37C VAL 3.7 12.6 - - - -
39C GLU* 1.3 81.6 - - - +
41C TRP* 1.3 71.4 + - - +
42C VAL* 3.7 16.6 - - + -
59C LEU 3.7 0.2 - - - +
60C HIS* 3.8 1.4 - - - -
61C VAL* 2.9 61.9 + - + +
63C LEU* 3.8 23.6 - - + -
107C LEU* 4.6 3.1 - - + -
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Residues in contact with TRP 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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31C VAL* 3.3 4.2 - - - +
32C TYR* 2.7 57.8 + - + +
33C PRO 3.9 2.5 - - - -
34C SER* 3.8 22.9 - - - -
39C GLU* 4.0 13.7 - - - -
40C PHE* 1.3 75.6 - - - +
42C VAL* 1.3 64.7 + - - +
58C MET* 3.8 21.1 - - + -
59C LEU 3.1 9.0 - - - +
60C HIS* 3.4 32.8 - + - +
77C CYS* 3.6 27.2 - - - -
164C ILE* 4.3 10.3 - - + -
165C PRO* 3.6 35.2 - - + +
168C TYR* 3.5 45.5 - + + -
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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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24C LEU* 4.3 1.3 - - + -
29C ARG* 5.4 7.9 - - + +
30C LYS 3.4 9.4 - - - +
31C VAL* 4.2 16.4 - - + -
40C PHE* 3.7 28.9 - - + -
41C TRP* 1.3 79.9 - - - +
43C GLU* 1.3 76.0 + - - +
44C PHE 3.6 0.7 + - - -
58C MET* 3.7 3.7 - - - -
59C LEU* 2.8 39.8 + - + +
61C VAL* 4.0 10.8 - - + -
111C PHE* 4.1 36.8 - - + -
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Residues in contact with GLU 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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30C LYS* 3.0 59.5 + - + +
32C TYR* 4.5 4.7 + - + -
42C VAL* 1.3 84.4 - - - +
44C PHE* 1.3 63.7 + - - +
45C LYS* 3.9 22.0 + - - +
56C THR* 3.8 27.2 - - + +
57C TRP 3.6 5.4 - - - +
58C MET* 3.8 18.5 - - + +
111C PHE* 6.0 0.9 - - - +
157C PRO* 5.7 2.9 - - - +
161C LEU* 5.9 1.4 - - - +
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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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43C GLU* 1.3 77.4 - - - +
45C LYS* 1.3 82.1 + - - +
46C GLY* 4.3 1.1 - - - -
47C PRO* 4.7 1.3 - - + -
55C GLY 4.1 0.2 - - - +
56C THR* 3.5 4.0 - - - +
57C TRP* 2.8 43.9 + + - +
59C LEU* 3.6 32.8 - - + -
76C PHE* 4.1 23.3 - + - -
111C PHE* 3.7 24.9 - - + -
115C LEU* 3.7 31.6 - - + -
116C PRO* 3.9 17.9 - - + -
119C LEU* 3.8 24.7 - - + -
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Residues in contact with LYS 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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43C GLU* 3.9 24.1 + - - +
44C PHE* 1.3 95.2 - - - +
46C GLY* 1.3 68.2 + - - +
47C PRO* 3.7 1.0 - - - +
53C GLU 5.8 1.3 - - - +
55C GLY 3.5 4.7 - - - +
56C THR* 2.8 34.3 + - + +
116C PRO* 5.6 1.0 - - - +
157C PRO* 4.5 11.5 - - - +
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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