Contacts of the strand formed by residues 50 - 57 (chain C) in PDB entry 1YXU
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 GLY 50 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46C SER* 3.3 6.9 + - - -
47C GLY 3.1 30.9 + - - +
48C GLY 3.4 1.8 - - - -
49C PHE* 1.3 83.2 - - - +
51C SER* 1.3 63.6 + - - -
68C HIS 3.6 9.2 - - - -
69C VAL* 5.1 3.6 - - - -
70C GLU 6.0 0.4 - - - -
73C ARG* 4.8 6.2 - - - +
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Residues in contact with SER 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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43C LEU* 4.1 15.0 - - - -
45C GLY 3.6 6.1 - - - -
46C SER* 4.0 8.1 + - - -
49C PHE 4.2 0.6 + - - -
50C GLY* 1.3 76.3 + - - -
52C VAL* 1.3 62.1 + - - +
53C TYR* 4.2 14.0 - - - -
66C ILE 3.7 1.9 - - - +
67C LYS* 3.6 0.7 - - - +
68C HIS* 3.0 40.9 + - - +
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Residues in contact with VAL 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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43C LEU* 3.5 3.0 - - - +
44C LEU* 2.7 37.5 + - + -
45C GLY* 3.2 15.8 + - - +
49C PHE* 3.7 28.9 - - + -
51C SER* 1.3 75.3 - - - +
53C TYR* 1.3 65.4 + - - +
65C ALA* 3.9 20.4 - - + -
66C ILE 3.3 8.3 - - - +
67C LYS* 3.8 21.1 - - + +
750C AMP 4.1 28.3 - - + +
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Residues in contact with TYR 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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40C VAL* 4.0 21.8 - - + -
41C GLY 3.4 18.8 - - - +
42C PRO 3.4 4.9 - - - -
43C LEU* 3.9 27.7 - - + +
44C LEU* 4.2 3.8 - - - +
51C SER* 4.2 20.6 - - - -
52C VAL* 1.3 78.4 - - - +
54C SER* 1.3 61.4 + - - +
65C ALA* 3.4 6.9 - - - +
66C ILE* 2.8 38.2 + - + +
68C HIS* 4.0 31.2 - + - -
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Residues in contact with SER 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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41C GLY* 2.4 40.9 + - - -
42C PRO* 2.7 29.6 + - - +
44C LEU* 3.9 23.7 - - - +
53C TYR* 1.3 72.7 - - - +
55C GLY* 1.3 52.4 + - - +
64C VAL 3.9 4.0 - - - -
122C ARG* 3.2 30.0 + - - -
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Residues in contact with GLY 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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39C GLN 3.3 12.1 - - - -
41C GLY* 4.2 0.4 - - - -
53C TYR 3.7 2.4 + - - -
54C SER* 1.3 75.1 - - - +
56C ILE* 1.3 63.3 + - - +
64C VAL* 2.8 31.5 + - - -
66C ILE* 4.1 11.0 - - - +
122C ARG* 3.0 24.3 + - - -
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Residues in contact with ILE 56 (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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38C TYR* 3.5 4.9 - - - -
39C GLN* 2.9 53.3 + - + +
55C GLY* 1.3 80.7 - - - +
57C ARG* 1.3 74.8 + - - +
58C VAL* 3.3 2.2 + - + +
61C ASN* 4.0 27.4 - - + +
62C LEU 3.6 4.0 - - - -
63C PRO* 4.4 8.7 - - + -
64C VAL* 3.8 1.8 - - - +
66C ILE* 5.2 0.6 - - - +
122C ARG* 4.3 12.1 - - - +
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Residues in contact with ARG 57 (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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37C GLN* 4.0 12.7 + - - +
38C TYR* 3.5 37.4 + - + -
56C ILE* 1.3 70.4 - - - +
58C VAL* 1.3 62.0 + - - +
59C SER* 3.0 26.4 + - - +
60C ASP* 3.1 21.6 + - - +
61C ASN* 2.9 30.3 + - - -
62C LEU* 3.0 45.6 + - + +
64C VAL* 4.3 3.9 - - + +
107C LEU* 3.8 33.4 + - - +
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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