Contacts of the strand formed by residues 63 - 70 (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 PRO 63 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55C GLY 3.9 2.0 - - - +
56C ILE* 4.4 4.3 - - + -
61C ASN 3.4 8.0 - - - +
62C LEU* 1.3 100.3 - - + +
64C VAL* 1.3 62.7 + - - +
121C GLU* 4.3 0.9 - - - +
122C ARG* 3.4 57.4 + - - +
124C GLU* 5.2 10.3 - - + +
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Residues in contact with VAL 64 (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* 4.2 20.9 - - + -
55C GLY* 2.8 49.3 + - - -
56C ILE* 3.8 4.3 - - - +
57C ARG* 4.7 1.3 - - + -
62C LEU* 3.4 12.1 + - + +
63C PRO* 1.3 78.7 - - - +
65C ALA* 1.3 57.5 + - - +
66C ILE* 4.1 14.4 - - + -
107C LEU* 3.6 30.1 - - + -
119C ILE* 3.9 11.9 - - + -
120C LEU 3.3 8.7 - - - +
122C ARG* 2.9 19.4 + - - +
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Residues in contact with ALA 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C LEU* 5.0 0.9 - - + -
52C VAL* 3.9 15.3 - - + -
53C TYR 3.4 6.3 - - - +
64C VAL* 1.3 75.0 - - - +
66C ILE* 1.3 60.6 + - - +
67C LYS 3.9 0.6 + - - -
118C LEU 3.4 2.6 - - - +
119C ILE* 3.6 1.6 - - - -
120C LEU* 2.8 41.5 + - + +
122C ARG* 3.8 4.9 - - + +
750C AMP 3.5 39.0 - - + +
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Residues in contact with ILE 66 (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* 4.1 21.8 - - + -
40C VAL* 3.9 30.5 - - + -
51C SER 3.7 2.6 - - - +
52C VAL* 3.3 3.2 - - - -
53C TYR* 2.8 41.1 + - + +
54C SER 5.3 0.2 - - - -
55C GLY* 4.1 19.5 - - - +
64C VAL* 4.1 11.0 - - + -
65C ALA* 1.3 73.0 - - - +
67C LYS* 1.3 58.3 + - - +
68C HIS* 3.7 18.0 + - + -
117C VAL* 3.3 31.0 - - + -
118C LEU 3.4 2.0 - - - -
119C ILE* 4.0 15.9 - - + -
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Residues in contact with LYS 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C PHE* 2.9 34.5 + - - +
51C SER 3.6 3.6 - - - +
52C VAL* 3.8 16.8 - - + +
65C ALA 3.9 0.6 + - - -
66C ILE* 1.3 72.3 - - - +
68C HIS* 1.3 63.2 + - - +
69C VAL* 4.0 11.3 + - + +
89C GLU* 2.6 35.5 + - - +
116C PHE 3.4 2.3 - - - +
117C VAL* 3.2 5.3 - - - -
118C LEU* 2.8 43.1 + - + +
120C LEU* 3.9 19.1 - - + -
186C ASP* 3.1 22.0 + - - +
750C AMP 3.5 30.2 - - - -
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Residues in contact with HIS 68 (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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49C PHE 4.2 0.5 - - - +
50C GLY* 3.6 4.2 - - - -
51C SER* 3.0 38.2 + - - +
53C TYR* 4.0 24.7 - + + -
66C ILE* 3.7 32.2 + - + -
67C LYS* 1.3 74.6 - - - +
69C VAL* 1.3 62.1 - - - +
70C GLU 4.3 0.4 + - - -
112C ARG* 3.1 32.8 + - - -
115C SER* 4.5 8.1 - - - +
116C PHE 3.6 2.9 - - - -
117C VAL* 3.5 17.5 - - + +
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Residues in contact with VAL 69 (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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49C PHE 3.9 19.5 - - - +
50C GLY* 5.1 2.7 - - - -
67C LYS* 4.1 14.6 - - + +
68C HIS* 1.3 79.7 - - - +
70C GLU* 1.3 65.9 + - - +
71C LYS* 3.6 0.3 + - - -
73C ARG* 5.5 4.0 - - + +
74C ILE* 3.9 27.1 - - + +
87C PRO* 5.9 3.4 - - + -
89C GLU* 4.2 17.5 - - - +
115C SER* 3.1 5.5 - - - -
116C PHE* 3.0 39.3 + - + +
118C LEU* 5.0 8.3 - - + -
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Residues in contact with GLU 70 (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 GLY* 6.0 0.4 - - - -
68C HIS 4.3 1.0 + - - -
69C VAL* 1.3 74.4 - - - +
71C LYS* 1.3 67.8 + - - +
72C ASP* 4.4 10.5 - - + +
73C ARG* 3.2 35.3 + - + +
74C ILE* 3.3 14.3 + - - +
114C ASP* 3.7 16.3 - - + +
115C SER* 4.2 4.0 - - - -
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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