Contacts of the strand formed by residues 106 - 111 (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 LEU 106 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90C VAL* 4.4 8.7 - - + -
93C LEU* 3.9 43.9 + - + +
94C LYS* 4.1 25.4 - - + +
97C SER* 4.6 13.3 + - - -
104C ILE 3.9 2.6 + - - -
105C ARG* 1.3 74.8 + - - +
107C LEU* 1.3 62.9 + - - +
108C ASP* 3.1 27.1 - - - +
109C TRP* 4.2 19.3 - - + -
118C LEU* 4.0 26.9 - - + -
119C ILE 3.4 9.9 - - - +
120C LEU* 4.4 3.4 - - + -
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Residues in contact with LEU 107 (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* 5.0 0.9 - - - +
57C ARG* 3.8 28.1 + - - +
62C LEU* 3.8 13.9 - - + -
64C VAL* 3.6 30.5 - - + -
105C ARG* 3.7 45.8 + - + +
106C LEU* 1.3 74.4 - - - +
108C ASP* 1.3 68.6 + - + +
119C ILE* 2.9 20.9 + - + +
121C GLU* 4.2 21.3 - - + +
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Residues in contact with ASP 108 (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* 4.8 7.6 + - - -
38C TYR* 3.9 13.3 + - - +
94C LYS* 6.3 0.4 - - - +
106C LEU* 3.1 15.5 - - - +
107C LEU* 1.3 82.5 - - - +
109C TRP* 1.3 74.6 + - - +
110C PHE* 3.8 20.6 - - - -
119C ILE* 2.9 41.2 + - + -
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Residues in contact with TRP 109 (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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80C LEU* 3.9 22.6 - - + +
84C THR* 5.2 7.4 - - + -
86C VAL* 3.8 14.1 - - + -
90C VAL* 4.0 23.8 - - + +
94C LYS* 3.4 34.9 - - - +
106C LEU* 4.2 11.2 - - + -
108C ASP* 1.3 87.2 + - - +
110C PHE* 1.3 94.5 + - - +
111C GLU* 4.1 18.6 - - + -
116C PHE* 3.8 27.4 - + - -
117C VAL 3.3 12.6 - - - +
118C LEU* 4.4 12.8 - - + -
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Residues in contact with PHE 110 (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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34C LEU* 3.6 36.1 - - - -
35C GLU* 4.4 12.1 - - + -
37C GLN* 5.2 3.1 - - - -
38C TYR* 4.0 14.1 - + - -
108C ASP* 3.8 19.7 - - - -
109C TRP* 1.3 91.1 - - - +
111C GLU* 1.3 63.8 + - - +
112C ARG* 5.9 2.2 - - + -
116C PHE* 3.4 6.8 - - - -
117C VAL* 2.9 49.5 + - + +
119C ILE* 3.8 28.3 - - + -
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Residues in contact with GLU 111 (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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71C LYS* 3.0 20.1 + - - +
84C THR* 5.5 4.2 - - - +
85C ARG 4.2 7.3 - - - +
109C TRP* 4.1 12.7 - - + -
110C PHE* 1.3 77.0 - - - +
112C ARG* 1.3 73.9 - - - +
115C SER 3.8 2.0 - - - -
116C PHE* 3.4 39.2 - - + -
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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