Contacts of the strand formed by residues 111 - 118 (chain C) in PDB entry 4YO0
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 ALA 111 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57C ARG* 4.1 14.6 - - - +
58C GLN 3.4 17.0 - - - +
59C THR* 3.6 9.4 - - + -
108C GLU 5.7 0.2 - - - +
109C ASP 3.2 11.2 + - - +
110C THR* 1.3 79.0 - - - +
112C THR* 1.3 64.3 + - - +
113C TYR* 3.5 15.5 - - + -
131C MET* 3.6 10.3 - - - +
132C VAL 3.0 30.4 + - - +
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Residues in contact with THR 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C VAL 4.1 0.2 - - - +
57C ARG* 3.3 3.5 - - - +
58C GLN* 2.8 41.3 + - - +
111C ALA* 1.3 71.2 - - - +
113C TYR* 1.3 61.7 - - - +
114C TYR* 3.7 35.1 + - + +
128C GLN 5.4 0.4 - - - +
129C GLY* 3.9 17.5 - - - -
130C VAL 3.5 9.0 - - - +
131C MET* 3.8 16.7 - - - +
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Residues in contact with TYR 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C GLU* 2.6 23.9 - - - +
39C LEU* 3.4 30.1 - - + -
55C TRP* 4.4 5.2 - + + -
56C VAL 3.8 3.1 - - - -
57C ARG* 3.0 43.9 + - + -
67C ILE* 4.7 4.9 - - + -
87C PHE* 3.9 9.1 - + - -
100C LEU* 4.1 12.8 - - + -
102C MET* 3.4 23.2 - - + +
109C ASP* 2.6 31.5 + - - +
111C ALA* 3.5 22.0 - - + -
112C THR* 1.3 72.3 - - - +
114C TYR* 1.3 56.9 + - - +
129C GLY* 3.4 0.3 - - - -
130C VAL* 2.8 26.6 + - + +
132C VAL* 3.7 23.3 - - + -
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Residues in contact with TYR 114 (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 GLU* 3.2 3.8 - - - -
55C TRP* 3.3 10.1 - - - -
56C VAL* 2.7 45.6 + - + +
58C GLN* 3.3 26.0 + - + -
64C LEU* 4.5 7.4 - - + -
112C THR* 3.7 22.8 - - + +
113C TYR* 1.3 74.1 - - - +
115C CYS* 1.3 61.8 + - - +
126C TRP* 3.8 30.3 - + + -
127C GLY 3.6 10.1 - - - -
128C GLN 3.9 2.5 + - - -
129C GLY* 3.5 27.4 - - - -
58D GLN* 3.0 24.2 + - - -
61D GLY 5.8 0.2 - - - -
62D ARG 3.5 7.8 + - - -
63D SER* 3.7 20.9 - - - -
64D PRO* 4.0 7.9 - - + -
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Residues in contact with CYS 115 (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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23C LEU* 3.9 14.1 - - - -
25C GLU* 2.8 29.7 + - - -
41C CYS* 2.2 52.5 - - + -
54C ALA 3.3 4.5 - - - -
55C TRP* 4.0 7.4 - - + -
98C HIS* 3.7 13.7 - - + +
114C TYR* 1.3 78.3 - - - +
116C ALA* 1.3 63.2 + - - +
126C TRP* 3.5 2.3 - - - -
127C GLY* 2.8 23.5 + - - -
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Residues in contact with ALA 116 (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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23C LEU* 4.0 4.3 - - - -
53C MET* 3.5 8.0 - - - +
54C ALA* 2.8 36.1 + - + +
56C VAL* 5.2 3.8 - - + -
98C HIS* 4.7 0.2 + - - -
115C CYS* 1.3 77.5 - - - +
117C LYS* 1.3 58.5 + - - +
123C PHE* 3.6 33.0 - - + -
125C TYR 3.3 12.8 - - - +
126C TRP* 4.3 16.4 - - + -
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Residues in contact with LYS 117 (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 VAL* 4.4 4.5 - - + -
23C LEU* 3.6 15.4 - - + +
46C PHE* 3.7 34.5 - - + -
51C TYR* 3.3 33.4 - - + -
52C GLY 3.8 4.7 - - - -
53C MET* 3.6 21.3 - - + -
116C ALA* 1.3 73.2 - - - +
118C THR* 1.3 77.9 + - - +
119C SER* 4.3 2.0 - - - -
123C PHE* 3.3 9.0 - - - +
124C ASP* 2.8 54.0 + - - +
125C TYR* 3.0 18.8 + - + +
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Residues in contact with THR 118 (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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51C TYR* 3.3 8.7 - - - +
52C GLY* 3.1 26.4 + - - +
53C MET 5.0 0.7 - - - +
54C ALA* 4.9 6.3 - - + -
69C SER* 5.5 3.6 - - - +
117C LYS* 1.3 93.2 + - - +
119C SER* 1.3 59.7 + - - +
122C TYR 3.5 4.9 - - - -
123C PHE* 3.6 19.7 - - + -
124C ASP* 3.7 2.0 - - - -
6F MET* 3.4 26.9 - - + -
7F PRO 5.9 0.7 - - - +
8F GLY 5.8 1.6 - - - -
9F ALA* 3.7 14.9 - - + +
12F ASP* 2.7 29.7 + - - +
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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