Contacts of the strand formed by residues 106 - 113 (chain D) 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 106 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57D GLN* 3.6 31.4 - - + -
58D GLN 3.6 10.8 - - - +
59D HIS* 3.7 9.6 - - + +
60D GLU 5.7 0.9 - - - +
104D ASP 3.2 8.1 + - - +
105D GLU* 1.3 77.6 - - - +
107D ASP* 1.3 62.8 + - - +
108D TYR* 3.6 9.4 - - + -
124D LYS* 4.6 7.0 - - - +
125D LEU 2.9 29.1 + - - -
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Residues in contact with ASP 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C GLN* 5.2 0.7 + - - -
56D TYR 3.8 0.5 - - - +
57D GLN* 3.5 2.3 - - - -
58D GLN* 2.7 47.8 + - + +
106D ALA* 1.3 74.7 - - - +
108D TYR* 1.3 67.8 + - - +
109D PHE* 3.3 31.7 + - + -
121D GLY 5.1 0.9 - - - +
122D GLY* 3.3 7.6 - - - -
123D THR 3.1 27.8 + - - +
124D LYS* 4.3 7.6 - - + +
301D EDO 5.7 0.7 + - - -
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Residues in contact with TYR 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D GLN* 3.0 9.2 + - - -
39D LEU* 3.7 28.7 - - + -
55D TRP* 4.6 5.8 - - + -
56D TYR 3.3 12.3 - - - +
57D GLN* 3.0 38.8 + - + -
67D MET* 4.3 3.8 - - + -
82D PHE* 3.7 24.0 - + - -
95D LEU* 3.7 20.4 - - + -
97D ILE* 4.2 2.9 - - + -
104D ASP* 2.6 38.2 + - - +
106D ALA* 3.6 18.6 - - + -
107D ASP* 1.3 71.8 + - - +
109D PHE* 1.3 62.2 + - - +
122D GLY* 3.3 0.5 - - - -
123D THR* 2.9 34.3 + - - +
125D LEU* 3.9 13.7 - - + -
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Residues in contact with PHE 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C GLN* 3.7 18.2 - - - -
63C GLY* 4.7 2.5 - - - -
64C LEU* 3.6 41.7 - - + -
25D GLN* 3.6 2.0 - - - -
54D ASN 3.9 0.2 - - - +
55D TRP* 3.4 6.3 - - - -
56D TYR* 2.8 50.5 + - + +
58D GLN* 3.5 27.6 - - + -
64D PRO* 5.9 0.4 - - + -
107D ASP* 3.3 37.0 - - + -
108D TYR* 1.3 75.7 - - - +
110D CYS* 1.3 63.7 + - - +
119D PHE* 4.8 1.1 - - + -
120D GLY 3.4 18.6 - - - -
121D GLY 3.6 10.5 - - - -
122D GLY* 3.5 16.2 - - - -
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Residues in contact with CYS 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D LEU* 4.0 2.5 - - - -
25D GLN* 3.2 23.3 + - - +
41D CYS* 2.1 52.9 - - + -
53D VAL* 4.3 2.9 - - + -
54D ASN 3.2 8.5 - - - +
55D TRP* 3.9 16.4 - - + -
109D PHE* 1.3 73.7 - - - +
111D HIS* 1.3 63.0 + - - +
119D PHE* 3.4 7.4 - - - -
120D GLY* 2.9 31.4 + - - -
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Residues in contact with HIS 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121C VAL 4.1 0.2 - - - -
122C TYR* 4.0 1.8 - - - -
123C PHE* 3.7 8.4 - + - -
23D LEU* 3.9 3.6 - - - -
52D TYR 3.9 0.3 - - - +
53D VAL* 3.3 6.2 - - - -
54D ASN* 2.9 56.6 + - - +
56D TYR* 3.1 39.2 + + + -
110D CYS* 1.3 79.7 - - - +
112D SER* 1.4 85.3 + - - +
113D TYR* 4.7 1.6 - + - -
117D ILE* 3.5 19.8 - - + +
118D VAL 3.3 11.7 - - - -
119D PHE* 3.8 14.4 - + + -
6F MET* 3.3 35.1 - - - -
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Residues in contact with SER 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D PHE* 4.0 14.4 - - - -
23D LEU* 3.6 15.7 - - - +
43D ARG* 4.7 4.6 + - - -
48D ILE* 5.2 1.2 + - - -
51D ASN* 3.8 9.9 + - - +
52D TYR 2.6 24.1 + - - -
53D VAL* 4.0 12.0 - - - +
111D HIS* 1.4 83.7 - - - +
113D TYR* 1.3 76.4 + - - +
118D VAL 3.0 27.4 + - - +
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Residues in contact with TYR 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121C VAL* 3.2 36.7 - - + +
21D PHE* 3.6 13.2 - - - -
43D ARG* 4.2 1.9 + - - -
51D ASN* 3.0 46.8 + - + +
52D TYR* 3.7 25.0 + - + -
54D ASN* 4.9 0.2 - - - -
111D HIS* 4.5 1.1 - + - -
112D SER* 1.3 89.5 + - - +
114D SER* 1.4 70.8 + - - +
116D GLY 3.1 15.9 - - - +
117D ILE* 4.2 13.9 - - + -
4F VAL* 3.0 28.9 + - + -
5F ALA 3.7 3.4 - - - -
6F MET* 3.5 40.2 - - + -
7F PRO* 4.2 1.6 - - + -
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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