Contacts of the strand formed by residues 106 - 115 (chain q) in PDB entry 5K0Y
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 q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1q MET* 3.3 31.7 - - + +
56q ASN 3.8 15.0 - - - +
57q ASP* 3.6 21.8 - - - +
58q LYS* 3.5 9.3 + - - -
63q MET* 3.7 28.5 - - + -
98q ARG* 3.6 24.2 - - - +
102q VAL* 3.9 17.7 - - + -
104q ALA 3.3 2.3 - - - +
105q ASN* 1.4 78.9 - - - +
107q SER* 1.4 62.1 + - - +
108q VAL 4.0 9.6 - - - +
109q LEU* 3.4 33.2 - - + -
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Residues in contact with SER 107 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A G 3.4 38.4 + - - +
157A U 3.9 7.4 + - - -
1q MET* 3.5 4.8 - - - +
2q LYS* 3.3 20.4 + - - +
56q ASN 3.1 6.3 + - - -
57q ASP 3.4 9.4 + - - -
58q LYS* 3.4 27.9 + - - +
105q ASN 3.8 1.6 + - - -
106q LEU* 1.4 72.3 - - - +
108q VAL* 1.4 66.4 + - - +
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Residues in contact with VAL 108 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A G 3.9 11.9 - - - +
156A G 3.5 33.9 - - - +
164A A 6.1 0.2 - - + -
1q MET* 4.8 0.7 - - - -
2q LYS* 3.3 22.7 - - + +
4q ASN* 3.7 20.9 - - + -
15q LEU* 4.6 3.8 - - + -
55q GLY* 3.3 4.4 - - - -
56q ASN* 3.1 29.8 + - - +
106q LEU* 3.4 10.0 - - - +
107q SER* 1.4 85.8 - - - +
109q LEU* 1.4 72.6 + - - +
110q ASN* 4.1 12.6 - - - +
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Residues in contact with LEU 109 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1q MET* 3.7 26.3 - - + -
2q LYS 3.5 4.0 + - - -
3q LEU* 3.7 21.9 - - + -
4q ASN 2.9 24.4 + - - -
24q LEU* 6.0 0.7 - - + -
27q PHE* 3.9 29.4 - - + +
28q TYR* 5.1 3.8 - - + -
52q ILE* 3.7 31.6 - - + -
54q GLY 3.8 6.5 - - - +
63q MET* 4.9 0.2 - - - -
102q VAL* 3.8 9.9 - - + -
106q LEU* 3.4 24.5 - - + -
108q VAL* 1.4 75.4 - - - +
110q ASN* 1.4 59.7 + - - +
111q LEU* 3.6 11.5 + - + +
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Residues in contact with ASN 110 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A A 3.4 26.3 + - - -
165A G 3.5 31.1 + - - +
4q ASN* 3.3 31.7 + - - +
6q SER* 5.4 0.7 + - - -
52q ILE* 4.2 0.3 - - - +
53q SER* 3.0 37.7 + - - +
54q GLY 3.0 19.0 + - - +
55q GLY* 3.5 20.0 - - - -
56q ASN* 4.6 0.8 + - - -
108q VAL* 4.1 7.9 - - - +
109q LEU* 1.4 69.2 - - - +
111q LEU* 1.3 62.6 + - - +
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Residues in contact with LEU 111 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A G 5.2 0.7 + - - -
3q LEU* 4.1 26.9 - - + -
4q ASN 3.1 19.1 + - - +
5q ILE* 4.2 16.2 - - + -
6q SER* 3.2 14.8 + - - -
27q PHE* 4.0 41.7 - - + -
50q VAL* 3.6 23.6 - - + -
51q ARG 4.0 2.5 - - - -
52q ILE* 4.0 21.1 - - + -
109q LEU* 4.1 19.3 - - + +
110q ASN* 1.3 82.3 - - - +
112q VAL* 1.4 65.0 + - - +
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Residues in contact with VAL 112 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A G 4.3 2.0 - - - +
166A A 3.5 30.1 - - - +
167A G 5.5 0.7 - - - +
6q SER* 3.8 7.0 - - - +
8q PRO* 3.9 22.9 - - + -
50q VAL* 3.4 4.1 - - - -
51q ARG* 2.8 58.6 + - - +
53q SER* 3.5 19.5 - - - +
111q LEU* 1.4 78.2 - - - +
113q ILE* 1.4 73.9 + - - +
114q VAL* 3.6 5.5 + - + +
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Residues in contact with ILE 113 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5q ILE* 3.6 24.5 - - + -
6q SER 3.0 18.9 + - - +
7q PHE* 3.9 27.5 - - + -
8q PRO* 3.1 24.3 - - - +
45q TRP* 5.3 1.1 - - + -
48q TYR* 3.6 37.7 - - + -
49q VAL 3.6 7.4 - - - +
50q VAL* 4.2 7.2 - - + -
111q LEU 4.2 0.2 - - - -
112q VAL* 1.4 73.9 - - - +
114q VAL* 1.4 61.2 + - - +
115q LYS 3.4 26.7 - - - +
116q LYS* 4.1 0.9 - - - +
121q ILE* 5.2 0.4 - - + -
124q LEU* 3.9 16.8 - - + -
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Residues in contact with VAL 114 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1773A G 5.6 3.4 + - - +
7q PHE* 5.7 3.0 - - - -
8q PRO* 5.4 2.6 - - + +
35q GLU* 3.3 25.1 - - - +
49q VAL* 3.1 20.8 + - + +
51q ARG* 3.7 34.3 - - + +
112q VAL* 4.0 6.1 - - + +
113q ILE* 1.4 77.8 - - - +
115q LYS* 1.4 77.8 + - + +
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Residues in contact with LYS 115 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1773A G 3.7 49.7 + - - +
1774A G 5.3 3.1 + - - -
35q GLU* 6.0 3.2 - - - +
47q GLY 5.0 1.1 - - - +
48q TYR* 3.4 2.8 - - - -
49q VAL* 3.1 47.2 + - + +
113q ILE* 3.4 8.8 - - - +
114q VAL* 1.4 95.9 - - + +
116q LYS* 1.4 66.1 + - - +
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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