Contacts of the strand formed by residues 94 - 98 (chain Q) in PDB entry 5IYB
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 ILE 94 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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300A ALA* 5.1 16.2 - - + -
44Q LYS* 4.5 5.2 - - - +
45Q GLU* 3.8 39.3 + - + +
46Q GLU* 6.1 0.9 - - - +
74Q CYS* 5.2 4.5 - - - -
75Q ARG 4.4 1.6 - - - -
76Q MET* 4.4 23.6 - - + -
77Q ARG* 6.1 0.2 - - - -
92Q TYR* 3.5 21.1 - - + +
93Q PHE* 1.3 79.4 - - - +
95Q ASN* 1.3 66.3 + - - +
96Q TYR* 3.7 31.2 - - + +
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Residues in contact with ASN 95 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42Q CYS* 2.4 47.6 + - - +
43Q VAL 3.9 6.0 + - - -
44Q LYS* 4.7 1.4 - - - +
74Q CYS* 3.3 27.7 - - - +
75Q ARG* 3.3 33.2 + - + +
77Q ARG* 4.2 26.2 - - + +
94Q ILE* 1.3 76.0 - - - +
96Q TYR* 1.3 80.9 + - - +
97Q ARG* 4.4 4.3 + - - +
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Residues in contact with TYR 96 (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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37Q LEU* 4.1 9.8 - - + +
41Q SER 3.1 14.6 - - - +
42Q CYS* 3.9 3.5 - - - -
43Q VAL* 4.2 7.8 + - - +
45Q GLU* 3.3 54.4 + - + -
48Q MET* 4.6 18.4 - - - -
60Q ARG* 4.9 4.5 - - - +
63Q LEU* 3.9 28.7 - - + +
64Q ASN* 5.8 0.7 + - - -
67Q LYS* 5.1 8.3 - - + -
72Q ILE* 3.9 34.1 - - + -
73Q LYS 3.6 2.7 - - - -
74Q CYS* 4.1 12.8 - - - -
94Q ILE* 3.7 23.3 - - + +
95Q ASN* 1.3 85.0 + - - +
97Q ARG* 1.3 60.5 + - - +
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Residues in contact with ARG 97 (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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37Q LEU* 4.6 8.7 - - - +
40Q ASN* 3.6 24.1 + - - +
41Q SER 3.4 16.8 - - - +
42Q CYS* 4.3 11.1 - - - -
72Q ILE* 3.6 2.2 - - - -
73Q LYS* 2.7 68.0 + - + +
74Q CYS* 4.8 5.7 + - - +
75Q ARG* 3.2 38.8 - - - +
95Q ASN* 4.4 6.0 + - - +
96Q TYR* 1.3 77.4 - - - +
98Q THR* 1.3 69.1 + - - +
100Q VAL* 5.0 9.1 - - - +
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Residues in contact with THR 98 (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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34Q LEU* 4.4 7.9 + - + +
37Q LEU* 3.2 43.9 + - - +
38Q ILE* 3.7 10.9 + - + +
40Q ASN* 6.2 0.4 - - - +
71Q PHE 3.9 14.1 + - - +
72Q ILE* 4.7 0.2 - - - +
97Q ARG* 1.3 82.2 - - - +
99Q LEU* 1.3 77.4 + - - +
100Q VAL* 3.5 11.6 + - - +
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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