Contacts of the strand formed by residues 75 - 80 (chain E) in PDB entry 3SKU
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 LYS 75 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137C TYR* 5.8 10.0 + - + +
216C SER 3.3 14.4 - - - +
217C ILE* 3.6 14.8 + - - +
218C GLY* 4.2 10.5 - - - +
68E GLN* 4.9 18.6 - - + +
69E LYS 3.9 4.9 - - - +
70E SER* 4.3 14.6 - - - +
71E THR* 4.9 2.2 - - - +
74E SER* 1.3 86.3 - - - +
76E GLN* 1.3 61.5 + - - +
123E ILE* 4.2 24.0 - - + -
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Residues in contact with GLN 76 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215C ASP 4.1 4.0 - - - +
216C SER* 3.7 17.0 + - - +
218C GLY* 4.4 0.2 - - - -
68E GLN* 3.3 4.1 - - - -
69E LYS* 2.5 56.3 + - + +
71E THR* 5.6 11.1 - - + +
75E LYS* 1.3 76.9 - - - +
77E ASN* 1.3 67.5 + - - +
91E ALA 4.4 3.1 - - - +
92E PRO* 4.1 11.3 - - - +
93E TYR* 3.8 26.9 + - - +
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Residues in contact with ASN 77 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214C VAL 3.7 0.2 + - - -
215C ASP* 2.7 45.1 + - - +
218C GLY* 3.3 19.0 - - - -
219C MET 2.6 25.7 + - - +
220C LEU* 3.0 16.9 - - + +
67E TRP 4.3 2.7 - - - -
68E GLN* 3.5 11.1 + - + +
76E GLN* 1.3 84.6 - - - +
78E VAL* 1.3 62.0 + - - +
79E ALA 5.3 0.2 - - - +
80E ILE* 5.2 2.7 - - + -
90E LEU* 3.7 33.2 - - + +
91E ALA 4.6 1.9 - - - +
93E TYR* 4.6 4.0 - - - -
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Residues in contact with VAL 78 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67E TRP* 2.9 28.2 + - + +
68E GLN 3.9 14.1 - - - +
69E LYS* 3.9 12.1 - - + +
76E GLN 4.2 0.7 - - - +
77E ASN* 1.3 77.6 - - - +
79E ALA* 1.3 67.0 + - + +
89E VAL* 3.4 2.1 - - - +
90E LEU* 2.8 39.0 + - - +
93E TYR* 3.6 43.7 - - + +
97E VAL* 4.8 9.6 - - + -
109E ILE* 5.3 4.7 - - + -
111E LEU* 6.6 0.2 - - + -
122E TYR* 4.6 12.8 - - + -
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Residues in contact with ALA 79 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65E VAL 4.0 0.2 - - - +
66E THR* 3.3 5.9 - - - +
67E TRP* 2.9 37.8 + - + +
78E VAL* 1.3 85.2 - - + +
80E ILE* 1.3 62.8 + - - +
88E SER 3.9 0.4 - - - -
89E VAL* 3.1 27.6 - - + -
97E VAL* 4.6 7.9 - - + -
99E PHE* 3.9 19.5 - - + -
109E ILE* 4.9 0.2 - - + -
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Residues in contact with ILE 80 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C HIS* 5.7 3.4 - - + -
134C ARG* 5.2 3.4 - - - +
215C ASP* 4.3 7.9 - - - +
220C LEU* 4.5 4.7 - - + -
221C PRO* 4.2 23.6 - - + -
64E GLN* 3.6 33.4 - - + +
65E VAL 3.4 2.5 - - - -
66E THR* 3.8 14.8 - - + -
77E ASN* 5.2 2.0 - - + -
79E ALA* 1.3 75.9 - - - +
81E TYR* 1.3 68.0 + - - +
82E ASN* 4.2 3.4 - - + +
87E VAL* 3.5 15.1 - - - +
88E SER* 3.0 34.9 + - - +
90E LEU* 4.1 26.2 - - + -
99E PHE* 3.7 4.1 - - - -
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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