Contacts of the strand formed by residues 64 - 72 (chain C) in PDB entry 3F98
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 SER 64 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58C ARG* 4.2 8.9 + - - +
62C PRO 4.0 1.8 + - - -
63C TYR* 1.3 78.2 - - - +
65C VAL* 1.3 61.8 + - - +
86C PRO* 3.5 6.2 - - - +
87C SER* 2.9 31.1 + - - -
88C GLN 4.7 1.5 + - - -
89C ASP 3.2 25.7 - - - -
90C ASN* 2.8 42.2 + - - +
133C ASN* 4.0 2.0 - - - -
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Residues in contact with VAL 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C ARG* 5.3 2.6 - - - +
63C TYR 3.9 0.7 - - - +
64C SER* 1.3 81.1 - - - +
66C GLY* 1.3 67.9 + - - +
84C TYR* 4.2 6.7 - - + -
85C TYR 3.3 3.6 - - - +
87C SER* 3.5 5.2 - - - -
131C PRO 4.6 5.3 + - - +
132C ALA* 3.3 13.6 - - + -
133C ASN* 2.7 33.7 + - - +
165C ILE* 3.5 28.0 - - + +
168C ALA* 3.6 20.2 - - + -
169C SER* 3.4 37.2 - - - +
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Residues in contact with GLY 66 (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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65C VAL* 1.3 80.0 - - - +
67C CYS* 1.3 62.0 + - - +
84C TYR* 3.3 5.2 - - - -
85C TYR* 2.8 52.4 + - - -
87C SER* 3.5 9.7 + - - -
132C ALA* 4.2 0.2 - - - -
133C ASN* 3.2 13.5 - - - -
136C SER* 4.5 0.4 - - - -
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Residues in contact with CYS 67 (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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66C GLY* 1.3 75.9 - - - +
68C THR* 1.3 62.6 + - - +
82C ARG* 3.5 40.6 - - - -
83C LEU 3.1 8.3 - - - +
84C TYR* 3.9 10.5 - - + -
85C TYR* 3.4 5.5 + - - -
95C THR* 3.6 33.2 - - - +
132C ALA* 3.7 10.5 - - + -
133C ASN 3.0 6.1 + - - -
134C TRP* 3.3 9.5 - - - -
135C ASN 2.8 30.7 + - - -
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Residues in contact with THR 68 (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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67C CYS* 1.3 74.9 - - - +
69C ASP* 1.3 71.0 + - - +
82C ARG* 3.5 2.3 - - - +
83C LEU* 2.8 47.2 + - + +
85C TYR* 3.9 6.5 - - + -
134C TRP* 3.7 10.1 - - - -
135C ASN* 2.7 27.0 + - - -
251C LEU* 3.7 9.0 - - - +
253C PHE* 3.6 34.3 - - + +
255C MET* 3.9 13.8 - - + +
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Residues in contact with ASP 69 (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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68C THR* 1.3 80.2 + - - +
70C LEU* 1.3 62.3 + - - +
80C PHE* 4.4 1.8 - - + -
81C LEU* 3.5 3.6 - - - +
82C ARG* 2.9 45.1 + - - +
99C PRO* 5.2 0.7 - - - +
134C TRP* 3.5 8.9 - - - -
157C ARG* 2.8 37.8 + - - -
247C ASN* 2.9 18.7 + - - -
249C LEU* 3.6 21.2 - - + +
251C LEU* 3.3 17.0 - - + +
255C MET* 4.0 1.7 - - - +
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Residues in contact with LEU 70 (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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68C THR* 5.8 0.7 - - + -
69C ASP* 1.3 75.7 - - - +
71C MET* 1.3 68.1 + - - +
72C PHE* 4.6 0.7 - - + -
79C THR 3.7 0.9 - - - +
80C PHE* 3.4 4.9 - - - -
81C LEU* 2.9 58.3 + - + +
83C LEU* 6.0 1.8 - - + -
235C LEU* 3.8 23.6 - - + -
236C ILE* 5.5 3.4 - - + -
239C ILE* 3.7 24.2 - - + -
245C VAL* 4.5 13.9 - - + -
247C ASN* 3.6 27.8 - - + +
249C LEU* 4.6 0.7 - - - -
255C MET* 3.8 25.4 - - + -
258C LEU* 6.1 0.4 - - + -
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Residues in contact with MET 71 (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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70C LEU* 1.3 74.2 - - - +
72C PHE* 1.3 62.9 + - - +
73C ASP 3.4 13.7 - - - +
74C HIS* 4.2 10.3 - - - +
79C THR 3.1 9.0 - - - +
80C PHE* 3.8 19.3 - - + -
180C ARG* 3.6 28.3 - - - +
188C TYR* 3.6 35.9 - - + +
189C TYR* 4.4 1.1 - - - -
190C PHE* 3.7 26.9 - - - -
247C ASN* 2.9 9.1 + - - +
248C ALA* 2.8 35.9 + - + +
249C LEU* 4.0 18.1 - - + +
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Residues in contact with PHE 72 (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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70C LEU* 4.2 2.6 - - + -
71C MET* 1.3 76.3 - - - +
73C ASP* 1.3 76.4 + - + +
79C THR* 2.8 36.2 + - - -
193C GLN* 5.9 4.7 - - - -
231C GLN* 4.9 1.2 + - - -
235C LEU* 3.9 24.7 - - + +
243C LYS* 5.7 9.0 - - + -
244C PRO 5.6 1.1 - - - -
245C VAL* 3.6 33.4 - - + -
246C LYS* 3.2 35.0 - - + +
248C ALA* 6.0 0.4 - - + -
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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