Contacts of the strand formed by residues 64 - 72 (chain C) in PDB entry 3I5D
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 64 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259B GLN* 4.6 18.8 - - + +
325B MET* 4.3 28.7 - - + +
326B VAL 5.1 3.6 - - - +
327B PHE* 3.4 51.4 - - + -
62C THR 3.8 0.4 + - - -
63C VAL* 1.3 76.0 - - - +
65C SER* 1.3 63.1 + - - +
195C ASN 4.2 0.7 - - - +
196C ILE* 3.6 3.1 - - - -
197C ARG* 2.8 47.1 + - + +
199C PRO* 4.4 13.2 - - + -
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Residues in contact with SER 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B MET* 4.1 15.0 - - - +
63C VAL* 3.8 5.8 + - - -
64C LEU* 1.3 79.4 - - - +
66C SER* 1.3 71.6 + - - +
67C VAL* 4.3 1.6 - - - +
194C ASN* 3.2 11.6 + - - -
195C ASN 4.0 3.1 - - - -
196C ILE* 4.0 3.1 - - - -
326C VAL* 3.2 45.0 - - - +
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Residues in contact with SER 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B VAL* 5.2 3.5 - - - +
282B LEU* 3.7 26.4 - - - +
321B ARG* 4.5 0.5 + - - -
323B ASP* 2.9 25.8 + - - -
325B MET* 4.4 7.2 - - - -
65C SER* 1.3 78.8 + - - +
67C VAL* 1.3 65.6 + - - +
68C THR* 5.5 0.7 + - - -
194C ASN* 2.9 15.9 + - - -
195C ASN* 3.1 26.2 + - - +
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Residues in contact with VAL 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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321B ARG* 2.9 25.6 + - - -
323B ASP* 4.9 0.8 + - - -
65C SER* 4.3 2.0 - - - +
66C SER* 1.3 78.5 + - - +
68C THR* 1.3 65.6 + - - +
69C THR* 5.4 0.4 - - + -
99C ASP 4.3 1.1 - - - +
100C GLY* 3.2 37.7 - - - +
192C ILE* 5.3 3.6 - - + -
193C LYS 3.4 8.7 - - - +
194C ASN* 3.7 19.7 - - + +
260C ILE* 5.2 0.2 - - + -
324C VAL* 3.6 33.2 - - + +
326C VAL* 3.9 11.0 - - + -
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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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255B VAL* 4.6 9.2 - - - +
295B TYR* 3.9 28.4 - - + -
321B ARG* 3.2 13.8 + - - +
66C SER* 5.5 0.5 + - - -
67C VAL* 1.3 81.0 + - - +
69C THR* 1.3 72.5 + - - +
70C LYS* 5.9 0.9 - - + -
99C ASP 4.8 0.9 - - - -
191C LEU 3.5 0.9 - - - +
192C ILE* 3.5 2.9 - - - -
193C LYS* 2.8 56.2 + - + +
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Residues in contact with THR 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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295B TYR* 5.7 1.6 - - - -
67C VAL* 5.4 0.9 - - + -
68C THR* 1.3 86.6 - - - +
70C LYS* 1.3 62.5 + - - +
71C VAL* 5.4 0.9 - - - -
98C GLU 4.8 3.8 + - - -
99C ASP 4.3 6.8 + - - -
100C GLY 3.6 24.8 + - - +
102C PHE* 3.8 33.6 - - + +
190C VAL* 4.0 11.4 - - + -
191C LEU* 3.2 8.5 - - - +
192C ILE* 4.5 7.2 - - + -
324C VAL* 4.4 12.8 - - + -
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Residues in contact with LYS 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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292B ALA* 5.5 7.2 - - + -
296B ASN 5.7 4.5 - - - +
68C THR* 5.9 1.1 - - + -
69C THR* 1.3 75.6 - - - +
71C VAL* 1.3 64.9 + - - +
72C LYS* 3.8 2.6 + - - +
189C THR 3.9 0.5 - - - +
190C VAL* 3.6 0.7 - - - -
191C LEU* 2.9 44.1 + - + +
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Residues in contact with VAL 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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69C THR* 5.5 1.1 - - - +
70C LYS* 1.3 72.8 - - - +
72C LYS* 1.3 65.1 + - - +
89C VAL* 3.6 37.7 - - + +
90C ALA* 4.5 12.6 - - - +
94C ILE* 3.6 18.5 - - + +
102C PHE* 3.5 39.7 - - + -
104C VAL* 4.7 4.7 - - + -
188C PHE* 4.4 9.6 - - + -
189C THR 3.4 8.1 - - - +
190C VAL* 3.7 13.5 - - + -
235C LEU* 5.1 1.8 - - + -
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Residues in contact with LYS 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 LYS 3.8 2.2 + - - +
71C VAL* 1.3 75.2 - - - +
73C GLY* 1.3 59.0 + - - +
89C VAL* 3.7 4.0 - - - -
90C ALA* 6.2 0.4 - - - -
188C PHE* 3.6 2.9 - - - -
189C THR* 2.8 50.5 + - + +
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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