Contacts of the strand formed by residues 89 - 95 (chain C) in PDB entry 3OF6
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 VAL 89 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37C GLN* 3.0 43.7 + - + +
88C ALA* 1.3 77.7 - - - +
90C TYR* 1.3 63.2 + - - +
91C LEU* 3.8 24.3 + - + +
110C PRO 4.9 2.5 - - - +
111C GLY* 4.5 3.4 - - - -
112C THR 3.1 17.3 - - - +
113C ARG* 3.8 42.2 - - + +
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Residues in contact with TYR 90 (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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6C GLN* 3.3 6.2 + - - -
21C LEU* 3.7 28.0 - - + -
34C TRP* 4.1 11.2 - - + -
35C TYR 3.4 5.6 - - - +
36C GLN* 3.9 32.2 + - + -
46C LEU* 3.9 23.3 - - + -
65C PHE* 4.2 11.6 - + - -
77C LEU* 4.6 7.0 - - + -
79C ILE* 3.7 22.2 - - + +
86C ASP* 2.9 27.8 + - - +
88C ALA* 3.9 14.4 - - + -
89C VAL* 1.3 70.9 - - - +
91C LEU* 1.3 61.1 + - - +
111C GLY* 3.2 4.0 - - - -
112C THR 2.9 35.3 + - - +
114C LEU* 3.5 24.9 - - + -
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Residues in contact with LEU 91 (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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6C GLN* 3.5 2.9 - - - -
34C TRP* 3.2 21.0 - - - -
35C TYR* 3.0 38.2 + - + -
37C GLN* 3.3 37.2 - - + +
43C PRO* 4.7 2.0 - - + -
89C VAL* 4.0 20.6 - - + +
90C TYR* 1.3 73.3 - - - +
92C CYS* 1.3 61.2 + - - +
108C PHE* 4.2 27.4 - - + -
109C GLY 4.4 9.4 - - - +
110C PRO 4.6 2.7 - - - +
111C GLY* 3.9 19.1 - - - +
44E PRO* 5.5 1.8 - - + -
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Residues in contact with CYS 92 (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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4C VAL* 4.2 4.6 - - + +
6C GLN* 2.9 21.1 + - + +
23C CYS* 2.0 47.3 - - + -
25C PRO* 4.9 1.6 - - - -
32C LEU* 3.8 26.2 - - - -
33C PHE 3.5 5.6 - - - +
34C TRP* 4.6 4.9 - - + -
35C TYR* 5.6 0.2 - - - -
91C LEU* 1.3 76.1 - - - +
93C ALA* 1.3 66.8 + - - +
107C TYR 3.7 0.7 - - - +
108C PHE* 3.2 6.2 - - - +
109C GLY* 3.0 26.6 + - - +
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Residues in contact with ALA 93 (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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4C VAL* 5.5 0.2 - - - -
25C PRO* 5.5 0.2 - - - -
32C LEU* 3.2 11.4 - - - +
33C PHE* 3.0 43.4 + - + -
35C TYR* 4.4 0.4 - - + -
92C CYS* 1.3 77.3 - - - +
94C SER* 1.3 61.9 + - - +
106C GLN* 3.6 32.5 - - + +
107C TYR 3.2 9.4 - - - +
108C PHE* 4.2 13.7 - - + -
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Residues in contact with SER 94 (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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4C VAL* 3.5 21.7 - - - +
25C PRO* 3.6 23.9 - - - +
26C ILE 3.9 0.3 + - - -
29C HIS* 3.1 30.0 + - - -
31C SER 3.2 9.0 - - - -
33C PHE* 4.9 0.4 - - - -
93C ALA* 1.3 76.8 - - - +
95C SER* 1.3 60.7 + - - +
106C GLN* 4.7 0.2 - - - -
107C TYR* 3.1 33.7 + - - +
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Residues in contact with SER 95 (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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29C HIS* 3.2 10.0 - - - -
30C VAL 3.4 4.9 + - - -
31C SER* 3.2 36.8 + - - -
33C PHE* 3.5 13.3 - - - -
94C SER* 1.3 75.7 - - - +
96C LEU* 1.3 65.0 + - - +
97C GLY 2.8 23.1 + - - -
100C TYR 4.2 2.0 + - - -
105C GLU 3.0 28.7 - - - -
106C GLN* 4.2 4.2 - - - +
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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