Contacts of the helix formed by residues 94 - 101 (chain C) in PDB entry 6PSI
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 94 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5C LYS* 3.5 32.3 - - - +
52C GLU* 3.1 13.4 + - - -
93C PHE* 1.3 78.3 - - - +
95C GLU* 1.3 70.2 + - - +
96C PHE* 3.6 6.9 - - - +
97C PHE* 3.1 21.1 + - - +
98C GLN* 2.9 25.8 + - - +
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Residues in contact with GLU 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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1C MET* 2.8 42.9 + - - +
3C ALA* 3.3 32.1 + - - +
5C LYS* 5.7 0.2 - - - +
94C SER* 1.3 76.4 - - - +
96C PHE* 1.3 76.3 + - - +
98C GLN* 3.2 23.1 + - + +
99C GLU* 2.9 32.2 + - - +
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Residues in contact with PHE 96 (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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2C ALA* 5.1 1.6 - - - -
3C ALA 3.5 20.2 - - - +
4C LYS* 3.7 26.9 - - + -
5C LYS* 3.5 23.6 - - + -
7C TYR* 3.3 39.3 - + - -
66C TYR* 4.6 3.8 - + - -
69C TYR* 3.5 46.2 - + - -
94C SER* 3.6 9.0 - - - +
95C GLU* 1.3 81.4 + - - +
97C PHE* 1.3 58.3 + - - +
99C GLU* 3.2 23.8 + - + +
100C LEU* 3.0 38.2 + - + +
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Residues in contact with PHE 97 (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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7C TYR* 3.6 16.2 - - - +
52C GLU* 3.5 24.0 - - + +
55C ALA* 4.3 0.9 - - + -
56C VAL* 3.5 23.6 - - + -
85C PHE* 3.4 33.9 - + - -
90C VAL* 3.6 27.1 - - + -
93C PHE* 3.5 34.8 - + + -
94C SER* 3.1 24.5 + - - +
96C PHE* 1.3 76.4 - - - +
98C GLN* 1.3 57.9 + - - +
100C LEU* 4.6 0.9 - - - -
101C PHE* 3.0 42.5 + + + +
105C LEU* 3.8 8.0 - - + +
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Residues in contact with GLN 98 (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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90C VAL 4.8 7.0 - - - +
91C GLU* 3.9 15.4 + - - +
93C PHE 2.9 25.0 + - - +
94C SER 2.9 15.3 + - - +
95C GLU* 3.2 23.0 + - - +
97C PHE* 1.3 75.0 - - - +
99C GLU* 1.3 55.5 - - - +
102C GLY* 3.0 22.1 - - - -
105C LEU* 3.6 29.8 - - + +
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Residues in contact with GLU 99 (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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1C MET* 3.0 26.5 + - - +
2C ALA* 3.0 29.6 + - - -
69C TYR* 5.5 3.3 + - - +
75C PRO* 3.4 25.0 - - + +
95C GLU 2.9 15.0 + - - +
96C PHE* 3.2 26.8 + - + +
98C GLN* 1.3 75.6 - - - +
100C LEU* 1.3 64.8 + - + +
101C PHE 3.3 0.2 - - - -
102C GLY* 3.2 11.6 + - - -
103C PRO* 4.3 2.3 - - - +
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Residues in contact with LEU 100 (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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7C TYR* 4.6 7.0 - - + +
56C VAL* 4.4 12.6 - - + -
65C ILE* 4.4 12.1 - - + -
66C TYR* 4.9 4.3 - - + -
69C TYR* 3.7 37.0 - - + -
75C PRO* 3.7 11.1 - - + +
76C PRO* 3.3 43.4 - - + +
83C TYR* 4.2 3.6 + - - -
96C PHE* 3.0 33.4 + - + +
97C PHE* 3.3 1.3 + - - -
99C GLU* 1.3 79.4 - - + +
101C PHE* 1.3 90.8 + - + +
102C GLY 3.6 0.2 - - - -
103C PRO* 5.3 0.3 - - - +
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Residues in contact with PHE 101 (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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7C TYR* 4.7 0.2 - - - -
56C VAL* 3.6 46.4 - - + -
62C LYS* 5.1 5.4 - - + -
65C ILE* 4.8 15.7 - - + -
76C PRO* 5.9 0.2 - - + -
83C TYR* 3.2 42.2 - + + -
85C PHE* 3.8 22.0 - + + -
97C PHE* 3.0 36.0 + + - +
100C LEU* 1.3 100.0 - - + +
102C GLY* 1.4 66.2 + - - +
103C PRO* 3.6 3.6 - - - -
104C GLY 3.1 12.0 + - - -
105C LEU* 3.2 22.3 + - + +
143C ARG* 4.7 6.7 - - - -
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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