Contacts of the helix formed by residues 92 - 104 (chain C) in PDB entry 3ESF
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 92 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90C GLU 5.3 0.2 + - - -
91C PRO* 1.3 74.8 - - - +
93C GLY* 1.3 68.3 + - - +
94C LYS 3.6 1.2 + - - -
95C LEU* 3.8 6.6 + - - +
96C ALA* 3.5 14.3 + - - -
188C TRP* 5.5 0.2 - - - +
192C GLU* 4.4 8.9 - - - +
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Residues in contact with GLY 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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92C SER* 1.3 77.0 - - - +
94C LYS* 1.3 79.1 + - - -
96C ALA* 3.4 2.2 + - - +
97C GLU* 3.2 32.8 + - - +
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Residues in contact with LYS 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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92C SER 3.6 0.8 + - - -
93C GLY* 1.3 83.0 - - - -
95C LEU* 1.3 57.7 + - - +
97C GLU* 3.4 6.8 + - - +
98C ALA* 3.0 28.8 + - - +
192C GLU* 3.2 27.7 + - + +
195C PHE* 4.1 18.5 - - + -
196C THR* 4.4 15.3 - - + -
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Residues in contact with LEU 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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91C PRO* 3.8 18.8 - - + -
92C SER 3.8 6.2 + - - +
93C GLY 3.4 0.6 - - - -
94C LYS* 1.3 76.7 - - - +
96C ALA* 1.3 61.5 + - - +
98C ALA* 3.2 3.4 + - - +
99C ILE* 2.8 47.4 + - + +
128C LEU* 5.0 2.2 - - + -
137C LEU* 4.4 7.2 - - + -
157C ILE* 4.6 11.4 - - + -
188C TRP* 3.9 12.6 - - + +
191C ALA* 3.7 26.9 - - + -
192C GLU* 3.9 24.3 - - + +
195C PHE* 4.2 31.1 - - + -
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Residues in contact with ALA 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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91C PRO* 3.5 37.9 - - + +
92C SER* 3.5 18.3 + - - -
93C GLY 3.4 3.2 + - - +
95C LEU* 1.3 78.8 - - - +
97C GLU* 1.3 68.5 + - - +
99C ILE* 3.5 5.1 + - - +
100C ARG* 3.2 27.7 + - - +
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Residues in contact with GLU 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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93C GLY* 3.2 25.6 + - - +
94C LYS* 3.8 6.3 - - - +
96C ALA* 1.3 81.4 - - - +
98C ALA* 1.3 55.7 - - - +
100C ARG* 3.3 23.1 + - + +
101C ALA* 2.9 30.0 + - - +
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Residues in contact with ALA 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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94C LYS 3.0 12.8 + - - +
95C LEU 3.5 6.3 - - - +
97C GLU* 1.3 74.5 - - - +
99C ILE* 1.3 59.9 + - - +
101C ALA* 3.3 7.4 + - - +
102C SER* 2.9 34.5 + - - -
135C LYS 6.0 0.4 - - - +
137C LEU* 3.7 7.9 - - + -
195C PHE* 3.3 39.7 - - + -
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Residues in contact with ILE 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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91C PRO* 3.7 28.0 - - + -
95C LEU* 2.8 30.0 + - + +
96C ALA* 3.8 5.4 - - - +
97C GLU 3.4 0.2 - - - -
98C ALA* 1.3 72.4 - - - +
100C ARG* 1.3 54.0 + - + +
102C SER 3.2 0.3 + - - -
103C PHE* 2.8 46.0 + - + +
105C SER 4.0 0.7 - - - +
106C PHE* 3.9 23.8 - - + +
109C PHE* 3.8 37.0 - - + -
128C LEU* 4.6 6.7 - - + -
137C LEU* 3.8 17.9 - - + -
188C TRP* 4.2 13.2 - - + -
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Residues in contact with ARG 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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96C ALA 3.2 12.2 + - - +
97C GLU* 3.6 26.9 + - + +
99C ILE* 1.3 74.9 - - + +
101C ALA* 1.3 59.1 + - - +
104C GLY* 2.8 43.5 + - - +
105C SER* 4.1 26.9 - - - +
106C PHE* 4.4 7.7 - - + +
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Residues in contact with ALA 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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97C GLU 2.9 16.7 + - - +
98C ALA* 3.3 7.8 + - - +
100C ARG* 1.3 75.6 - - - +
102C SER* 1.3 59.6 - - - +
104C GLY 4.8 0.2 - - - -
136C LYS* 3.5 22.7 + - - +
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Residues in contact with SER 102 (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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98C ALA 2.9 16.8 + - - -
99C ILE 4.0 2.0 - - - -
101C ALA* 1.3 79.4 - - - +
103C PHE* 1.3 66.1 + - - +
104C GLY 3.8 0.2 - - - -
135C LYS 4.7 0.7 + - - -
136C LYS* 3.6 18.0 - - - +
137C LEU* 2.9 50.1 + - - +
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Residues in contact with PHE 103 (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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99C ILE* 2.8 33.7 + - + +
102C SER* 1.3 76.0 - - - +
104C GLY* 1.3 55.5 + - - +
105C SER 3.2 17.8 + - - +
108C LYS* 3.5 21.9 - - + +
109C PHE* 3.5 44.0 - + + +
112C GLU* 3.5 26.0 - - - -
128C LEU* 3.9 8.5 - - + -
137C LEU* 3.7 40.8 - - + -
138C LYS* 3.8 13.2 - - - -
139C VAL* 4.0 16.8 - - + -
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Residues in contact with GLY 104 (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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100C ARG* 2.8 36.8 + - - +
101C ALA 4.8 0.2 - - - -
102C SER 3.8 0.8 - - - -
103C PHE* 1.3 75.2 - - - +
105C SER* 1.3 62.8 + - - +
108C LYS* 5.2 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