Contacts of the helix formed by residues 95 - 107 (chain C) in PDB entry 3K9S
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 GLN 95 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93C THR* 3.2 33.5 + - + +
94C LEU* 1.3 80.2 - - - +
96C GLY* 1.3 68.9 + - - +
97C ASP 3.7 1.0 + - - -
98C LEU* 4.0 7.3 + - - +
99C LYS* 3.6 20.8 + - - +
194C TRP* 5.4 0.2 - - - +
195C ASP* 4.9 7.4 + - - +
198C ALA* 5.3 5.9 - - - +
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Residues in contact with GLY 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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95C GLN* 1.3 76.6 + - - +
97C ASP* 1.3 67.0 + - - -
99C LYS* 3.3 4.1 + - - +
100C ALA* 3.0 23.0 + - - +
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Residues in contact with ASP 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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95C GLN 3.7 0.6 + - - -
96C GLY* 1.3 72.7 - - - -
98C LEU* 1.3 57.4 + - - +
100C ALA* 3.0 9.8 + - - +
101C ALA* 2.8 29.1 + - - +
201C PHE* 4.3 16.6 - - + -
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Residues in contact with LEU 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 LEU* 3.9 9.6 - - + -
95C GLN 4.0 7.3 + - - +
96C GLY 3.3 0.4 - - - -
97C ASP* 1.3 78.8 - - - +
99C LYS* 1.3 57.9 + - - +
101C ALA* 3.1 1.3 + - - +
102C ILE* 2.8 49.1 + - + +
131C LEU* 4.8 2.2 - - + -
138C LEU* 4.3 7.6 - - + -
163C ILE* 4.6 9.4 - - + -
194C TRP* 3.8 32.1 - - + +
197C ALA* 3.8 19.1 - - + -
198C ALA* 3.8 22.9 - - + +
201C PHE* 3.9 36.9 - - + -
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Residues in contact with LYS 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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93C THR* 6.1 0.6 - - - +
94C LEU* 3.8 40.8 + - + +
95C GLN* 3.6 22.9 + - - +
96C GLY 3.3 9.3 + - - +
97C ASP 3.3 0.6 - - - -
98C LEU* 1.3 77.1 - - - +
100C ALA* 1.3 57.8 + - - +
102C ILE* 3.2 5.4 + - - +
103C GLU* 2.9 55.4 + - - +
109C VAL* 4.1 15.3 - - + -
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Residues in contact with ALA 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 GLY 3.0 14.7 + - - +
97C ASP* 3.3 12.1 - - - +
99C LYS* 1.3 75.6 - - - +
101C ALA* 1.3 57.0 + - - +
103C GLU* 3.3 14.9 + - - +
104C ARG* 3.0 27.5 + - - +
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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 ASP 2.8 12.6 + - - +
98C LEU 3.5 7.4 - - - +
100C ALA* 1.3 74.0 - - - +
102C ILE* 1.3 67.2 + - - +
104C ARG* 3.2 25.4 + - - +
105C ASP* 3.0 27.9 + - - +
138C LEU* 3.8 11.4 - - + -
201C PHE* 3.5 28.7 - - + -
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Residues in contact with ILE 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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94C LEU* 4.0 22.7 - - + -
98C LEU* 2.8 39.0 + - + +
99C LYS* 3.5 5.6 - - - +
101C ALA* 1.3 77.9 - - - +
103C GLU* 1.3 62.2 + - - +
106C PHE* 3.1 31.2 + - + +
108C SER 4.4 0.6 + - - +
109C VAL* 4.3 16.8 - - + -
112C PHE* 3.5 35.9 - - + -
131C LEU* 4.4 9.9 - - + -
138C LEU* 3.8 19.1 - - + -
194C TRP* 4.2 14.1 - - + -
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Residues in contact with GLU 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 LYS* 2.9 44.6 + - - +
100C ALA* 3.7 12.4 - - - +
101C ALA 3.2 0.2 - - - -
102C ILE* 1.3 78.6 - - - +
104C ARG* 1.3 54.6 + - - +
107C GLY* 2.8 34.5 + - - +
108C SER* 3.8 12.0 - - - +
109C VAL* 4.2 23.4 + - + +
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Residues in contact with ARG 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 ALA 3.0 12.6 + - - +
101C ALA* 3.2 29.5 + - - +
103C GLU* 1.3 78.9 - - - +
105C ASP* 1.3 76.9 + - - +
106C PHE 3.8 0.2 + - - -
107C GLY* 4.1 2.6 + - - -
136C ASP* 4.2 18.8 + - - +
138C LEU* 6.2 0.2 - - - +
201C PHE* 4.6 7.9 - - - -
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Residues in contact with ASP 105 (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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101C ALA 3.0 14.7 + - - +
104C ARG* 1.3 104.7 + - - +
106C PHE* 1.3 76.3 + - + +
107C GLY 3.6 0.2 - - - -
136C ASP 4.1 4.0 - - - +
137C LYS* 3.5 31.0 - - + +
138C LEU* 2.7 45.6 + - + +
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Residues in contact with PHE 106 (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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102C ILE* 3.1 23.0 + - + +
105C ASP* 1.3 81.5 - - + +
107C GLY* 1.3 58.3 + - - +
108C SER 3.2 3.6 - - - +
111C ASN* 2.8 30.9 - - + +
112C PHE* 3.8 46.2 - + + +
115C GLU* 3.2 36.6 - - - -
131C LEU* 4.0 12.6 - - + -
138C LEU* 3.8 38.8 - - + -
139C ALA* 3.9 13.2 - - - -
140C VAL* 3.9 11.9 - - + -
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Residues in contact with GLY 107 (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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103C GLU* 2.8 23.8 + - - +
104C ARG 4.1 3.0 + - - -
105C ASP 3.6 1.2 - - - -
106C PHE* 1.3 75.9 - - - +
108C SER* 1.3 63.6 + - - +
111C ASN* 3.9 5.6 - - - -
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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