Contacts of the helix formed by residues 95 - 107 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93A THR* 3.1 31.5 + - + +
94A LEU* 1.3 78.8 - - - +
96A GLY* 1.3 69.8 + - - +
97A ASP 3.8 0.2 + - - -
98A LEU* 3.9 7.4 + - - +
99A LYS* 3.4 21.2 + - - -
195A ASP* 4.9 5.6 - - - +
198A ALA* 5.5 4.2 - - - +
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Residues in contact with GLY 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A GLN* 1.3 76.4 - - - +
97A ASP* 1.3 67.6 + - - -
99A LYS* 3.2 3.4 + - - +
100A ALA* 3.0 22.8 + - - +
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Residues in contact with ASP 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A GLY* 1.3 71.4 - - - -
98A LEU* 1.3 66.5 + - - +
100A ALA* 3.2 7.2 + - - +
101A ALA* 2.9 24.1 + - - +
104A ARG* 5.3 0.2 + - - -
201A PHE* 4.0 20.2 - - + -
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Residues in contact with LEU 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A LEU* 4.0 9.0 - - + -
95A GLN 3.9 6.7 + - - +
96A GLY 3.3 0.6 - - - -
97A ASP* 1.3 78.0 - - - +
99A LYS* 1.3 63.5 + - - +
101A ALA 3.1 0.9 + - - -
102A ILE* 3.0 27.3 + - + +
131A LEU* 4.8 1.8 - - + -
138A LEU* 4.1 16.2 - - + -
163A ILE* 4.4 9.2 - - + -
194A TRP* 3.9 19.7 - - + +
197A ALA* 3.7 19.3 - - + +
198A ALA* 3.6 39.4 - - + +
201A PHE* 3.7 35.2 - - + -
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Residues in contact with LYS 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A LEU* 3.6 39.4 + - + +
95A GLN* 3.4 27.3 + - - +
96A GLY 3.2 3.6 + - - +
98A LEU* 1.3 78.4 - - - +
100A ALA* 1.3 64.7 + - - +
102A ILE* 3.2 4.6 + - - +
103A GLU* 3.0 55.2 + - - +
109A VAL* 4.0 14.8 - - + -
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Residues in contact with ALA 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A GLY 3.0 13.0 + - - +
97A ASP* 3.6 10.3 - - - +
99A LYS* 1.3 79.0 - - - +
101A ALA* 1.3 56.4 + - - +
103A GLU* 3.5 13.1 + - - +
104A ARG* 3.0 38.8 + - - +
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Residues in contact with ALA 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A ASP 2.9 11.2 + - - +
98A LEU 3.5 4.7 - - - +
100A ALA* 1.3 76.2 - - - +
102A ILE* 1.3 59.4 + - - +
104A ARG* 3.4 29.3 + - - +
105A ASP* 2.9 36.3 + - - +
138A LEU* 3.6 14.4 - - + -
201A PHE* 3.5 26.9 - - + -
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Residues in contact with ILE 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A LEU* 3.9 28.3 - - + -
98A LEU* 3.0 26.2 + - + +
99A LYS* 3.6 7.2 - - - +
101A ALA* 1.3 75.2 - - - +
103A GLU* 1.3 54.5 + - - +
105A ASP 3.3 0.2 + - - -
106A PHE* 2.8 44.1 + - + +
108A SER 4.2 5.8 - - - +
109A VAL* 4.2 13.2 - - + -
112A PHE* 3.5 49.6 - - + -
131A LEU* 4.4 7.0 - - + -
138A LEU* 3.6 18.8 - - + -
194A TRP* 4.2 7.2 - - + -
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Residues in contact with GLU 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A LYS* 3.0 45.0 + - - +
100A ALA* 3.8 12.8 - - - +
102A ILE* 1.3 75.2 - - - +
104A ARG* 1.3 56.2 + - - +
107A GLY* 2.7 38.5 + - - +
108A SER* 3.8 10.3 - - - +
109A VAL* 4.0 21.7 + - + +
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Residues in contact with ARG 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A ALA* 3.0 32.1 + - - +
101A ALA* 3.4 29.3 - - - +
103A GLU* 1.3 77.7 - - - +
105A ASP* 1.3 78.4 + - - +
107A GLY* 4.2 2.8 + - - -
136A ASP 4.7 12.5 + - - -
137A LYS* 6.0 0.6 - - - +
201A PHE* 4.6 7.5 - - - -
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Residues in contact with ASP 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A ALA* 2.9 21.2 + - - +
104A ARG* 1.3 97.0 + - - +
106A PHE* 1.3 71.5 + - + +
136A ASP 4.3 2.9 - - - +
137A LYS* 3.5 24.8 - - - +
138A LEU* 2.9 45.1 + - + +
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Residues in contact with PHE 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A ILE* 2.8 32.5 + - + +
105A ASP* 1.3 76.9 - - + +
107A GLY* 1.3 58.2 + - - +
108A SER 3.2 4.0 - - - +
111A ASN* 3.2 25.7 + - + +
112A PHE* 3.7 55.0 - + + +
115A GLU* 3.3 33.4 - - - -
131A LEU* 4.2 3.8 - - + -
138A LEU* 3.7 28.3 - - + -
139A ALA* 3.8 27.4 - - - -
140A VAL* 4.1 13.9 - - + -
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Residues in contact with GLY 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A GLU* 2.7 24.4 + - - +
104A ARG 4.2 2.8 + - - -
105A ASP 3.6 1.4 - - - -
106A PHE* 1.3 77.8 - - - +
108A SER* 1.3 61.0 + - - +
111A ASN* 4.4 4.3 - - - -
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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