Contacts of the helix formed by residues 102 - 113 (chain P) in PDB entry 3K9Q
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 ASP 102 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100P TYR 3.0 1.6 + - - -
101P THR* 1.3 80.1 - - - +
103P LYS* 1.3 66.4 + - - +
104P ASP* 3.0 17.5 + - - +
105P LYS* 3.0 50.1 + - + +
106P ALA* 3.0 24.7 + - - +
119P ILE* 4.3 3.8 - - - +
123P ALA* 3.9 1.9 - - - +
124P THR* 2.7 34.6 + - - +
125P GLY* 4.2 3.6 + - - -
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Residues in contact with LYS 103 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102P ASP* 1.3 72.7 - - - +
104P ASP* 1.3 70.7 + - - +
106P ALA* 3.3 2.3 + - - +
107P GLN* 3.1 27.7 + - + +
124P THR 2.9 14.6 + - - +
125P GLY* 4.2 2.5 - - - -
126P ASP* 2.9 52.1 + - + +
127P LEU* 3.8 21.1 - - + +
144P THR* 4.7 14.2 + - - -
145P VAL* 4.3 22.4 - - + +
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Residues in contact with ASP 104 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102P ASP* 3.0 13.0 + - - +
103P LYS* 1.3 83.9 - - - +
105P LYS* 1.3 62.7 + - + +
107P GLN* 3.1 22.0 - - - +
108P ALA 4.3 0.7 + - - -
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Residues in contact with LYS 105 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99P PHE 3.7 21.9 + - - +
100P TYR* 3.4 23.7 - - + -
101P THR* 4.7 10.3 + - - +
102P ASP* 3.0 35.7 + - + +
103P LYS 3.4 0.4 - - - -
104P ASP* 1.3 75.9 - - + +
106P ALA* 1.3 62.8 + - - +
108P ALA* 3.2 22.7 + - - +
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Residues in contact with ALA 106 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95P GLU* 5.2 0.2 - - + -
100P TYR* 3.7 23.7 + - + +
102P ASP 3.0 17.7 + - - +
103P LYS 3.8 3.6 - - - +
105P LYS* 1.3 72.3 - - - +
107P GLN* 1.3 66.2 + - - +
108P ALA 2.9 4.1 + - - -
109P HIS* 3.0 24.0 + - + +
117P VAL* 3.8 18.9 - - + +
119P ILE* 3.9 16.2 - - + -
145P VAL* 4.0 11.7 - - + -
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Residues in contact with GLN 107 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103P LYS* 3.1 17.5 + - + +
104P ASP* 3.1 22.0 - - - +
106P ALA* 1.3 77.9 - - - +
108P ALA* 1.3 52.1 + - - +
110P ILE* 2.7 61.6 + - - +
111P GLU* 3.1 31.1 + - - +
144P THR* 4.7 5.4 + - - -
145P VAL* 4.3 10.0 - - - +
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Residues in contact with ALA 108 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79P ASP* 5.3 0.7 - - - +
80P ALA* 4.3 9.0 - - + -
81P SER* 3.6 32.1 - - - +
100P TYR* 4.4 6.1 - - + -
104P ASP 4.3 1.0 + - - +
105P LYS 3.2 16.8 + - - +
106P ALA 2.9 0.4 - - - -
107P GLN* 1.3 78.1 - - - +
109P HIS* 1.3 61.1 + - - +
111P GLU* 3.4 15.9 + - - +
112P ALA* 3.0 23.4 + - - +
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Residues in contact with HIS 109 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8P ASN* 3.2 29.9 + - + -
80P ALA* 3.4 21.8 - - + +
83P LEU* 4.3 1.1 - - + -
85P TRP* 3.1 29.1 + - - -
93P VAL* 3.6 28.5 - - + +
95P GLU* 2.9 23.3 + - + -
100P TYR* 4.6 3.6 - + - -
106P ALA* 3.0 19.9 + - - -
108P ALA* 1.3 77.1 - - - +
110P ILE* 1.3 61.3 + - - +
112P ALA* 3.3 2.2 + - - -
113P GLY 3.1 6.4 + - - -
114P ALA* 3.0 24.0 + - + +
117P VAL* 3.5 28.5 - - + -
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Residues in contact with ILE 110 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106P ALA 4.4 0.2 - - - +
107P GLN* 2.7 50.5 + - - +
109P HIS* 1.3 72.7 - - - +
111P GLU* 1.3 57.3 + - - +
113P GLY* 2.9 20.4 + - - -
114P ALA 3.5 16.2 - - - +
115P LYS 3.6 25.8 - - - +
116P LYS* 3.9 3.8 - - - -
117P VAL* 4.0 12.3 - - + -
144P THR* 3.8 31.9 - - + +
145P VAL* 4.6 2.9 - - + -
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Residues in contact with GLU 111 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81P SER* 4.2 15.5 - - - +
104P ASP 5.5 0.2 - - - +
107P GLN* 3.1 39.7 + - + +
108P ALA* 3.7 16.1 + - - +
110P ILE* 1.3 77.9 - - - +
112P ALA* 1.3 58.9 + - - +
113P GLY* 3.1 2.0 + - - -
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Residues in contact with ALA 112 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80P ALA 3.6 16.8 - - - +
81P SER 3.7 12.9 + - - +
83P LEU 3.3 21.3 - - - +
84P PRO* 4.9 0.2 - - - +
85P TRP* 3.4 14.9 + - + -
86P LYS* 3.0 23.2 + - - +
108P ALA 3.0 17.3 + - - +
109P HIS 3.6 6.3 - - - +
110P ILE 3.2 0.2 - - - -
111P GLU* 1.3 74.9 - - - +
113P GLY* 1.3 56.3 + - - +
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Residues in contact with GLY 113 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85P TRP* 3.8 12.6 - - - +
86P LYS* 3.7 22.4 - - - +
89P ASN* 5.5 0.7 - - - -
90P ILE 4.0 4.0 + - - +
109P HIS 3.1 0.6 + - - -
110P ILE 2.9 10.9 + - - -
111P GLU 3.1 2.2 - - - -
112P ALA* 1.3 80.7 - - - +
114P ALA* 1.3 67.6 + - - +
115P LYS* 3.8 6.2 + - - +
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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