Contacts of the helix formed by residues 108 - 122 (chain D) in PDB entry 3Q2K
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 ARG 108 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106D ALA* 3.5 4.1 - - - +
107D THR* 1.3 95.4 + - - +
109D TRP* 1.3 68.3 + - - +
110D GLU* 4.5 3.6 - - + +
111D ASP* 3.0 38.4 + - - +
112D GLY 3.0 9.7 + - - -
178D TRP* 5.1 3.6 + - - +
179D GLU* 3.0 54.9 + - - +
329D LEU* 4.4 4.0 - - - -
113H LYS* 6.1 3.2 - - - +
350H ASP* 6.2 0.4 - - - -
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Residues in contact with TRP 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108D ARG* 1.3 72.4 - - - +
110D GLU* 1.3 62.7 + - + +
112D GLY* 3.1 3.6 + - - -
113D LYS* 3.0 55.1 + - + +
326D LEU* 3.5 44.2 - - + -
329D LEU* 4.1 12.8 - - + +
330D ALA* 3.6 28.5 - - + -
333D THR* 3.5 26.7 + - + +
337D ARG* 3.9 19.5 - - - +
349D LEU* 3.6 30.5 - - + +
350D ASP 2.8 27.1 + - - -
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Residues in contact with GLU 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108D ARG* 3.2 3.7 - - + +
109D TRP* 1.3 80.0 - - + +
111D ASP* 1.3 70.0 + - - +
113D LYS* 3.3 20.8 + - - +
114D ARG* 3.1 44.2 + - - +
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Residues in contact with ASP 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83D GLY 5.3 0.7 - - - +
86D PRO* 3.6 25.8 - - + +
87D TRP* 3.5 27.2 + - + -
90D ILE* 5.5 0.2 - - - +
106D ALA* 4.3 1.1 - - + -
107D THR* 5.1 1.4 + - - -
108D ARG* 3.0 35.4 + - + +
110D GLU* 1.3 81.8 - - - +
112D GLY* 1.3 53.9 + - - +
114D ARG* 3.0 23.4 + - - +
115D MET* 2.8 39.0 + - - +
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Residues in contact with GLY 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105D MET* 4.1 1.6 - - - +
106D ALA* 3.5 18.7 - - - +
108D ARG 3.0 9.3 + - - -
109D TRP 3.1 5.6 + - - -
111D ASP* 1.3 77.7 - - - +
113D LYS* 1.3 59.9 + - - +
115D MET* 3.4 9.8 + - - +
116D VAL* 3.3 24.4 + - - +
326D LEU* 3.6 9.6 - - - +
329D LEU* 3.7 11.9 - - - -
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Residues in contact with LYS 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A ARG* 5.7 6.7 - - - +
109D TRP* 3.0 67.0 + - + +
110D GLU* 3.9 17.5 - - - +
111D ASP 3.2 0.4 - - - -
112D GLY* 1.3 72.1 - - - +
114D ARG* 1.3 66.1 + - - +
116D VAL* 3.3 3.1 + - - +
117D LYS* 3.0 24.0 + - - +
326D LEU* 4.4 15.3 - - + -
350D ASP* 3.5 19.8 + - - -
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Residues in contact with ARG 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87D TRP* 3.4 23.9 - - - -
90D ILE* 3.2 27.8 - - + -
110D GLU* 3.1 38.5 + - - +
111D ASP* 3.0 34.9 + - - +
113D LYS* 1.3 74.6 - - - +
115D MET* 1.3 63.6 + - - +
117D LYS* 3.7 24.6 - - - +
118D ALA* 3.1 23.8 + - + +
117H LYS* 5.7 1.7 - - - +
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Residues in contact with MET 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85D HIS 4.1 4.5 - - - +
86D PRO* 3.0 33.4 - - + +
89D ALA* 3.8 23.0 - - + +
90D ILE* 4.2 10.1 - - - +
101D SER* 4.4 9.2 - - - +
105D MET* 3.2 57.0 - - + +
111D ASP 2.8 17.2 + - - +
112D GLY* 3.4 11.0 - - - +
114D ARG* 1.3 74.2 - - - +
116D VAL* 1.3 61.7 + - - +
118D ALA* 3.5 2.1 + - - +
119D CYS* 3.2 28.4 + - - -
126D LEU* 4.3 17.0 - - + -
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Residues in contact with VAL 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105D MET* 3.8 11.2 - - + -
112D GLY 3.3 12.8 + - - +
113D LYS 3.3 7.0 + - - +
115D MET* 1.3 75.2 - - - +
117D LYS* 1.3 67.2 + - - +
119D CYS* 3.5 3.5 + - - +
120D ASP* 3.1 22.9 + - - +
126D LEU* 3.9 12.6 - - + -
322D GLY* 3.8 28.0 - - - +
323D ARG* 3.5 43.1 - - + +
326D LEU* 3.9 16.6 - - + -
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Residues in contact with LYS 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A TRP* 5.4 15.5 - - + -
113D LYS 3.0 15.7 + - - +
114D ARG* 3.7 26.7 - - - +
116D VAL* 1.3 77.8 - - - +
118D ALA* 1.3 59.6 + - - +
120D ASP* 3.1 11.3 + - + +
121D GLU* 2.9 36.1 + - - +
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Residues in contact with ALA 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90D ILE* 4.2 33.2 - - + +
93D ALA* 4.0 5.5 - - + +
94D GLN* 5.3 4.7 - - - +
114D ARG* 3.1 17.7 + - + +
115D MET 4.0 3.1 - - - +
117D LYS* 1.3 77.8 - - - +
119D CYS* 1.3 67.0 + - - +
121D GLU* 3.4 7.8 + - - +
122D ALA* 3.0 24.6 + - - +
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Residues in contact with CYS 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89D ALA* 4.5 6.3 - - - -
93D ALA* 4.0 21.1 - - - -
99D VAL* 4.0 20.0 - - - -
115D MET 3.2 17.9 + - - +
116D VAL 4.0 4.3 - - - +
117D LYS 3.4 0.2 - - - -
118D ALA* 1.3 75.5 - - - +
120D ASP* 1.3 58.4 + - - +
122D ALA* 3.5 0.8 + - - -
123D GLY 3.1 4.2 + - - -
124D VAL* 2.9 44.6 + - - +
125D ARG 4.4 2.7 - - - -
126D LEU* 3.9 30.7 - - + -
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Residues in contact with ASP 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116D VAL* 3.1 21.0 + - - +
117D LYS* 3.1 14.8 + - + +
119D CYS* 1.3 72.6 - - - +
121D GLU* 1.3 68.9 + - - +
122D ALA 3.0 1.6 - - - -
123D GLY* 2.9 14.4 + - - -
124D VAL 5.6 0.5 - - - +
323D ARG* 2.9 41.5 + - - -
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Residues in contact with GLU 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117D LYS* 2.9 21.6 + - + +
118D ALA* 3.5 9.4 - - - +
120D ASP* 1.3 78.8 - - - +
122D ALA* 1.3 61.4 + - + +
123D GLY* 3.3 0.5 + - - -
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Residues in contact with ALA 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93D ALA* 3.6 30.5 - - + +
94D GLN* 4.7 1.6 - - - +
96D GLY* 5.6 1.2 - - - -
118D ALA 3.0 16.4 + - - +
119D CYS 4.0 1.1 - - - +
120D ASP 3.0 1.0 - - - -
121D GLU* 1.3 79.4 - - + +
123D GLY* 1.3 62.6 + - - +
124D VAL* 3.3 17.4 + - + +
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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