Contacts of the helix formed by residues 100 - 112 (chain D) in PDB entry 4R0C
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 GLY 100 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96D ALA 3.6 0.6 + - - -
97D GLU 3.3 12.8 + - - -
98D GLN 3.3 3.4 - - - -
99D SER* 1.3 77.9 + - - +
101D LEU* 1.3 55.7 + - - +
102D LEU 3.1 3.3 + - - -
103D SER* 3.1 11.9 + - - -
104D VAL* 2.8 36.5 + - - +
246D PRO* 4.8 5.1 - - - +
310D TYR* 4.3 3.8 - - - -
316D GLN* 5.6 3.4 - - - -
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Residues in contact with LEU 101 (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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96D ALA* 3.6 6.0 + - + +
99D SER* 3.2 19.1 + - - +
100D GLY* 1.3 76.9 - - - +
102D LEU* 1.3 65.0 + - + +
104D VAL* 3.5 1.5 - - - +
105D SER* 2.7 46.3 + - - +
253D MET* 3.8 17.3 - - + -
256D THR* 3.8 13.5 - - + -
303D ALA* 4.5 4.3 - - - +
306D CYS* 3.8 41.7 - - + +
307D GLY* 3.8 3.6 - - - +
310D TYR* 3.9 27.1 - - + -
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Residues in contact with LEU 102 (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 LEU* 4.5 11.7 - - + +
96D ALA* 4.0 32.6 + - + +
97D GLU* 4.5 9.0 - - - +
100D GLY 3.1 1.0 - - - -
101D LEU* 1.3 88.9 - - + +
103D SER* 1.3 64.5 + - - +
105D SER* 4.0 5.6 - - - -
106D LEU* 3.1 32.8 + - + +
131D LEU* 4.5 14.6 - - + +
132D THR* 3.6 33.7 - - + -
135D ALA* 5.1 1.8 - - - -
303D ALA* 5.5 4.7 - - + -
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Residues in contact with SER 103 (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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97D GLU* 4.4 9.0 + - - -
100D GLY* 3.1 13.5 + - - -
102D LEU* 1.3 78.7 - - - +
104D VAL* 1.3 59.5 + - - +
106D LEU* 3.9 2.4 - - - +
107D ALA* 2.9 33.6 + - - +
135D ALA* 3.3 28.9 - - - +
139D VAL* 4.1 15.0 - - - +
140D LEU* 5.1 0.6 - - - +
246D PRO* 3.7 23.6 - - - -
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Residues in contact with VAL 104 (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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100D GLY 2.8 14.2 + - - +
101D LEU 3.5 11.9 - - - +
103D SER* 1.3 78.5 - - - +
105D SER* 1.3 63.4 + - - +
107D ALA* 3.9 1.6 - - - +
108D SER* 3.0 30.0 + - - -
111D ARG* 5.2 0.5 + - - -
246D PRO* 3.5 25.0 - - + +
247D GLN 3.5 33.0 - - - +
248D ILE* 3.5 10.3 - - + +
253D MET* 4.0 12.3 - - + -
310D TYR* 3.4 28.3 - - + +
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Residues in contact with SER 105 (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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101D LEU* 2.7 26.2 + - - +
102D LEU* 4.1 7.0 - - - -
103D SER 3.2 0.8 - - - -
104D VAL* 1.3 77.2 - - - +
106D LEU* 1.3 68.1 + - - +
108D SER* 3.3 8.8 - - - -
109D LEU* 3.3 22.9 + - - +
253D MET* 3.2 24.6 - - - +
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Residues in contact with LEU 106 (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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102D LEU* 3.1 23.1 + - + +
103D SER* 4.0 2.2 - - - +
105D SER* 1.3 76.4 - - - +
107D ALA* 1.3 67.2 + - - +
109D LEU* 3.0 28.0 + - + +
110D VAL* 3.4 8.5 + - - +
125D ALA* 3.6 23.7 - - + +
128D LEU* 4.6 20.6 - - + +
129D SER* 3.4 36.1 - - - -
132D THR* 5.2 7.0 - - + +
135D ALA* 5.5 3.1 - - + -
136D GLY 5.4 2.0 - - - +
140D LEU* 3.6 21.5 - - + -
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Residues in contact with ALA 107 (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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103D SER 2.9 19.5 + - - +
104D VAL 3.9 3.8 - - - +
106D LEU* 1.3 75.4 - - - +
108D SER* 1.3 62.7 + - - +
110D VAL* 3.0 5.7 + - - +
111D ARG* 2.8 42.4 + - - +
139D VAL* 4.7 5.6 - - + -
140D LEU* 4.0 4.5 - - - +
143D LEU* 3.8 24.2 - - + -
245D ALA* 4.5 8.3 - - + -
246D PRO* 4.4 5.2 - - + +
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Residues in contact with SER 108 (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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104D VAL 3.0 17.0 + - - -
105D SER* 3.3 12.8 - - - -
107D ALA* 1.3 77.4 - - - +
109D LEU* 1.3 57.5 + - - +
111D ARG* 3.0 11.2 + - - +
112D ARG* 2.7 58.5 + - - +
248D ILE* 3.1 29.8 - - - +
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Residues in contact with LEU 109 (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 SER 3.3 9.6 + - - +
106D LEU* 3.0 21.8 + - + +
108D SER* 1.3 78.4 - - - +
110D VAL* 1.3 60.3 + - - +
112D ARG* 3.8 5.1 + - + +
113D SER* 3.5 11.8 + - - -
121D THR* 3.0 25.5 - - + +
124D PHE* 4.5 25.4 - - + -
125D ALA* 4.8 11.2 - - + -
128D LEU* 5.1 6.3 - - + -
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Residues in contact with VAL 110 (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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106D LEU 3.4 3.8 + - - +
107D ALA 3.0 8.1 + - - +
109D LEU* 1.3 74.9 - - - +
111D ARG* 1.3 66.6 + - - +
113D SER* 3.2 18.2 + - - +
118D LEU* 4.1 7.2 - - + +
121D THR* 3.7 10.8 - - + +
122D VAL* 3.5 44.4 - - + +
125D ALA* 4.2 12.6 - - + -
140D LEU* 5.2 8.5 - - + +
143D LEU* 3.8 24.2 - - + -
144D ALA* 5.1 1.8 - - + -
147D VAL* 4.1 23.1 - - + +
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Residues in contact with ARG 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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104D VAL 5.2 0.6 + - - -
107D ALA* 2.8 35.2 + - - +
108D SER* 3.7 10.8 + - - +
110D VAL* 1.3 74.2 - - - +
112D ARG* 1.3 60.9 + - + +
113D SER 3.1 8.8 + - - +
143D LEU* 4.3 19.1 - - + +
147D VAL* 4.8 10.3 - - + -
243D VAL* 5.4 6.8 - - - +
244D ASP* 4.2 3.4 - - - +
245D ALA* 2.9 49.3 + - - +
246D PRO 3.2 16.4 + - - -
247D GLN* 4.3 15.4 - - - +
248D ILE* 5.4 2.2 - - - +
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Residues in contact with ARG 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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108D SER* 2.7 39.9 + - - +
109D LEU* 4.0 6.0 - - + +
111D ARG* 1.3 73.8 - - + +
113D SER* 1.3 62.8 + - - +
114D SER 3.8 0.3 + - - -
248D ILE* 3.9 21.8 - - - +
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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