Contacts of the helix formed by residues 102 - 124 (chain D) in PDB entry 3C5C
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 SER 102 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28D ARG* 3.9 7.7 + - - -
99D SER* 2.9 28.2 + - - +
100D VAL 3.3 1.6 + - - -
101D ASP* 1.3 80.3 - - - +
103D ARG* 1.3 63.8 + - - +
104D GLN* 3.5 9.9 + - - +
105D SER* 2.9 39.4 + - - -
106D PHE* 3.1 7.6 + - - +
143D GLN* 3.6 2.9 - - - +
144D VAL* 4.3 2.9 - - - -
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Residues in contact with ARG 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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102D SER* 1.3 72.4 - - - +
104D GLN* 1.3 59.3 + - + +
106D PHE* 3.2 23.2 + - - +
107D ASP* 2.9 50.6 + - - +
143D GLN* 2.9 50.9 + - + +
144D VAL* 3.9 8.9 - - - +
148D GLU* 2.9 36.8 + - - -
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Residues in contact with GLN 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D ARG* 3.6 40.0 + - - +
102D SER* 3.1 4.2 + - - +
103D ARG* 1.3 82.5 - - + +
105D SER* 1.3 61.1 + - - +
107D ASP* 3.5 7.5 + - - +
108D SER* 3.0 26.3 + - - -
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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
----------------------------------------------------------
28D ARG* 3.8 28.3 + - - +
29D ARG 5.8 0.2 - - - -
31D ALA* 4.4 7.4 - - - -
97D VAL 4.7 1.4 - - - +
98D TYR* 3.5 11.8 - - - +
99D SER* 2.8 35.5 + - - -
102D SER* 2.9 25.9 + - - -
104D GLN* 1.3 78.4 - - - +
106D PHE* 1.3 58.2 + - - +
108D SER* 3.3 2.4 + - - -
109D SER* 2.9 23.4 + - - -
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Residues in contact with PHE 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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98D TYR* 3.7 41.1 - + + -
102D SER 3.1 8.8 + - - +
103D ARG* 3.6 36.6 - - - +
104D GLN 3.2 0.2 - - - -
105D SER* 1.3 77.9 + - - +
107D ASP* 1.3 71.5 + - - +
109D SER* 2.6 21.6 + - - -
110D SER* 3.4 4.9 + - - -
144D VAL* 3.7 25.4 - - + -
148D GLU* 3.4 37.5 - - + -
149D GLY* 4.3 0.2 - - - -
152D LEU* 3.4 30.1 - - + +
155D ARG* 6.3 1.3 - - - -
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Residues in contact with ASP 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 ARG* 2.9 45.1 + - - +
104D GLN* 3.8 7.9 - - - +
106D PHE* 1.3 82.1 - - - +
108D SER* 1.3 57.8 + - - +
110D SER* 2.7 26.8 + - - -
111D SER* 3.6 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
----------------------------------------------------------
28D ARG* 3.4 33.6 - - - +
104D GLN 3.0 16.8 + - - -
105D SER 3.6 7.9 - - - -
106D PHE 3.2 0.2 - - - -
107D ASP* 1.3 74.1 - - - +
109D SER* 1.3 65.3 + - - +
111D SER* 3.0 24.5 + - - -
112D TYR* 3.2 18.9 - - - -
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Residues in contact with SER 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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27D GLY* 5.6 0.2 - - - -
28D ARG 5.6 0.2 - - - +
96D VAL* 3.7 21.6 - - - +
97D VAL 4.6 4.0 - - - -
98D TYR* 3.8 17.0 - - - -
105D SER 2.9 13.9 + - - -
106D PHE* 2.6 21.7 + - - -
108D SER* 1.3 77.4 - - - +
110D SER* 1.3 61.6 + - - +
112D TYR* 3.2 7.1 + - - +
113D LEU* 3.0 26.3 + - - +
131D LEU* 4.1 7.4 - - - -
152D LEU* 3.2 18.0 - - - +
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Residues in contact with SER 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 PHE 3.4 3.8 + - - -
107D ASP* 2.7 23.4 + - - -
109D SER* 1.3 82.2 + - - +
111D SER* 1.3 55.5 + - - +
113D LEU* 3.3 5.4 + - - +
114D GLU* 2.8 39.6 + - - +
152D LEU* 3.7 28.0 - - - -
155D ARG* 3.9 18.4 + - - -
156D PHE* 3.8 0.8 - - - -
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Residues in contact with SER 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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107D ASP 3.6 5.1 + - - -
108D SER* 3.0 23.4 + - - -
110D SER* 1.3 78.9 + - - +
112D TYR* 1.3 63.1 + - - +
114D GLU* 3.4 16.7 - - - +
115D LEU* 3.1 26.2 + - - +
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Residues in contact with TYR 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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26D LEU* 4.0 19.1 - - + -
27D GLY* 3.5 44.4 + - - -
28D ARG* 3.9 4.2 - - - -
75D THR* 6.0 0.2 - - - -
77D ASP* 2.7 42.8 + - - +
84D CYS* 5.9 0.9 - - - -
87D TYR* 3.8 17.7 - - - -
96D VAL* 4.0 16.8 - - + -
108D SER* 3.2 28.6 + - - -
109D SER* 3.2 8.1 + - - +
111D SER* 1.3 78.3 - - - +
113D LEU* 1.3 60.1 + - - +
115D LEU* 3.2 11.3 + - + +
116D LEU* 3.0 34.7 + - - +
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Residues in contact with LEU 113 (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 VAL* 3.7 27.4 - - + -
109D SER 3.0 18.3 + - - +
110D SER 3.6 6.3 - - - +
112D TYR* 1.3 75.7 - - - +
114D GLU* 1.3 55.2 + - - +
116D LEU* 3.5 7.7 + - + +
117D ALA* 3.0 27.7 + - - +
129D ALA* 4.4 13.0 - - + -
130D LEU 5.5 0.4 - - - +
131D LEU* 4.2 13.0 - - + -
152D LEU* 3.9 26.7 - - + +
156D PHE* 3.5 39.3 - - + +
158D CYS* 4.2 24.9 - - + -
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Residues in contact with GLU 114 (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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110D SER* 2.8 26.6 + - - +
111D SER* 3.4 23.4 + - - +
112D TYR 3.2 0.2 - - - -
113D LEU* 1.3 70.3 - - - +
115D LEU* 1.3 58.8 + - - +
117D ALA* 3.2 4.3 + - - +
118D LEU* 3.0 35.8 + - + +
155D ARG* 3.3 23.4 + - - -
156D PHE* 3.4 19.5 - - + -
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Residues in contact with LEU 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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84D CYS* 3.3 42.8 - - + -
87D TYR* 3.4 22.7 - - + +
88D LEU* 4.1 13.2 - - + -
111D SER 3.1 15.2 + - - +
112D TYR* 3.4 17.7 - - + +
114D GLU* 1.3 75.5 - - - +
116D LEU* 1.3 62.9 + - + +
118D LEU* 3.5 13.3 + - + +
119D HIS* 3.1 24.3 + - - +
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Residues in contact with LEU 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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26D LEU* 4.0 10.8 - - + -
87D TYR* 4.8 1.1 - - + -
88D LEU* 3.5 27.8 - - + -
94D PHE* 3.7 55.2 - - + -
96D VAL* 4.0 20.6 - - + -
112D TYR 3.0 18.9 + - - +
113D LEU* 3.7 8.7 - - + +
114D GLU 3.3 0.2 - - - -
115D LEU* 1.3 76.4 - - + +
117D ALA* 1.3 63.2 + - - +
119D HIS* 3.3 2.8 + - - +
120D ALA* 3.0 24.3 + - - +
127D ILE 6.0 1.1 - - - +
129D ALA* 4.1 12.8 - - + -
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Residues in contact with ALA 117 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113D LEU 3.0 16.0 + - - +
114D GLU* 3.2 10.3 + - - +
116D LEU* 1.3 76.3 - - - +
118D LEU* 1.3 62.8 + - - +
120D ALA* 3.4 5.7 + - - +
121D LYS* 3.1 22.8 + - - +
156D PHE* 4.1 16.6 - - + -
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Residues in contact with LEU 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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114D GLU* 3.0 20.3 + - + +
115D LEU* 3.6 15.5 - - + +
117D ALA* 1.3 74.9 - - - +
119D HIS* 1.3 58.2 + - - +
121D LYS* 3.3 8.2 + - + +
122D GLU* 2.9 51.5 + - + +
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Residues in contact with HIS 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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85D GLU* 5.3 5.9 + - + -
88D LEU* 3.4 53.7 + - + +
89D ASN* 2.8 35.8 + - - -
94D PHE* 6.5 0.2 - + - -
115D LEU 3.1 14.9 + - - +
116D LEU 3.3 4.7 + - - +
118D LEU* 1.3 79.4 - - - +
120D ALA* 1.3 56.4 + - - +
122D GLU* 3.2 11.0 + - - -
123D THR* 2.8 70.6 + - + +
125D ARG* 4.5 7.8 - - + -
127D ILE* 5.7 1.1 - - + -
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Residues in contact with ALA 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 LEU 3.0 12.5 + - - +
117D ALA* 3.6 9.9 - - - +
119D HIS* 1.3 77.9 - - - +
121D LYS* 1.3 56.4 + - - +
124D GLN* 2.8 34.5 + - - +
125D ARG 3.3 26.7 - - - +
126D SER* 5.1 3.4 - - - -
127D ILE 5.4 1.6 - - - +
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Residues in contact with LYS 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 ALA 3.1 14.0 + - - +
118D LEU* 3.7 11.2 - - + +
120D ALA* 1.3 76.4 - - - +
122D GLU* 1.3 62.3 + - + +
124D GLN* 4.4 7.9 + - - +
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Residues in contact with GLU 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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44C ARG* 5.4 9.6 - - - +
45C PHE 4.0 1.9 - - - +
46C ILE* 3.6 17.2 - - - +
118D LEU* 2.9 44.1 + - + +
119D HIS* 3.2 13.6 + - - +
121D LYS* 1.3 74.1 - - + +
123D THR* 1.3 66.6 + - + +
124D GLN* 3.6 0.6 - - - +
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Residues in contact with THR 123 (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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45C PHE* 3.4 36.6 - - + +
46C ILE* 3.7 1.9 - - - -
47C SER* 2.8 31.9 + - - -
119D HIS* 2.8 55.1 + - + +
122D GLU* 1.3 80.8 - - + +
124D GLN* 1.3 64.5 + - - +
125D ARG* 3.0 25.0 + - - +
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Residues in contact with GLN 124 (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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46C ILE* 4.5 17.5 - - + -
47C SER* 3.5 1.3 - - - -
48C GLU* 3.1 40.2 - - + +
120D ALA* 2.8 14.9 + - - +
121D LYS* 4.4 6.6 + - - +
122D GLU 3.6 1.2 - - - +
123D THR* 1.3 79.2 - - - +
125D ARG* 1.3 58.3 + - - +
126D SER* 3.1 10.5 + - - -
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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