Contacts of the helix formed by residues 116 - 131 (chain D) in PDB entry 4GQS
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 ASN 116 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96D GLY* 3.7 4.6 - - - -
97D ARG* 2.6 50.3 + - - +
114D PHE 4.1 6.7 + - - -
115D SER* 1.3 77.7 - - - +
117D GLY* 1.3 73.0 + - - +
119D ARG* 3.4 10.9 - - - +
120D TRP* 3.2 14.0 + - - -
371D THR* 6.6 0.4 - - + -
433D ARG* 3.6 3.9 + - - +
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Residues in contact with GLY 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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116D ASN* 1.3 82.1 - - - +
118D LYS* 1.3 65.8 + - - +
120D TRP* 3.2 12.5 + - - +
121D LYS* 3.6 12.4 + - - +
371D THR* 6.1 3.2 - - - +
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Residues in contact with LYS 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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117D GLY* 1.3 68.7 - - - -
119D ARG* 1.3 69.5 + - - +
120D TRP 2.8 1.9 + - - -
121D LYS* 2.8 21.6 + - + +
122D GLU* 2.9 20.7 + - + +
281D GLU* 4.9 11.0 - - - +
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Residues in contact with ARG 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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109D GLY 2.9 28.6 + - - -
110D PHE* 3.0 35.2 - - - +
111D GLY 4.1 1.0 + - - +
115D SER* 4.3 9.4 - - - -
116D ASN 3.4 11.6 + - - +
118D LYS* 1.3 75.8 - - - +
120D TRP* 1.3 62.7 + - - +
122D GLU* 3.5 1.4 + - - +
123D ILE* 3.1 31.9 + - - +
281D GLU* 3.4 34.0 - - + +
286D ASN* 2.6 33.0 + - - +
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Residues in contact with TRP 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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95D SER* 4.0 18.4 - - - -
112D ILE* 3.1 23.3 - - + -
115D SER* 3.2 28.0 + - - +
116D ASN* 3.2 3.6 + - - +
117D GLY 3.5 10.3 - - - +
118D LYS 2.8 4.2 + - - -
119D ARG* 1.3 74.0 - - - +
121D LYS* 1.3 95.4 + - + +
122D GLU 3.1 0.2 + - - -
123D ILE* 3.2 1.9 + - - +
124D ARG* 2.7 59.3 + - + +
432D LYS* 3.3 45.5 - - + -
433D ARG* 2.9 37.7 - - - +
501D HEM 2.6 20.6 + - - -
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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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92D GLU* 2.7 44.1 + - - -
95D SER* 4.9 0.9 - - - -
117D GLY 3.6 8.0 + - - +
118D LYS* 2.8 15.5 + - + +
120D TRP* 1.3 106.1 - - + +
122D GLU* 1.3 57.6 + - + +
124D ARG* 4.2 4.7 - - - -
125D ARG* 2.9 70.9 + - - +
432D LYS* 4.4 2.2 - - - +
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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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118D LYS* 2.9 20.4 + - + +
119D ARG 3.7 4.3 - - - +
121D LYS* 1.3 74.9 - - + +
123D ILE* 1.3 66.8 + - - +
125D ARG* 4.2 5.0 - - - +
126D PHE* 3.3 23.9 + - - +
281D GLU* 3.2 38.6 - - + +
282D PHE* 4.0 23.1 - - + -
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Residues in contact with ILE 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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111D GLY 4.3 10.5 - - - +
112D ILE* 3.9 22.9 - - + +
119D ARG* 3.1 20.1 + - - +
120D TRP 4.0 1.3 - - - +
122D GLU* 1.3 73.7 - - - +
124D ARG* 1.3 66.1 + - - +
126D PHE* 3.5 7.3 + - + +
127D SER* 2.9 26.9 + - - +
267D PHE* 4.1 21.5 - - + -
281D GLU* 3.6 28.9 - - + +
282D PHE* 4.4 9.4 - - + -
286D ASN* 4.2 14.1 - - + +
290D THR* 3.5 26.9 - - + +
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Residues in contact with ARG 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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112D ILE* 3.7 14.0 - - + +
120D TRP* 2.7 49.7 + - + +
121D LYS* 3.9 4.7 - - - +
123D ILE* 1.3 71.1 - - - +
125D ARG* 1.3 62.4 + - + +
127D SER* 2.7 26.2 + - - -
128D LEU* 2.8 35.1 + - + +
432D LYS 2.9 27.5 + - - -
433D ARG* 3.3 10.3 + - - +
434D ILE* 2.6 48.5 + - - +
435D CYS 4.7 0.6 + - - -
436D VAL* 3.2 27.6 - - - +
501D HEM 3.4 12.0 + - - -
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Residues in contact with ARG 125 (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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92D GLU* 4.8 0.4 + - - -
121D LYS* 2.9 64.1 + - - +
122D GLU* 4.2 7.0 - - - +
124D ARG* 1.3 84.1 - - + +
126D PHE* 1.3 64.4 + - - +
128D LEU* 3.3 20.0 + - + +
129D MET* 3.3 24.9 + - + +
432D LYS* 4.2 13.1 - - - +
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Residues in contact with PHE 126 (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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122D GLU 3.3 17.3 + - - +
123D ILE* 3.6 8.1 - - + +
124D ARG 3.0 0.6 + - - -
125D ARG* 1.3 77.4 - - - +
127D SER* 1.3 69.7 + - - +
129D MET* 3.2 21.4 + - + +
130D THR* 3.2 35.2 + - - -
263D PHE* 3.6 30.3 - + - -
266D CYS* 4.1 12.3 - - + -
267D PHE* 3.9 42.6 - + + -
270D LYS* 4.8 13.0 - - + -
282D PHE* 4.0 28.7 - + + -
290D THR* 6.4 0.7 - - + -
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Residues in contact with SER 127 (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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112D ILE* 4.2 9.3 - - - +
123D ILE* 2.9 20.6 + - - +
124D ARG 2.7 15.2 + - - -
126D PHE* 1.3 71.9 - - - +
128D LEU* 1.3 55.8 + - - -
129D MET 2.8 15.8 + - - -
130D THR 3.0 5.7 + - - -
131D LEU* 3.0 28.9 - - - +
263D PHE* 3.9 21.1 - - - -
290D THR* 4.5 6.2 - - - +
294D LEU* 4.6 5.8 - - - +
436D VAL* 4.2 14.4 - - - -
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Residues in contact with LEU 128 (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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124D ARG* 2.8 68.2 + - + +
125D ARG* 3.3 10.7 + - + +
127D SER* 1.3 78.0 - - - +
129D MET* 1.3 60.5 + - + +
131D LEU* 3.9 16.8 + - - +
434D ILE* 6.0 1.3 - - + -
436D VAL* 3.3 31.6 - - + +
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Residues in contact with MET 129 (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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125D ARG* 3.3 24.4 + - + +
126D PHE* 3.2 16.5 + - + +
127D SER 2.8 5.3 + - - -
128D LEU* 1.3 74.7 - - + +
130D THR* 1.3 58.1 + - - +
131D LEU 2.9 14.1 + - - -
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Residues in contact with THR 130 (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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126D PHE* 3.2 29.5 + - - -
127D SER 3.0 2.5 + - - -
129D MET* 1.3 74.4 - - - +
131D LEU* 1.3 62.8 + - - +
181D ILE* 5.1 5.9 - - - +
262D ASP 5.5 0.7 - - - +
263D PHE* 3.6 36.3 - - + -
266D CYS* 4.1 26.1 - - + -
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Residues in contact with LEU 131 (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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127D SER* 3.0 27.1 - - - +
128D LEU* 4.1 12.9 - - - +
129D MET 2.9 8.0 - - - -
130D THR* 1.3 88.9 - - - +
181D ILE* 5.0 15.5 - - + -
263D PHE* 3.5 24.5 - - + -
294D LEU* 4.9 9.6 - - + -
436D VAL* 3.5 33.2 - - + +
437D GLY* 5.4 0.4 - - - -
440D LEU* 6.3 1.6 - - + -
501D HEM 4.4 16.6 - - + -
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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