Contacts of the helix formed by residues 111 - 123 (chain D) in PDB entry 5GQQ
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 111 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105D ASP* 5.1 2.4 - - - +
109D MET 4.0 0.4 + - - -
110D ILE* 1.3 73.4 - - - +
112D LYS* 1.3 54.0 + - - +
113D ASN* 2.6 38.9 + - - +
114D GLU* 2.9 42.4 + - - +
115D LEU* 2.6 37.9 + - - +
135D ILE* 4.0 6.7 - - - -
144D GLY 4.6 4.5 - - - +
145D GLN* 3.7 24.4 + - + +
202D CA 4.2 1.6 - - - -
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Residues in contact with LYS 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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111D ASP* 1.3 77.4 + - - +
113D ASN* 1.3 70.8 + - - +
115D LEU* 3.1 6.3 + - - +
116D LYS* 3.0 23.3 + - + +
128D ASP* 3.9 27.4 + - - +
129D GLN* 4.9 4.0 + - - -
131D HIS* 4.4 16.9 - - + -
132D ASP* 2.9 42.1 + - - +
135D ILE* 3.5 23.6 - - + +
144D GLY 4.9 0.4 + - - -
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Residues in contact with ASN 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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111D ASP* 2.6 15.6 + - - +
112D LYS* 1.3 84.1 - - - +
114D GLU* 1.3 62.2 + - + +
116D LYS* 3.4 6.6 + - - +
117D GLN* 3.2 25.2 + - - +
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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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102D TYR* 3.2 25.3 - - - +
103D ASP* 3.2 2.9 - - - +
104D ARG* 2.9 25.9 + - + +
105D ASP* 2.7 17.1 + - - +
109D MET 3.2 3.5 - - - +
110D ILE* 3.3 7.7 - - + -
111D ASP* 2.9 43.1 + - - +
113D ASN* 1.3 75.4 - - + +
115D LEU* 1.3 59.0 + - - +
117D GLN* 3.1 9.5 + - - +
118D ALA* 2.9 28.6 + - - +
202D CA 2.4 30.0 - - - -
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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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110D ILE* 3.6 8.7 - - + +
111D ASP 2.6 22.1 + - - +
112D LYS* 3.1 7.1 + - - +
114D GLU* 1.3 73.4 - - - +
116D LYS* 1.3 52.1 + - - +
118D ALA* 3.1 2.9 + - + +
119D LEU* 2.7 57.6 + - + +
131D HIS* 4.5 9.4 - - + +
134D LEU* 4.3 21.5 - - + -
135D ILE* 4.1 13.2 - - + +
138D PHE* 4.5 8.7 - - + -
146D ILE* 3.6 27.1 - - + -
151D PHE* 3.9 26.7 - - + -
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Residues in contact with LYS 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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112D LYS* 3.0 12.8 + - + +
113D ASN* 3.9 9.0 - - - +
115D LEU* 1.3 75.6 - - - +
117D GLN* 1.3 55.7 + - + +
119D LEU* 4.0 0.2 - - - +
120D SER* 2.8 45.5 + - - -
126D LEU 3.8 18.4 + - - -
128D ASP* 4.1 30.0 + - - +
131D HIS* 3.6 33.1 - - + +
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Residues in contact with GLN 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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102D TYR* 3.4 21.5 - - + +
104D ARG* 3.5 34.0 + - + +
113D ASN 3.2 13.9 + - - +
114D GLU* 3.1 11.6 + - - +
116D LYS* 1.3 78.5 - - - +
118D ALA* 1.3 60.9 + - - +
120D SER* 4.0 4.6 - - - -
121D GLY* 3.1 18.0 + - - -
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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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102D TYR* 3.4 35.9 - - + -
110D ILE* 4.9 0.9 - - + -
114D GLU 2.9 12.0 + - - +
115D LEU* 3.5 8.7 - - + +
117D GLN* 1.3 77.0 - - - +
119D LEU* 1.3 62.3 + - - +
121D GLY* 3.3 3.1 + - - -
122D PHE* 3.2 31.6 + - + -
151D PHE* 4.2 26.2 - - + -
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Residues in contact with LEU 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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115D LEU* 2.7 43.2 + - + +
116D LYS 4.0 2.0 - - - +
118D ALA* 1.3 73.7 - - - +
120D SER* 1.3 62.9 + - - +
122D PHE* 3.2 33.8 + - + +
124D TYR* 3.2 34.5 + - + +
126D LEU* 3.8 13.5 - - + -
131D HIS* 4.2 12.8 - - - +
134D LEU* 3.5 31.9 - - + -
138D PHE* 5.3 2.9 - - + -
155D CYS* 4.7 7.4 - - - -
158D LEU* 4.0 19.7 - - + -
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Residues in contact with SER 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 LYS* 2.8 31.6 + - - -
117D GLN* 4.0 5.4 - - - -
119D LEU* 1.3 72.9 - - - +
121D GLY* 1.3 62.1 + - - +
123D GLY* 3.1 10.4 + - - -
124D TYR 3.6 12.6 - - - -
125D ARG* 3.7 27.4 + - - -
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Residues in contact with GLY 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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102D TYR* 3.8 18.7 + - - -
117D GLN 3.1 12.5 + - - -
118D ALA 3.3 5.5 + - - -
120D SER* 1.3 76.3 - - - +
122D PHE* 1.3 63.4 + - - +
123D GLY 3.3 0.4 + - - -
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Residues in contact with PHE 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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95D TRP* 4.3 10.8 - + - -
98D VAL* 3.6 36.3 - - + -
102D TYR* 4.6 6.5 - + - -
118D ALA* 3.2 18.4 + - + -
119D LEU* 3.2 26.0 + - + +
120D SER 3.1 0.8 - - - -
121D GLY* 1.3 80.9 - - - +
123D GLY* 1.3 57.7 + - - +
124D TYR* 3.5 19.5 - + + -
151D PHE* 4.1 11.9 - + - -
155D CYS* 3.7 26.9 - - + -
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Residues in contact with GLY 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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120D SER 3.1 10.3 + - - -
121D GLY 3.3 0.8 + - - -
122D PHE* 1.3 80.2 - - - +
124D TYR* 1.3 66.1 + - - +
125D ARG* 3.6 19.4 + - - -
166D ARG* 5.7 3.4 + - - -
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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