Contacts of the helix formed by residues 121 - 138 (chain D) in PDB entry 5JGH
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 121 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119D PRO 3.7 0.8 + - - -
120D ALA* 1.3 78.7 - - - +
122D PRO* 1.3 76.3 - - - +
123D PHE 3.3 2.9 - - - -
124D ILE* 3.2 21.1 + - - +
125D LYS* 3.2 11.6 + - - +
169D TYR* 4.1 7.4 - - - -
4E A 5.9 0.9 - - - -
5E T 4.9 11.2 - - - -
6E T 5.0 3.6 - - - -
19F T 4.5 5.0 + - - -
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Residues in contact with PRO 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121D GLY* 1.3 82.7 - - - +
123D PHE* 1.3 62.7 + - - +
125D LYS* 3.5 3.9 + - + +
126D TYR* 3.2 22.2 + - - +
154D TRP* 4.0 10.3 - - + -
165D TYR* 3.7 28.5 - - + +
166D ILE* 3.8 16.2 - - + +
168D GLU* 6.0 0.2 - - - +
169D TYR* 3.7 22.9 - - + -
5E T 3.5 29.2 - - - +
6E T 3.6 21.8 - - - +
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Residues in contact with PHE 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121D GLY 3.3 0.6 - - - -
122D PRO* 1.3 76.8 - - - +
124D ILE* 1.3 68.5 + - + +
126D TYR* 3.2 2.5 + + - +
127D ALA* 2.8 36.1 + - + +
147D MET* 4.4 4.0 - - - -
150D ILE* 3.7 28.7 - - + -
151D GLY* 3.7 25.1 - - - -
154D TRP* 3.6 34.6 - + + -
3E T 3.2 44.9 - - + -
4E A 3.2 46.0 + - - +
5E T 4.5 5.1 + - - +
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Residues in contact with ILE 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120D ALA* 3.7 20.6 - - + -
121D GLY* 3.2 13.3 + - - +
123D PHE* 1.3 88.0 - - + +
125D LYS* 1.3 56.9 + - - +
126D TYR 3.2 0.2 + - - -
127D ALA* 3.3 4.1 + - + +
128D ASN* 2.7 44.7 + - - +
3E T 4.2 1.8 - - - +
4E A 4.1 17.7 - - + +
19F T 3.5 26.9 - - + +
20F A 3.4 56.8 - - + +
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Residues in contact with LYS 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120D ALA* 4.8 12.5 - - + +
121D GLY 3.2 12.1 + - - +
122D PRO* 4.0 4.9 - - + +
124D ILE* 1.3 80.2 - - - +
126D TYR* 1.3 64.7 + - - +
128D ASN* 3.5 24.7 + - + +
129D GLU* 3.2 35.0 + - + +
165D TYR* 4.4 5.2 - - + -
168D GLU* 3.5 31.9 - - - +
21F A 5.9 0.6 + - - -
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Residues in contact with TYR 126 (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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122D PRO 3.2 16.2 + - - +
123D PHE* 3.6 4.7 - + - +
124D ILE 3.1 0.6 - - - -
125D LYS* 1.3 77.2 - - - +
127D ALA* 1.3 68.1 + - - +
129D GLU* 2.6 26.0 + - - +
130D VAL* 3.1 32.8 + - + +
150D ILE* 3.7 21.5 - - + -
153D LYS* 3.3 39.3 + - - +
154D TRP* 3.5 39.9 - + + -
157D LEU* 3.8 25.0 - - + +
161D ILE* 5.9 0.7 - - + -
165D TYR* 3.6 40.3 - + + -
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Residues in contact with ALA 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123D PHE* 2.8 31.7 + - + +
124D ILE* 3.6 5.8 - - + +
126D TYR* 1.3 73.7 - - - +
128D ASN* 1.3 60.0 + - - +
129D GLU 3.1 0.2 + - - -
130D VAL* 4.0 1.1 - - - -
131D ARG* 2.8 37.4 + - - +
147D MET* 4.4 18.2 - - + -
150D ILE* 3.6 30.3 - - + -
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Residues in contact with ASN 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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120D ALA* 5.5 0.6 - - - +
124D ILE* 2.7 39.5 + - - +
125D LYS* 3.7 29.6 - - + +
126D TYR 3.1 0.4 + - - -
127D ALA* 1.3 73.9 - - - +
129D GLU* 1.3 62.4 + - + +
131D ARG* 2.4 46.3 + - - +
132D SER* 5.1 2.1 + - - -
147D MET* 5.3 0.3 - - - +
20F A 3.7 23.1 + - - +
21F A 3.9 11.6 + - - +
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Residues in contact with GLU 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 LYS* 3.2 22.1 + - + +
126D TYR 2.6 14.9 + - - +
128D ASN* 1.3 76.2 - - + +
130D VAL* 1.3 61.3 + - + +
131D ARG 3.8 0.2 + - - -
132D SER* 4.4 9.0 + - - -
133D GLN 5.2 0.2 + - - -
165D TYR* 2.1 47.6 + - - +
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Residues in contact with VAL 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 TYR* 3.1 53.4 + - + +
127D ALA* 3.6 9.4 - - - +
129D GLU* 1.3 79.0 - - + +
131D ARG* 1.3 69.0 + - - +
132D SER 3.1 3.9 + - - -
133D GLN* 3.2 12.5 + - + +
134D VAL* 2.9 34.3 + - + +
150D ILE* 4.0 11.0 - - + -
153D LYS* 4.6 4.7 - - - +
165D TYR* 5.4 0.9 - - - +
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Residues in contact with ARG 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127D ALA 2.8 22.2 + - - +
128D ASN* 2.4 45.8 + - - +
129D GLU 3.5 1.2 - - - -
130D VAL* 1.3 77.1 - - - +
132D SER* 1.3 60.5 + - - +
134D VAL* 3.2 1.0 + - - +
135D PHE* 2.8 31.6 + - + +
143D GLN* 3.3 22.9 + - - -
146D LEU* 4.7 12.4 - - + +
147D MET* 3.1 33.3 - - - +
150D ILE* 3.8 17.0 - - + -
21F A 3.0 37.0 + - - -
22F A 4.4 5.9 + - - -
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Residues in contact with SER 132 (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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128D ASN 5.1 1.9 + - - -
129D GLU 4.4 8.2 + - - -
130D VAL 3.1 0.8 - - - -
131D ARG* 1.3 82.5 - - - +
133D GLN* 1.3 60.1 + - - +
135D PHE* 3.6 5.9 + - - +
136D ALA* 3.3 20.8 + - - +
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Residues in contact with GLN 133 (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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129D GLU 5.2 0.6 + - - +
130D VAL* 3.2 15.2 + - + +
132D SER* 1.3 76.3 - - - +
134D VAL* 1.3 63.4 + - + +
136D ALA* 3.2 7.8 + - + +
137D GLN* 3.0 54.3 + - + +
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Residues in contact with VAL 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130D VAL* 2.9 23.1 + - + +
131D ARG 3.7 2.7 - - - +
133D GLN* 1.3 77.2 - - + +
135D PHE* 1.3 62.6 + - - +
137D GLN* 3.3 12.4 + - - +
138D HIS* 3.1 27.2 + - + +
146D LEU* 3.6 19.1 - - + -
149D ILE* 4.0 18.2 - - + -
150D ILE* 3.8 25.1 - - + -
153D LYS* 3.5 35.0 - - + -
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Residues in contact with PHE 135 (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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131D ARG* 2.8 19.1 + - + +
132D SER* 3.9 6.1 - - - +
134D VAL* 1.3 78.1 - - - +
136D ALA* 1.3 59.2 + - - +
138D HIS 2.9 33.5 - - - +
139D PRO* 3.2 30.5 - - + +
141D LYS 3.8 13.0 - - - -
146D LEU* 3.6 29.8 - - + +
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Residues in contact with ALA 136 (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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132D SER 3.3 11.1 + - - +
133D GLN* 3.2 12.8 + - + +
135D PHE* 1.3 81.6 - - - +
137D GLN* 1.3 62.0 + - + +
138D HIS 3.5 0.7 + - - -
139D PRO* 3.8 11.5 - - - +
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Residues in contact with GLN 137 (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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133D GLN* 3.0 52.3 + - - +
134D VAL* 3.8 16.7 - - - +
135D PHE 3.2 0.2 - - - -
136D ALA* 1.3 77.6 - - + +
138D HIS* 1.3 79.7 + - + +
139D PRO* 3.7 5.2 - - - +
153D LYS* 5.8 2.1 + - - +
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Residues in contact with HIS 138 (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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134D VAL* 3.1 27.9 + - + +
135D PHE* 2.9 19.4 + - - +
137D GLN* 1.3 94.5 + - + +
139D PRO* 1.3 67.2 - - - +
140D ASP* 3.2 8.5 + - - +
141D LYS* 3.4 35.4 + - + +
146D LEU* 4.2 3.8 - - + +
149D ILE* 3.9 31.0 - - + +
155G GLN 5.0 2.7 - - - -
156G SER* 4.6 14.1 + - - -
157G LEU 5.8 0.9 - - - -
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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