Contacts of the helix formed by residues 107 - 126 (chain D) in PDB entry 5YL4
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 THR 107 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D ALA 3.3 5.1 + - - +
103D LYS* 3.4 14.6 + - - -
105D HIS 3.9 0.6 - - - -
106D TYR* 1.3 81.8 - - + +
108D GLU* 1.3 77.4 + - - +
109D GLY 3.4 1.1 - - - -
110D ALA* 3.3 16.0 + - - +
111D GLU* 3.0 21.3 + - - +
401D GLU* 3.0 48.6 + - + +
133E VAL* 5.2 0.2 - - + -
134E ARG* 4.6 16.1 - - + +
137E LYS* 4.1 17.9 - - + -
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Residues in contact with GLU 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68D LEU* 3.8 19.9 - - + +
95D SER* 2.9 26.2 + - - -
96D GLY 3.0 15.6 + - - +
103D LYS* 3.1 40.8 + - + +
107D THR* 1.3 89.2 + - - +
109D GLY* 1.3 61.8 + - - +
111D GLU* 3.3 30.2 + - - +
112D LEU* 3.6 4.7 + - - +
401D GLU* 4.8 2.5 - - - +
137E LYS* 5.8 2.9 - - - +
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Residues in contact with GLY 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68D LEU* 4.0 13.6 - - - +
103D LYS 2.9 11.1 + - - -
104D GLY 3.3 19.7 - - - -
108D GLU* 1.3 73.2 - - - +
110D ALA* 1.3 58.6 + - - +
111D GLU 3.2 0.4 - - - -
112D LEU* 3.2 2.4 + - - -
113D VAL* 3.0 30.3 + - - +
147D MET* 3.8 16.9 - - - +
150D LEU* 4.5 1.6 - - - -
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Residues in contact with ALA 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104D GLY 4.0 3.8 + - - -
105D HIS 4.1 6.6 + - - +
106D TYR 3.2 28.7 - - - +
107D THR 3.3 5.7 + - - +
109D GLY* 1.3 77.2 - - - +
111D GLU* 1.3 59.0 + - + +
113D VAL* 3.2 19.8 - - + +
114D ASP* 4.7 3.5 + - - +
150D LEU* 3.9 15.2 - - + +
134E ARG* 3.2 19.3 - - - +
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Residues in contact with GLU 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107D THR* 3.0 25.4 + - - +
108D GLU* 3.3 20.1 + - - +
109D GLY 3.2 0.8 - - - -
110D ALA* 1.3 76.5 - - + +
112D LEU* 1.3 62.8 + - - +
113D VAL 3.6 0.2 + - - -
114D ASP* 4.5 6.2 + - - +
115D SER* 4.7 2.8 + - - -
134E ARG* 5.6 4.7 - - - -
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Residues in contact with LEU 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66D VAL* 4.7 0.9 - - + -
67D ASP 3.6 26.7 - - - +
68D LEU* 4.1 18.6 - - + -
91D VAL* 3.9 23.6 - - + +
92D PHE 4.3 4.7 - - - +
93D GLY* 3.8 24.2 - - - +
108D GLU 3.6 2.2 + - - +
109D GLY 3.2 3.8 + - - +
111D GLU* 1.3 78.5 - - - +
113D VAL* 1.3 62.1 + - - +
114D ASP 3.4 0.7 - - - -
115D SER* 2.6 36.5 + - - +
116D VAL* 3.4 6.2 + - - +
147D MET* 3.9 22.7 - - + -
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Residues in contact with VAL 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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109D GLY 3.0 14.3 + - - +
110D ALA* 3.2 21.8 - - - +
111D GLU 3.3 0.2 - - - -
112D LEU* 1.3 76.7 - - - +
114D ASP* 1.3 73.0 + - - +
116D VAL* 3.3 3.6 + - - +
117D LEU* 2.9 32.1 + - + +
147D MET* 4.1 8.7 - - + +
150D LEU* 3.7 30.5 - - + -
151D LEU* 4.2 25.6 - - + +
154D LYS* 4.4 19.7 - - + -
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Residues in contact with ASP 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 ALA 5.1 3.1 - - - -
111D GLU 4.5 5.7 + - - +
112D LEU 3.3 0.8 + - - -
113D VAL* 1.3 87.2 - - - +
115D SER* 1.3 61.1 + - - +
117D LEU* 3.3 17.9 + - - +
118D ASP* 3.0 35.9 + - - +
121D ARG* 4.8 2.4 + - - +
154D LYS* 5.6 2.3 + - - +
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Residues in contact with SER 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91D VAL* 3.8 9.8 - - - +
111D GLU 4.7 2.4 + - - -
112D LEU* 2.6 40.6 + - - +
114D ASP* 1.3 73.1 - - - +
116D VAL* 1.3 63.0 + - - +
118D ASP* 3.6 17.8 - - - +
119D VAL* 3.5 18.4 - - - +
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Residues in contact with VAL 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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7D ILE* 5.5 1.8 - - + -
64D ILE* 4.1 10.8 - - + -
66D VAL* 3.8 28.5 - - + -
91D VAL* 3.4 27.8 - - + -
112D LEU* 3.6 10.8 - - + +
113D VAL 3.3 7.3 + - - +
114D ASP 3.3 0.2 - - - -
115D SER* 1.3 76.0 + - - +
117D LEU* 1.3 57.2 + - - +
119D VAL* 2.8 24.9 + - - +
120D VAL* 3.0 15.0 + - + +
147D MET* 3.8 20.6 - - + -
151D LEU* 3.4 26.0 - - + -
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Residues in contact with LEU 117 (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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113D VAL* 2.9 23.2 + - + +
114D ASP* 3.5 24.0 - - - +
116D VAL* 1.3 75.3 - - - +
118D ASP* 1.3 56.5 + - - +
120D VAL* 3.8 8.7 - - + +
121D ARG* 3.0 50.3 + - + +
151D LEU* 4.7 6.7 - - + -
154D LYS* 4.0 37.9 - - + +
155D ILE* 4.1 27.6 - - + +
158D GLU* 4.4 19.1 - - - +
159D TYR* 6.5 1.1 - - + -
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Residues in contact with ASP 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114D ASP* 3.0 21.6 + - - +
115D SER* 3.6 16.0 - - - +
116D VAL 3.1 0.4 + - - -
117D LEU* 1.3 76.7 - - - +
119D VAL* 1.3 58.2 + - + +
121D ARG* 2.9 25.7 + - - +
122D LYS* 3.0 29.5 + - - +
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Residues in contact with VAL 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64D ILE* 3.8 20.4 - - + -
86D ARG* 5.4 1.1 - - - +
88D ASP 4.1 10.1 - - - +
89D ASN* 3.6 39.3 - - - +
91D VAL* 3.5 23.3 - - + -
115D SER 3.5 16.4 - - - +
116D VAL 2.8 10.9 + - - +
118D ASP* 1.3 69.2 - - + +
120D VAL* 1.3 65.3 + - - +
122D LYS* 3.5 8.2 + - + +
123D GLU* 3.1 25.2 + - + +
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Residues in contact with VAL 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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5D VAL* 4.9 0.4 - - + -
7D ILE* 4.2 16.2 - - + -
64D ILE* 3.6 23.3 - - + -
116D VAL* 3.0 27.3 + - + +
117D LEU* 3.8 13.0 - - + +
119D VAL* 1.3 75.5 - - - +
121D ARG* 1.3 54.1 + - - +
123D GLU* 3.0 3.5 + - - +
124D SER* 2.7 39.9 + - - +
133D PHE* 3.7 32.3 - - + -
155D ILE* 4.5 15.9 - - + -
159D TYR* 4.4 9.2 - - + -
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Residues in contact with ARG 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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114D ASP* 4.8 2.8 + - - +
117D LEU* 3.0 47.2 + - + +
118D ASP* 2.9 33.8 + - - +
120D VAL* 1.3 75.5 - - + +
122D LYS* 1.3 56.7 + - - +
124D SER* 4.2 0.2 - - - -
125D GLU* 3.0 34.0 + - - +
158D GLU* 2.7 41.8 + - - +
159D TYR* 3.6 20.0 + - + +
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Residues in contact with LYS 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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86D ARG* 3.1 43.7 - - - +
88D ASP* 5.9 0.4 - - - -
118D ASP 3.0 18.3 + - - +
119D VAL* 3.8 8.7 - - - +
120D VAL 3.2 0.2 - - - -
121D ARG* 1.3 77.0 - - - +
123D GLU* 1.3 65.5 + - + +
125D GLU* 4.1 11.0 - - - +
126D SER* 3.4 19.2 + - - -
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Residues in contact with GLU 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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5D VAL* 4.5 10.3 - - + -
52D ASN* 3.0 28.5 + - - -
61D PRO 5.1 0.7 - - - +
62D ARG* 3.6 23.8 - - + +
64D ILE* 4.4 7.4 - - + -
86D ARG* 3.9 17.3 + - - +
89D ASN* 2.7 36.7 + - - +
119D VAL* 3.1 19.9 + - + +
120D VAL 3.0 4.3 + - - +
122D LYS* 1.3 78.6 - - + +
124D SER* 1.3 61.7 + - - +
126D SER* 2.9 21.7 + - - -
127D CYS* 3.4 16.4 - - - -
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Residues in contact with SER 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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5D VAL* 4.0 4.5 - - - +
120D VAL* 2.7 18.5 + - - +
123D GLU* 1.3 72.9 - - - +
125D GLU* 1.3 60.2 + - - +
127D CYS* 3.4 26.2 + - - +
130D LEU* 3.6 21.1 - - - +
133D PHE* 3.6 20.4 - - - -
159D TYR* 3.2 36.1 + - - -
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Residues in contact with GLU 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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121D ARG 3.0 21.2 + - - +
122D LYS* 4.1 12.2 - - - +
123D GLU 3.3 0.2 - - - -
124D SER* 1.3 76.9 - - - +
126D SER* 1.3 59.5 + - - +
127D CYS 3.2 5.4 + - - +
159D TYR* 4.9 1.1 + - - +
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Residues in contact with SER 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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3D GLU* 5.1 0.3 - - - +
52D ASN* 5.1 6.5 + - - -
122D LYS 3.4 11.9 + - - -
123D GLU* 2.9 23.2 + - - -
125D GLU* 1.3 75.6 - - - +
127D CYS* 1.3 62.0 + - - +
128D ASP 3.5 2.9 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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