Contacts of the helix formed by residues 108 - 125 (chain B) in PDB entry 5DQZ
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 108 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104B LYS* 3.4 15.7 + - + +
105B LEU 3.4 1.0 - - - +
106B ALA 4.6 0.2 - - - -
107B LEU* 1.3 78.2 - - - +
109B GLU* 1.3 62.8 + - - +
110B ASP* 3.1 25.4 + - - +
111B LEU* 3.8 24.1 - - + +
112B ARG* 2.8 30.9 + - - +
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Residues in contact with GLU 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B ALA 5.5 0.9 - - - +
107B LEU 3.5 10.1 + - - +
108B ASP* 1.3 76.2 + - - +
110B ASP* 1.3 62.0 + - - +
112B ARG* 3.3 34.4 + - - +
113B LEU* 2.9 29.3 + - - +
134B VAL* 5.3 4.0 - - - +
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Residues in contact with ASP 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B ASP* 3.1 22.5 + - - +
109B GLU* 1.3 77.1 + - - +
111B LEU* 1.3 62.3 + - + +
113B LEU* 3.2 9.6 + - - +
114B LYS* 3.0 35.9 + - + +
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Residues in contact with LEU 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B LYS* 3.9 25.8 - - + +
105B LEU* 3.8 24.5 - - + +
108B ASP* 3.3 34.2 + - + +
110B ASP* 1.3 74.6 - - + +
112B ARG* 1.3 66.9 + - - +
114B LYS* 3.0 14.3 + - + +
115B VAL* 2.9 27.9 + - - +
275B GLY* 3.5 26.4 - - - +
277B ILE* 4.4 19.3 - - + -
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Residues in contact with ARG 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B LEU 3.2 12.4 + - - +
106B ALA 3.9 14.6 - - - +
108B ASP 2.8 18.4 + - - +
109B GLU* 3.3 34.7 + - - +
111B LEU* 1.3 76.6 - - - +
113B LEU* 1.3 57.5 + - - +
115B VAL* 3.2 3.9 + - - +
116B VAL* 2.9 35.3 + - + +
134B VAL* 3.9 27.8 - - + +
138B ARG* 5.0 5.9 - - - +
205B GLY 5.2 0.2 + - - -
206B PHE* 2.9 51.6 + - + +
207B VAL 4.4 4.2 + - - -
209B THR* 4.0 19.0 + - - +
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Residues in contact with LEU 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B GLU 2.9 18.5 + - - +
110B ASP* 3.4 9.9 - - - +
112B ARG* 1.3 76.9 - - - +
114B LYS* 1.3 57.7 + - + +
116B VAL* 3.4 3.3 + - + +
117B ARG* 2.9 46.2 + - + +
131B ARG* 6.1 1.1 - - - -
132B ARG 3.4 28.0 - - - +
133B SER* 4.5 2.9 - - - -
134B VAL* 3.8 26.0 - - + +
137B LEU* 4.1 16.2 - - + -
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Residues in contact with LYS 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B ASP* 3.0 19.9 + - + +
111B LEU* 3.0 14.5 + - + +
113B LEU* 1.3 74.8 - - + +
115B VAL* 1.3 63.9 + - - +
117B ARG* 3.3 12.2 + - - +
118B LYS* 3.0 23.0 + - - +
274B ALA* 3.6 18.9 - - - +
275B GLY* 4.1 16.4 + - - +
276B GLU* 2.8 32.3 + - - +
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Residues in contact with VAL 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B LEU* 4.2 22.4 - - + -
111B LEU 2.9 18.0 + - - +
112B ARG 3.5 7.0 - - - +
114B LYS* 1.3 75.7 - - - +
116B VAL* 1.3 57.6 + - - +
118B LYS* 3.1 5.7 + - - +
119B MET* 2.9 40.2 + - + +
206B PHE* 3.9 26.5 - - + -
271B VAL* 3.6 40.5 - - + +
272B LEU* 4.2 8.7 - - + +
274B ALA* 4.5 0.7 - - - -
275B GLY 4.2 4.5 - - - +
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Residues in contact with VAL 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B ARG* 2.9 24.1 + - + +
113B LEU* 3.7 6.3 - - - +
115B VAL* 1.3 75.0 - - - +
117B ARG* 1.3 58.1 + - - +
119B MET* 3.1 11.2 + - - +
120B PHE* 2.9 27.4 + - + +
134B VAL* 4.2 20.9 - - + -
137B LEU* 3.8 26.2 - - + -
206B PHE* 3.9 28.0 - - + +
207B VAL* 3.9 25.4 - - + -
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Residues in contact with ARG 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B LEU* 2.9 39.6 + - + +
114B LYS* 3.5 10.1 - - - +
115B VAL 3.3 0.2 - - - -
116B VAL* 1.3 75.8 - - - +
118B LYS* 1.3 58.4 + - - +
120B PHE* 3.2 10.3 + - - +
121B GLU* 2.9 27.5 + - - +
127B PRO* 4.9 5.9 - - - +
128B ALA* 2.9 37.5 + - + +
129B PRO 3.1 23.6 + - - -
130B ALA* 4.8 3.6 - - - +
131B ARG 4.5 8.2 - - - +
132B ARG* 4.6 9.1 + - - +
137B LEU* 4.3 14.5 - - + +
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Residues in contact with LYS 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B LYS 3.0 7.0 + - - +
115B VAL 3.4 7.0 - - - +
117B ARG* 1.3 75.6 - - - +
119B MET* 1.3 65.6 + - - +
121B GLU* 2.9 32.5 + - - +
122B LEU* 2.9 44.0 + - + +
270B ASP* 3.5 33.2 + - - -
271B VAL* 4.1 11.4 - - - +
274B ALA* 3.4 34.5 - - + -
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Residues in contact with MET 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B VAL* 2.9 20.7 + - + +
116B VAL* 3.1 10.3 + - - +
118B LYS* 1.3 75.9 - - - +
120B PHE* 1.3 57.8 + - - +
122B LEU* 3.4 4.3 + - - +
123B ARG* 2.9 32.0 + - - +
206B PHE* 3.7 30.3 - - + -
207B VAL* 4.0 21.3 - - + -
215B PHE* 4.3 6.3 - - + -
218B ASP* 3.8 32.1 - - + +
219B ILE* 4.9 1.8 - - + -
222B ILE* 3.8 30.0 - - + +
271B VAL* 3.7 25.6 - - + -
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Residues in contact with PHE 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B VAL* 2.9 13.0 + - + +
117B ARG* 3.4 11.7 - - - +
119B MET* 1.3 77.2 - - - +
121B GLU* 1.3 62.5 + - - +
123B ARG* 4.5 1.8 - - - +
124B PHE* 3.0 60.7 + + + +
126B GLU* 3.6 12.8 - - + -
127B PRO 4.2 2.2 - - - -
128B ALA* 3.5 42.0 - - + -
129B PRO* 4.7 3.4 - - + -
137B LEU* 4.5 21.5 - - + -
140B ILE* 3.8 34.5 - - + -
141B GLU* 4.9 1.6 - - + -
144B ARG* 4.1 16.8 - - - -
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Residues in contact with GLU 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B ARG 2.9 13.7 + - - +
118B LYS* 2.9 40.7 + - - +
120B PHE* 1.3 77.9 - - - +
122B LEU* 1.3 59.3 + - - +
125B GLY* 3.0 29.0 + - - -
126B GLU* 3.4 27.4 - - - +
127B PRO* 4.5 17.4 - - + +
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Residues in contact with LEU 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B LYS* 2.9 44.7 + - + +
119B MET* 3.8 3.4 - - - +
121B GLU* 1.3 80.2 - - - +
123B ARG* 1.3 62.3 + - - +
125B GLY* 4.5 2.3 + - - -
222B ILE* 4.1 16.1 - - + +
226B ASP* 5.0 4.5 - - - +
267B LEU* 4.3 19.7 - - + +
270B ASP* 4.2 16.4 - - - +
271B VAL* 3.7 30.1 - - + -
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Residues in contact with ARG 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B MET 2.9 18.7 + - - +
120B PHE* 3.7 4.5 - - - +
122B LEU* 1.3 79.7 - - - +
124B PHE* 1.3 87.7 + - + +
141B GLU* 2.6 36.4 + - - -
145B VAL* 3.2 29.4 - - - +
221B ASP* 3.1 41.7 + - - +
222B ILE* 3.7 27.1 - - + +
224B LYS* 5.3 0.2 - - - +
225B PHE* 3.4 23.6 - - + -
226B ASP* 4.7 10.7 - - - +
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Residues in contact with PHE 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B PHE* 3.0 57.2 + + + +
123B ARG* 1.3 113.5 - - + +
125B GLY* 1.3 61.3 + - - +
126B GLU* 4.7 5.6 - - + +
141B GLU* 4.1 21.3 - - + -
144B ARG* 3.6 58.4 + - + +
145B VAL* 5.1 1.6 - - + -
148B THR* 5.6 3.4 - - - -
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Residues in contact with GLY 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B GLU* 3.0 14.0 + - - -
122B LEU 4.5 1.9 + - - -
123B ARG 3.7 1.2 - - - -
124B PHE* 1.3 79.1 - - - +
126B GLU* 1.3 64.6 + - - +
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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