Contacts of the helix formed by residues 111 - 123 (chain A) in PDB entry 1DG3
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 111 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A ASN* 2.7 34.9 + - - +
19A GLY* 3.3 35.8 + - - +
20A ARG 3.5 2.4 - - - +
21A LEU* 3.6 27.9 - - + +
108A ASP 4.9 0.4 + - - -
109A ASN 3.2 1.2 - - - -
110A GLN* 1.3 84.6 - - - +
112A ASP* 1.3 66.6 + - - +
113A SER 3.3 2.9 - - - -
114A TRP* 3.0 31.6 + - + +
115A ILE* 3.0 14.3 + - - +
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Residues in contact with ASP 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A ASN* 4.2 10.6 + - - -
76A LYS* 5.9 0.2 - - - -
100A GLY 4.3 6.8 - - - +
101A LEU* 3.3 25.8 - - + +
102A GLY* 3.0 33.8 + - - -
104A VAL* 5.0 1.6 - - - +
105A GLU* 4.0 4.2 - - - +
108A ASP 4.8 0.2 - - - +
109A ASN* 3.5 36.6 + - - +
110A GLN 3.6 0.6 - - - -
111A ASN* 1.3 77.4 - - - +
113A SER* 1.3 62.2 + - - +
115A ILE* 3.3 3.5 + - - +
116A PHE* 3.2 19.6 + - - +
143A TYR* 4.6 5.9 + - - +
144A TYR* 3.9 14.1 + - + -
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Residues in contact with SER 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A GLN 5.3 1.0 + - - -
111A ASN 3.3 0.8 - - - -
112A ASP* 1.3 75.6 - - - +
114A TRP* 1.3 64.1 + - - +
116A PHE* 3.5 2.8 + - - +
117A ALA* 3.1 23.2 + - - +
143A TYR* 4.0 5.5 + - - -
144A TYR* 3.9 19.8 - - - +
147A GLU* 2.6 26.6 + - - -
148A LEU* 5.8 0.3 - - - +
151A ARG* 3.2 36.4 + - - -
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Residues in contact with TRP 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A LEU* 3.9 16.6 - - + -
110A GLN 4.8 3.8 - - - -
111A ASN* 3.0 32.8 + - - +
113A SER* 1.3 76.8 - - - +
115A ILE* 1.3 60.6 + - - +
117A ALA* 3.3 5.3 + - + +
118A LEU* 2.8 35.0 + - + +
151A ARG* 3.1 64.0 - - + +
304A ILE* 3.5 41.2 - - + +
308A ASP 4.3 6.1 - - - -
309A LEU* 4.0 24.2 - - + -
310A PRO* 3.6 15.0 - - + -
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Residues in contact with ILE 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A ILE* 4.8 4.3 - - + -
16A ASN* 4.2 15.3 - - + +
21A LEU* 4.0 22.7 - - + -
77A GLY* 3.9 27.6 - - - +
78A ILE* 3.7 27.0 - - + +
98A THR* 3.9 23.1 - - + -
99A GLU 5.7 0.9 - - - +
101A LEU* 4.2 10.3 - - + -
111A ASN 3.0 18.2 + - - +
112A ASP* 3.6 9.0 - - - +
113A SER 3.3 0.2 - - - -
114A TRP* 1.3 77.4 - - - +
116A PHE* 1.3 63.3 + - - +
118A LEU* 3.4 7.4 + - + -
119A ALA* 3.0 22.9 + - - +
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Residues in contact with PHE 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A VAL* 4.1 18.2 - - + -
101A LEU* 4.5 6.9 - - + +
112A ASP 3.2 9.9 + - - +
113A SER 3.7 7.6 - - - +
114A TRP 3.3 0.2 - - - -
115A ILE* 1.3 80.6 - - - +
117A ALA* 1.3 63.5 + - - +
119A ALA* 3.2 8.4 + - - +
120A VAL* 3.1 29.1 + - + +
126A PHE* 3.6 35.1 - + - -
128A TYR* 4.4 2.7 - + - -
142A LEU* 3.9 29.2 - - + -
144A TYR* 3.4 43.1 - + + -
145A VAL* 4.0 20.6 - - + -
148A LEU* 4.1 16.8 - - + -
178A PHE* 5.9 1.3 - + - -
230A PHE* 5.5 2.2 - + - -
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Residues in contact with ALA 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A SER 3.1 15.1 + - - +
114A TRP* 3.3 9.4 + - + +
116A PHE* 1.3 80.8 - - - +
118A LEU* 1.3 61.7 + - + +
120A VAL* 3.2 4.9 + - - +
121A LEU* 3.0 27.4 + - + +
148A LEU* 4.0 25.6 - - + -
151A ARG* 4.3 16.2 - - + +
152A ILE* 3.9 14.8 - - + +
310A PRO* 6.3 1.1 - - + -
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Residues in contact with LEU 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A ILE* 4.0 26.5 - - + -
21A LEU* 4.3 12.6 - - + -
78A ILE* 4.0 9.6 - - + -
114A TRP 2.8 25.0 + - - +
115A ILE* 3.8 14.1 - - + +
116A PHE 3.3 0.2 - - - -
117A ALA* 1.3 76.7 - - + +
119A ALA* 1.3 62.9 + - - +
121A LEU* 3.2 8.6 + - + +
122A LEU* 3.0 36.6 + - + +
297A VAL* 6.3 0.2 - - - -
300A TYR* 3.7 37.0 - - + -
301A VAL* 4.8 3.4 - - + +
304A ILE* 4.0 26.2 - - + -
310A PRO* 5.0 1.3 - - + -
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Residues in contact with ALA 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A ALA* 4.0 15.0 - - + +
44A VAL* 4.2 9.2 - - + -
78A ILE* 4.0 11.4 - - + +
96A LEU* 5.3 4.5 - - + -
98A THR* 4.6 5.8 - - + -
115A ILE 3.0 14.8 + - - +
116A PHE* 3.2 10.7 + - - +
118A LEU* 1.3 76.1 - - - +
120A VAL* 1.3 59.0 + - - +
122A LEU* 3.8 3.2 + - - +
123A SER* 2.8 30.7 + - - -
126A PHE* 3.6 18.0 - - + -
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Residues in contact with VAL 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A PHE* 3.1 28.5 + - + +
117A ALA* 3.4 8.7 - - - +
118A LEU 3.2 0.2 - - - -
119A ALA* 1.3 79.8 - - - +
121A LEU* 1.3 62.7 + - - +
122A LEU 3.4 0.3 + - - -
123A SER* 3.6 5.8 + - - +
126A PHE* 3.5 25.8 - - + -
148A LEU* 4.3 6.7 - - + -
152A ILE* 4.3 4.5 - - + -
174A PHE 5.5 0.2 - - - +
175A PHE* 3.7 47.6 - - + -
176A PRO* 3.4 21.7 - - + +
230A PHE* 4.5 11.0 - - + -
280A LYS* 4.3 1.2 + - - -
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Residues in contact with LEU 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A ALA* 3.0 17.4 + - + +
118A LEU* 3.2 11.6 + - + +
120A VAL* 1.3 77.5 - - - +
122A LEU* 1.3 59.2 + - - +
152A ILE* 4.0 35.2 - - + -
174A PHE* 4.1 21.8 - - + -
175A PHE* 5.5 0.7 - - + -
280A LYS* 2.8 21.0 + - - +
282A LEU* 5.9 0.9 - - - +
296A LEU* 5.0 1.9 - - - +
300A TYR* 3.8 45.9 + - + +
310A PRO* 3.6 33.2 - - + +
312A MET* 4.8 6.3 - - + +
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Residues in contact with LEU 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A LEU* 5.1 5.2 - - + -
14A ILE* 4.4 17.7 - - + -
40A VAL* 3.4 20.2 - - - +
78A ILE* 4.9 5.4 - - + -
96A LEU* 3.9 23.1 - - + -
118A LEU* 3.0 28.0 + - + +
119A ALA 4.6 0.2 - - - +
121A LEU* 1.3 77.0 - - - +
123A SER* 1.3 58.2 + - - +
280A LYS* 3.6 13.0 - - - +
293A LEU* 4.0 19.6 - - + +
296A LEU* 4.0 28.7 - - + -
297A VAL* 4.1 22.7 - - + +
300A TYR* 4.0 17.3 - - + -
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Residues in contact with SER 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A VAL* 3.6 11.7 - - - -
42A ALA* 4.0 13.7 - - - +
96A LEU* 4.9 0.7 - - - -
119A ALA 2.8 21.7 + - - -
120A VAL 3.6 1.8 + - - +
121A LEU 3.5 1.0 - - - -
122A LEU* 1.3 79.7 - - - +
124A SER* 1.3 60.5 + - - +
125A THR 3.6 17.9 + - - -
126A PHE* 4.1 1.2 - - - -
174A PHE 5.0 0.5 - - - +
176A PRO* 3.4 30.7 - - - +
280A LYS* 2.8 25.7 + - - +
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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