Contacts of the helix formed by residues 117 - 127 (chain A) in PDB entry 3DDN
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 GLN 117 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113A ALA 3.0 10.8 + - - -
114A ALA* 3.5 12.4 + - - +
115A SER 4.5 2.5 - - - +
116A ARG* 1.3 81.9 - - - +
118A ILE* 1.3 64.8 + - - +
119A PRO* 3.3 5.7 - - - -
120A ALA* 3.4 9.9 + - + +
121A ALA* 3.0 20.3 + - - +
134A SER 5.4 0.6 + - - -
135A PHE* 3.5 30.2 - - + +
136A SER 2.9 43.3 + - - +
137A GLY* 4.0 0.7 + - - -
274A GLN* 6.2 5.0 - - - +
276A VAL* 5.4 1.8 - - - -
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Residues in contact with ILE 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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112A LEU 4.3 2.9 - - - +
113A ALA* 3.1 22.1 + - + +
116A ARG* 3.0 35.9 - - + +
117A GLN* 1.3 76.1 - - - +
119A PRO* 1.3 63.5 - - + +
121A ALA* 3.2 1.0 + - - +
122A ASP* 2.8 28.1 + - - +
106B HIS* 3.8 17.7 - - + +
109B ALA* 4.6 12.1 - - + +
110B LEU* 4.9 4.3 - - + -
113B ALA* 3.8 15.3 - - + -
119B PRO* 3.7 10.8 - - + -
276B VAL* 3.6 30.3 - - + -
278B THR* 4.3 12.5 - - + +
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Residues in contact with PRO 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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113A ALA* 3.7 11.4 - - + +
117A GLN 3.6 3.8 - - - -
118A ILE* 1.3 94.1 - - + +
120A ALA* 1.3 56.8 + - - +
122A ASP* 3.2 2.3 + - - +
123A ALA* 2.8 30.1 + - - +
276A VAL* 3.8 32.3 - - + -
118B ILE* 4.1 12.8 - - + -
119B PRO* 4.2 18.8 - - + +
122B ASP* 3.9 27.4 - - + +
126B ARG* 5.7 1.1 - - - +
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Residues in contact with ALA 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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117A GLN* 3.4 13.5 + - + +
119A PRO* 1.3 78.5 - - - +
121A ALA* 1.3 58.1 + - - +
123A ALA* 3.1 9.1 + - - +
124A SER* 2.9 28.9 + - - -
135A PHE* 3.9 15.8 - - + -
273A ALA* 5.0 21.8 - - + +
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Residues in contact with ALA 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 GLN 3.0 17.5 + - - +
118A ILE 3.6 3.1 - - - +
120A ALA* 1.3 75.7 - - - +
122A ASP* 1.3 63.0 + - - +
124A SER* 2.7 20.0 + - - -
125A LEU* 3.3 9.7 + - - +
135A PHE* 3.5 15.4 - - + -
277B VAL 3.8 4.1 - - - +
278B THR* 3.7 13.9 - - + -
279B PRO* 3.7 22.8 - - + +
281B LEU* 3.8 13.7 - - + -
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Residues in contact with ASP 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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118A ILE 2.8 17.7 + - - +
119A PRO 3.5 4.4 - - - +
121A ALA* 1.3 76.7 - - - +
123A ALA* 1.3 57.9 + - - +
125A LEU* 3.4 3.5 + - - +
126A ARG* 2.5 72.4 + - - +
119B PRO* 3.8 20.9 - - + +
276B VAL* 3.2 10.3 - - + +
277B VAL* 2.9 35.0 + - - +
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Residues in contact with ALA 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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119A PRO 2.8 14.0 + - - +
120A ALA* 3.1 13.2 + - - +
122A ASP* 1.3 75.6 + - - +
124A SER* 1.3 60.1 + - - +
126A ARG* 3.0 9.7 + - - +
127A GLU* 2.9 39.2 + - + +
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Residues in contact with SER 124 (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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120A ALA 2.9 12.6 + - - -
121A ALA* 2.7 25.0 + - - -
123A ALA* 1.3 76.0 - - - +
125A LEU* 1.3 64.8 + - - +
127A GLU* 3.2 15.8 + - - +
128A HIS 3.4 0.2 + - - -
129A THR 3.1 24.5 + - - +
131A LYS* 3.5 32.2 + - - +
135A PHE* 3.9 16.4 - - - -
279B PRO* 4.5 3.8 - - - +
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Residues in contact with LEU 125 (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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121A ALA 3.3 5.7 + - - +
122A ASP 3.8 1.3 - - - +
123A ALA 3.3 0.4 - - - -
124A SER* 1.3 82.9 + - - +
126A ARG* 1.3 57.4 + - - +
127A GLU 3.3 0.2 - - - -
128A HIS* 3.2 11.3 + - - -
129A THR 3.4 17.0 - - - +
130A TRP* 3.7 14.6 - - + -
259B PHE* 4.0 8.3 - - + -
264B CYS 3.6 23.1 - - - +
265B THR* 5.2 0.2 - - - -
270B PHE* 3.0 36.7 - - + +
277B VAL* 3.5 36.8 - - + +
278B THR* 3.4 36.3 - - - +
279B PRO* 3.5 10.3 - - + -
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Residues in contact with ARG 126 (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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122A ASP* 2.5 57.2 + - - +
123A ALA* 3.0 13.2 + - - +
125A LEU* 1.3 74.4 - - - +
127A GLU* 1.3 57.1 + - + +
128A HIS* 3.1 25.1 + - - -
119B PRO* 5.3 1.4 - - - +
269B LEU 4.1 1.4 + - - -
270B PHE* 3.0 36.4 + - - +
271B GLU* 5.6 0.3 - - - +
272B LEU 3.0 29.3 + - - -
273B ALA* 4.0 8.5 + - - +
275B VAL 2.7 17.6 + - - -
276B VAL* 4.1 0.4 - - - +
277B VAL* 4.2 10.4 - - - +
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Residues in contact with GLU 127 (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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123A ALA* 2.9 21.5 + - - +
124A SER* 3.2 15.8 + - - +
126A ARG* 1.3 76.7 - - + +
128A HIS* 1.3 74.2 + - - +
129A THR* 3.0 12.4 + - - +
131A LYS* 4.8 3.5 + - - -
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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