Contacts of the helix formed by residues 117 - 127 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113B ALA 2.9 10.6 + - - -
114B ALA* 3.8 8.7 + - - +
115B SER 3.5 5.3 - - - +
116B ARG* 1.3 81.6 + - - +
118B ILE* 1.3 65.7 + - - +
119B PRO* 3.4 4.9 - - - -
120B ALA* 3.3 9.1 + - + +
121B ALA* 2.9 20.6 + - - +
134B SER 5.0 2.1 - - - +
135B PHE* 3.7 28.6 - - + +
136B SER 2.9 49.3 + - - +
137B GLY* 4.0 1.2 - - - +
273B ALA 6.1 1.1 - - - +
276B VAL* 5.4 2.2 - - - -
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Residues in contact with ILE 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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106A HIS* 3.6 31.0 - - + -
109A ALA* 4.3 11.2 - - + +
110A LEU* 4.1 6.7 - - + -
113A ALA* 4.0 16.4 - - + -
119A PRO* 4.1 7.9 - - + -
276A VAL* 3.7 29.6 - - + -
278A THR* 3.9 9.4 - - + -
112B LEU 4.4 0.7 - - - +
113B ALA* 3.0 26.2 + - + +
116B ARG* 3.0 17.8 + - + +
117B GLN* 1.3 76.0 - - - +
119B PRO* 1.4 62.4 - - + +
121B ALA* 3.1 5.2 + - - +
122B ASP* 2.7 33.3 + - - +
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Residues in contact with PRO 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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118A ILE* 3.7 14.4 - - + -
119A PRO* 4.2 18.2 - - + +
122A ASP* 3.8 26.7 - - + +
126A ARG* 5.3 0.7 - - - +
113B ALA* 3.8 3.8 - - + +
117B GLN 3.5 3.4 - - - -
118B ILE* 1.4 93.8 - - + +
120B ALA* 1.3 56.8 + - - +
122B ASP* 3.5 2.4 + - - +
123B ALA* 3.0 28.8 + - - +
276B VAL* 3.5 42.6 - - + -
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Residues in contact with ALA 120 (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 GLN* 3.3 13.4 + - + +
119B PRO* 1.3 75.7 - - - +
121B ALA* 1.3 66.7 + - - +
123B ALA* 3.1 7.2 + - - +
124B SER* 3.1 24.3 + - - -
135B PHE* 3.9 15.3 - - + -
273B ALA* 5.0 21.3 - - + +
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Residues in contact with ALA 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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277A VAL 4.0 2.0 - - - -
278A THR* 3.8 11.0 - - + -
279A PRO* 3.9 4.2 - - + +
281A LEU* 3.5 31.6 - - + -
117B GLN 2.9 18.6 + - - +
118B ILE 3.4 4.3 - - - +
120B ALA* 1.3 76.5 - - - +
122B ASP* 1.3 61.3 + - - +
124B SER* 2.8 17.8 + - - -
125B LEU* 3.5 13.2 + - - +
135B PHE* 3.4 17.6 - - + -
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Residues in contact with ASP 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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119A PRO* 3.9 25.6 - - + +
276A VAL* 3.6 7.9 - - + +
277A VAL* 3.1 34.5 + - - +
118B ILE 2.7 18.6 + - - +
119B PRO 3.8 4.2 - - - +
121B ALA* 1.3 72.9 - - - +
123B ALA* 1.3 64.3 + - - +
125B LEU* 3.3 5.9 + - - +
126B ARG* 2.6 66.7 + - - +
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Residues in contact with ALA 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 PRO 3.0 17.9 + - - +
120B ALA* 3.1 8.0 + - - +
122B ASP* 1.3 78.5 + - - +
124B SER* 1.3 60.2 + - - +
126B ARG* 2.8 25.2 + - - +
127B GLU* 3.0 25.4 + - - +
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Residues in contact with SER 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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279A PRO* 4.8 3.3 - - - +
120B ALA 3.1 11.9 + - - -
121B ALA 2.8 21.1 + - - -
123B ALA* 1.3 77.5 - - - +
125B LEU* 1.3 58.7 + - - +
127B GLU* 3.4 16.1 + - - +
128B HIS 3.4 0.2 + - - -
129B THR* 2.6 42.9 + - - -
131B LYS* 3.9 20.9 + - - +
135B PHE* 3.8 15.2 - - - -
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Residues in contact with LEU 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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259A PHE* 4.7 2.2 - - + -
264A CYS 3.7 21.3 - - - +
265A THR* 5.4 0.4 - - - -
270A PHE* 3.6 31.9 - - + -
277A VAL* 3.8 15.5 - - + -
278A THR* 3.5 19.3 - - - +
279A PRO* 3.4 40.2 - - + -
121B ALA 3.5 7.3 + - - +
122B ASP 3.3 6.8 + - - +
123B ALA 3.2 0.6 - - - -
124B SER* 1.3 82.0 + - - +
126B ARG* 1.3 56.0 + - - +
128B HIS* 2.7 24.9 + - - -
129B THR 3.3 18.2 - - - +
130B TRP* 3.8 16.6 - - + -
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Residues in contact with ARG 126 (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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119A PRO* 5.7 1.2 - - - +
269A LEU 3.8 2.6 + - - -
270A PHE* 2.9 39.8 + - + +
271A GLU* 4.4 1.1 - - - +
272A LEU 2.8 25.9 + - - -
273A ALA* 3.9 10.8 + - - +
275A VAL 2.4 31.9 + - - -
276A VAL* 4.2 0.4 - - - +
277A VAL* 4.4 7.2 - - + +
122B ASP* 2.6 43.3 + - - +
123B ALA* 2.8 11.9 + - - +
125B LEU* 1.3 76.3 - - + +
127B GLU* 1.3 59.2 + - - +
128B HIS* 3.2 20.9 + - - -
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Residues in contact with GLU 127 (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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123B ALA* 3.0 24.9 + - - +
124B SER* 3.5 15.9 + - - +
126B ARG* 1.3 77.0 - - - +
128B HIS* 1.3 74.4 + - - +
129B THR* 3.1 20.6 + - + +
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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