Contacts of the helix formed by residues 117 - 128 (chain A) in PDB entry 3SDG
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 HIS 117 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A GLU* 2.6 42.7 + - - +
79A VAL* 3.8 32.8 - - + +
82A GLN* 3.8 27.2 + - - -
113A THR 3.3 21.1 + - - +
114A PHE 3.0 6.8 + - - +
116A SER* 1.3 96.1 + - - +
118A LYS* 1.4 61.4 + - - +
119A ALA 3.3 2.9 + - - -
120A VAL* 3.4 3.5 + - + -
121A THR* 2.8 24.4 + - - -
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Residues in contact with LYS 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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38A GLU* 5.6 1.3 + - - +
114A PHE 3.7 9.0 - - - +
115A GLY* 3.3 22.9 + - - +
116A SER 3.8 1.0 - - - -
117A HIS* 1.4 75.4 - - - +
119A ALA* 1.3 58.5 + - - +
121A THR* 3.5 5.3 - - - -
122A ARG* 2.9 32.8 + - - +
187A PHE* 4.0 38.2 + - + +
196A GLU* 2.8 40.1 + - - -
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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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34A GLU* 4.2 1.1 - - + +
37A LEU* 3.6 17.1 - - + +
38A GLU* 3.6 56.7 + - - +
117A HIS 3.3 0.4 - - - -
118A LYS* 1.3 79.2 - - - +
120A VAL* 1.3 58.1 + - + +
122A ARG* 3.9 8.8 - - - +
123A ALA* 3.0 32.5 + - - +
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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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34A GLU* 3.5 38.8 + - + +
37A LEU* 4.8 4.7 - - + -
72A LEU* 4.2 3.4 - - + +
75A LEU* 4.0 25.8 - - + -
76A LEU* 3.9 30.4 - - + +
79A VAL* 3.9 23.1 - - + -
117A HIS* 3.4 10.8 + - + +
118A LYS 3.3 0.4 - - - -
119A ALA* 1.3 74.5 - - - +
121A THR* 1.3 56.4 + - - +
123A ALA* 4.0 3.8 - - - +
124A GLY* 2.7 34.3 + - - -
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Residues in contact with THR 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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76A LEU* 4.9 7.8 - - - +
79A VAL* 5.0 0.5 - - - +
114A PHE* 3.3 28.1 + - + -
117A HIS* 2.8 23.0 + - - +
118A LYS* 3.5 8.1 - - - +
120A VAL* 1.3 77.4 - - - +
122A ARG* 1.3 61.5 + - + +
124A GLY* 3.4 0.5 + - - -
125A GLN* 2.9 36.9 + - + +
184A PHE* 3.3 47.1 - - + -
187A PHE* 4.6 9.2 - - + -
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Residues in contact with ARG 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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37A LEU 5.8 2.9 - - - -
118A LYS 2.9 17.7 + - - +
119A ALA* 3.9 7.4 - - - +
121A THR* 1.3 79.7 - - - +
123A ALA* 1.3 65.9 + - - +
125A GLN* 3.2 6.7 + - - +
126A ALA* 3.1 23.1 + - + +
184A PHE* 6.5 0.4 - - - -
187A PHE 4.5 3.0 + - - -
188A ALA* 3.4 49.1 + - + +
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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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37A LEU* 4.1 21.8 - - + -
41A PRO* 6.4 0.2 - - + -
42A LEU* 5.2 5.4 - - + +
72A LEU* 3.6 25.1 - - + +
119A ALA 3.0 21.7 + - - +
122A ARG* 1.3 76.3 - - - +
124A GLY* 1.3 57.8 + - - +
126A ALA* 3.4 7.5 + - - +
127A ALA* 3.0 28.8 + - - +
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Residues in contact with GLY 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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72A LEU* 4.0 13.0 - - - +
76A LEU* 4.1 21.3 - - - -
120A VAL 2.7 23.3 + - - -
121A THR 3.8 0.9 - - - -
123A ALA* 1.3 75.6 - - - +
125A GLN* 1.3 63.4 + - - +
127A ALA* 3.2 5.6 + - - -
128A ARG* 3.3 2.8 + - - +
134A VAL* 3.2 25.4 - - - +
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Residues in contact with GLN 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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76A LEU* 5.4 4.0 - - - +
114A PHE* 5.9 0.2 - - - -
121A THR* 2.9 23.3 + - + +
122A ARG* 3.7 6.7 - - - +
124A GLY* 1.3 72.9 - - - +
126A ALA* 1.3 66.9 + - - +
128A ARG* 2.9 53.7 + - - +
129A ALA* 4.3 1.0 + - - +
138A TRP* 3.6 30.3 - - - -
180A GLU* 4.2 0.7 - - - +
184A PHE* 3.3 49.8 - - + -
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Residues in contact with ALA 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 ARG* 3.1 17.0 + - + +
123A ALA* 3.8 7.2 - - - +
124A GLY 3.3 0.2 - - - -
125A GLN* 1.3 76.5 - - - +
127A ALA* 1.3 61.2 + - - +
129A ALA* 3.3 21.0 + - - +
130A THR* 4.3 4.7 + - - +
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Residues in contact with ALA 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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42A LEU* 6.0 0.4 - - + -
72A LEU* 3.7 20.4 - - + -
123A ALA 3.0 17.5 + - - +
124A GLY 3.2 4.9 + - - +
125A GLN 3.1 0.8 - - - -
126A ALA* 1.3 74.5 - - - +
128A ARG* 1.3 60.0 + - - +
129A ALA 3.0 2.4 + - - -
130A THR* 3.2 10.2 + - - +
131A SER* 2.9 35.2 + - - -
134A VAL* 3.9 17.0 - - + -
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Residues in contact with ARG 128 (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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76A LEU* 5.9 0.2 - - + -
124A GLY 3.3 9.9 + - - +
125A GLN* 2.9 45.5 + - - +
127A ALA* 1.3 77.2 - - - +
129A ALA* 1.3 61.1 + - - +
130A THR 3.6 0.2 + - - -
131A SER 3.9 3.1 + - - +
134A VAL* 3.7 16.8 - - + +
135A ALA* 3.7 29.1 + - + +
138A TRP* 3.3 40.6 - - + +
139A SER* 5.9 2.0 - - - +
177A LEU* 6.3 0.4 - - - +
180A GLU* 2.9 26.1 + - - -
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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