Contacts of the helix formed by residues 111 - 122 (chain B) in PDB entry 4DJH
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 THR 111 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B LEU 3.7 11.9 - - - +
108B VAL* 2.6 20.8 + - - +
109B THR 3.0 1.2 - - - -
110B THR* 1.3 82.8 - - - +
112B MET* 1.3 63.8 + - - +
113B PRO* 3.3 1.8 - - - -
114B PHE* 3.0 12.9 + - + +
115B GLN* 2.9 21.3 + - - +
134B VAL* 4.1 22.4 - - + -
137B ILE* 3.7 25.4 - - + -
320B TYR* 2.7 21.3 + - - -
1300B JDC 3.4 18.3 - - - +
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Residues in contact with MET 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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66B TYR* 3.2 54.8 + - + +
69B VAL* 3.9 20.0 - - + -
70B PHE* 3.7 26.7 - - + +
109B THR* 3.0 19.6 + - - +
111B THR* 1.3 78.0 + - - +
113B PRO* 1.3 69.5 - - + +
115B GLN* 3.1 5.2 + - - +
116B SER 3.0 19.9 + - - -
320B TYR* 3.2 48.5 - - + +
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Residues in contact with PRO 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A VAL* 3.9 35.5 - - + +
63A THR* 4.1 10.6 + - + -
64A ALA* 4.8 3.8 - - + +
66B TYR* 3.1 13.9 - - - +
70B PHE* 3.8 17.5 - - + -
109B THR 3.6 5.4 - - - +
110B THR* 3.3 20.6 - - - +
112B MET* 1.3 96.9 - - + +
114B PHE* 1.3 62.7 + - + +
116B SER* 3.1 11.8 + - - +
117B THR* 3.0 21.5 + - - -
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Residues in contact with PHE 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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60A VAL* 3.9 28.7 - - + -
110B THR* 3.2 31.2 - - - -
111B THR* 3.0 15.5 + - + +
113B PRO* 1.3 78.3 - - + +
115B GLN* 1.3 58.3 + - - +
117B THR* 3.2 2.3 + - - -
118B VAL* 3.0 34.7 + - - +
124B TRP* 4.7 9.9 - + + -
126B PHE* 3.8 40.6 - + + -
130B LEU* 4.2 25.8 - - + -
134B VAL* 4.7 16.8 - - + -
1300B JDC 5.4 1.3 - - + -
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Residues in contact with GLN 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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66B TYR* 6.1 1.6 - - + -
111B THR 2.9 10.8 + - - +
112B MET* 3.5 7.6 - - - +
114B PHE* 1.3 75.3 - - - +
116B SER* 1.3 67.3 + - - +
118B VAL* 3.5 6.5 + - - +
119B TYR* 2.9 24.8 + - + +
312B TYR* 4.4 4.6 + - - -
313B TYR* 3.7 17.7 + - + -
316B ILE* 2.6 37.6 - - + +
320B TYR* 4.0 13.0 - - + +
1300B JDC 3.6 44.6 + - + +
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Residues in contact with SER 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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63A THR* 3.8 12.2 + - - +
66B TYR* 3.3 31.4 + - - -
112B MET 3.0 10.9 + - - -
113B PRO* 3.1 14.4 + - - +
115B GLN* 1.3 79.6 - - - +
117B THR* 1.3 60.5 + - - +
119B TYR* 3.4 7.4 - - - +
120B LEU* 3.1 36.2 + - - +
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Residues in contact with THR 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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59A PRO* 3.8 26.2 - - + +
60A VAL 4.5 2.1 + - - -
63A THR* 4.4 5.2 + - - -
113B PRO 3.0 15.1 + - - -
114B PHE 3.2 8.7 + - - -
115B GLN 3.1 0.6 - - - -
116B SER* 1.3 76.9 + - - +
118B VAL* 1.3 61.3 + - - +
120B LEU* 3.1 8.6 + - - +
121B MET* 2.9 52.2 + - + +
125B PRO* 4.1 5.8 - - + -
126B PHE* 3.5 25.9 - - + -
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Residues in contact with VAL 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 PHE 3.0 21.0 + - - +
115B GLN* 4.0 8.5 - - - +
117B THR* 1.3 75.1 - - - +
119B TYR* 1.3 53.6 + - - +
122B ASN* 2.7 34.2 + - - +
123B SER* 3.4 29.6 - - - +
124B TRP* 3.3 34.8 - - + +
125B PRO* 4.2 0.4 - - + -
126B PHE* 3.7 11.4 - - + -
209B GLU* 5.9 2.0 - - - +
1300B JDC 4.0 19.1 - - + +
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Residues in contact with TYR 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 GLN* 2.9 20.5 + - + +
116B SER* 3.4 9.2 - - - +
118B VAL* 1.3 77.8 - - - +
120B LEU* 1.3 84.6 + - + +
122B ASN* 3.4 13.7 + - - +
313B TYR* 3.4 59.0 - + + +
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Residues in contact with LEU 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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120A LEU* 3.5 45.8 - - + -
116B SER* 3.1 23.8 + - - +
117B THR* 3.7 6.1 - - - +
119B TYR* 1.3 103.2 - - + +
121B MET* 1.3 64.3 + - + +
122B ASN* 3.1 2.8 + - - +
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Residues in contact with MET 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A PRO* 5.6 6.7 - - - -
117B THR* 2.9 28.3 + - + +
120B LEU* 1.3 76.0 - - + +
122B ASN* 1.3 65.5 + - - +
123B SER* 3.0 27.3 + - - +
125B PRO* 3.4 41.7 - - + -
207B VAL* 5.6 1.0 - - - +
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Residues in contact with ASN 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 VAL* 2.7 22.3 + - - +
119B TYR* 3.7 9.5 + - - +
120B LEU 3.1 4.8 - - - +
121B MET* 1.3 79.1 - - - +
123B SER* 1.3 57.2 + - - +
207B VAL* 3.8 23.3 - - + +
209B GLU* 4.3 10.2 - - - +
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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