Contacts of the helix formed by residues 111 - 122 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107A LEU 3.6 13.2 - - - +
108A VAL* 2.6 22.3 + - - +
110A THR* 1.3 80.0 - - - +
112A MET* 1.3 59.8 + - - +
113A PRO* 3.4 1.1 - - - -
114A PHE* 3.0 13.7 + - + +
115A GLN* 2.8 24.6 + - - +
134A VAL* 4.5 14.6 - - + -
137A ILE* 3.8 28.5 - - + -
320A TYR* 2.7 23.5 + - - -
1300A JDC 3.5 22.9 - - - +
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Residues in contact with MET 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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66A TYR* 3.1 31.3 + - + +
69A VAL* 3.6 22.0 - - + +
70A PHE* 3.7 27.1 - - + -
109A THR* 3.0 30.8 + - + +
111A THR* 1.3 79.1 + - - +
113A PRO* 1.3 64.5 - - + +
115A GLN* 2.8 20.9 + - - +
116A SER* 2.9 13.5 + - - -
320A TYR* 3.4 59.7 - - + +
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Residues in contact with PRO 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A TYR* 3.0 13.6 - - - +
70A PHE* 3.8 17.9 - - + -
109A THR 3.7 2.5 - - - +
110A THR* 3.3 22.9 - - - +
111A THR 3.5 0.2 - - - -
112A MET* 1.3 95.4 - - + +
114A PHE* 1.3 63.4 + - + +
116A SER* 3.6 3.4 + - - +
117A THR* 3.2 27.4 + - - +
60B VAL* 4.1 25.6 - - + +
63B THR* 4.0 21.9 + - + -
64B ALA* 4.7 4.0 - - + +
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Residues in contact with PHE 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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110A THR* 3.2 26.7 - - - -
111A THR* 3.3 13.9 - - + +
112A MET 2.9 0.8 - - - -
113A PRO* 1.3 79.6 - - + +
115A GLN* 1.3 66.8 + - - +
118A VAL* 2.8 32.3 + - - +
124A TRP* 4.5 9.4 - + + -
126A PHE* 3.4 32.8 - + + -
130A LEU* 4.1 26.2 - - + -
134A VAL* 4.2 23.8 - - + -
1300A JDC 5.1 3.8 - - + -
60B VAL* 3.9 31.4 - - + -
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Residues in contact with GLN 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A TYR* 5.7 2.0 - - + -
111A THR 2.8 12.6 + - - +
112A MET* 2.8 9.8 + - - +
114A PHE* 1.3 76.5 - - - +
116A SER* 1.3 59.3 + - - +
118A VAL* 3.4 6.7 + - - +
119A TYR* 2.9 27.7 + - + +
312A TYR* 4.2 10.1 + - - -
313A TYR* 3.9 27.0 - - + -
316A ILE* 3.7 21.4 - - + +
320A TYR* 3.9 21.5 - - + +
1300A JDC 3.2 41.2 + - + +
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Residues in contact with SER 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A TYR* 3.3 36.6 + - - -
112A MET 2.9 10.2 + - - -
113A PRO* 3.6 5.5 + - - +
115A GLN* 1.3 76.1 - - - +
117A THR* 1.3 62.0 + - - +
119A TYR* 2.8 10.8 + - - +
120A LEU* 2.8 46.6 + - - +
63B THR* 4.1 8.1 + - - +
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Residues in contact with THR 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 PRO 3.2 13.4 + - - +
114A PHE 3.4 3.2 + - - +
116A SER* 1.3 81.8 + - - +
118A VAL* 1.3 64.4 + - - +
120A LEU* 3.5 13.5 + - - +
121A MET* 3.2 32.9 + - + +
125A PRO* 4.7 7.6 - - + -
126A PHE* 3.3 37.7 - - + -
59B PRO* 3.7 26.0 - - + +
63B THR* 4.6 8.4 + - - -
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Residues in contact with VAL 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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114A PHE 2.8 21.1 + - - +
115A GLN* 3.5 6.7 - - - +
117A THR* 1.3 77.7 - - - +
119A TYR* 1.3 57.0 + - - +
121A MET 3.4 0.2 + - - -
122A ASN* 2.6 36.3 + - - -
123A SER 3.4 25.3 + - - +
124A TRP* 3.4 35.7 - - + -
125A PRO* 4.4 0.9 - - + -
126A PHE* 4.0 11.9 - - + -
1300A JDC 4.0 19.5 - - + +
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Residues in contact with TYR 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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115A GLN* 2.9 15.4 + - + +
116A SER* 2.8 12.6 + - - +
118A VAL* 1.3 79.7 - - - +
120A LEU* 1.3 83.5 + - + +
122A ASN* 3.5 12.2 + - - +
309A LEU* 5.8 1.8 - - + -
313A TYR* 3.4 50.3 - + + +
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Residues in contact with LEU 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 SER* 2.8 27.6 + - - +
117A THR* 3.8 15.9 - - - +
119A TYR* 1.3 95.1 - - + +
121A MET* 1.3 62.7 + - + +
122A ASN* 4.9 1.0 - - - +
120B LEU* 3.5 45.8 - - + -
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Residues in contact with MET 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A THR* 3.2 20.1 + - + +
120A LEU* 1.3 79.0 - - + +
122A ASN* 1.3 70.3 + - - +
123A SER* 3.4 23.2 + - - +
125A PRO* 3.2 49.4 - - + -
59B PRO* 6.3 2.7 - - - -
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Residues in contact with ASN 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 VAL* 2.6 20.2 + - - -
119A TYR* 3.5 9.7 + - - +
120A LEU 3.3 3.6 - - - +
121A MET* 1.3 77.4 - - - +
123A SER* 1.3 57.7 + - - +
207A VAL* 3.5 32.6 - - + +
208A ILE 4.5 0.5 - - - +
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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