Contacts of the helix formed by residues 109 - 121 (chain A) in PDB entry 4CEJ
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 LEU 109 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61A LEU* 5.5 0.7 - - + -
63A VAL* 3.9 32.5 - - + +
64A THR 4.2 3.8 + - - -
108A THR* 1.3 74.9 - - - +
110A HIS* 1.3 59.0 + - + +
112A PHE* 3.3 22.7 + - + +
113A CYS* 2.9 41.9 + - - -
372A GLU* 6.0 0.9 - - + +
416A GLN* 3.5 60.3 - - + +
419A ILE* 4.7 9.6 - - + -
420A LEU* 4.3 20.2 - - + -
423A VAL* 6.5 0.2 - - + -
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Residues in contact with HIS 110 (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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65A PHE 5.8 0.9 - - - -
108A THR* 3.1 13.4 - - + +
109A LEU* 1.3 79.5 - - + +
111A SER* 1.3 56.8 + - - +
113A CYS* 3.3 9.5 + - - +
114A LEU* 2.9 27.2 + - - +
368A PHE* 3.5 45.0 + + + -
371A LEU* 3.7 19.0 - - + +
372A GLU* 4.0 29.6 + - + +
416A GLN* 4.4 12.4 + - - -
55X T 3.2 27.2 + - - -
56X T 4.2 16.2 - - - +
57X T 5.0 0.2 - - - -
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Residues in contact with SER 111 (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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67A ASN* 3.9 3.8 + - - -
107A SER* 3.5 25.4 - - - -
108A THR* 2.8 21.4 + - - -
110A HIS* 1.3 75.7 - - - +
112A PHE* 1.3 65.0 + - - +
114A LEU* 3.1 9.6 + - - +
115A GLN* 3.0 29.9 + - - +
57X T 2.5 28.7 + - - -
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Residues in contact with PHE 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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61A LEU* 3.8 26.9 - - + -
63A VAL* 5.4 1.1 - - + -
105A SER* 5.3 3.4 - - - -
107A SER* 4.1 4.6 + - - +
108A THR 3.3 8.0 + - - +
109A LEU* 3.3 27.3 + - + +
111A SER* 1.3 74.8 - - - +
113A CYS* 1.3 69.0 + - - +
115A GLN* 3.1 11.6 + - + +
116A VAL* 2.9 45.8 + - + +
375A CYS* 4.7 0.7 - - - -
379A LEU* 5.1 0.2 - - + -
397A TYR* 3.7 30.7 - + - -
401A PHE* 3.7 19.7 - + - -
419A ILE* 4.5 11.9 - - + -
423A VAL* 3.6 33.4 - - + -
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Residues in contact with CYS 113 (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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109A LEU* 2.9 30.4 + - - -
110A HIS* 3.4 11.7 - - - +
112A PHE* 1.3 76.0 - - - +
114A LEU* 1.3 57.7 + - - +
116A VAL* 3.1 3.8 + - - +
117A LEU* 2.9 34.5 + - - +
371A LEU* 3.7 25.6 - - + +
372A GLU* 4.0 9.9 - - - -
375A CYS* 3.7 32.1 - - + -
419A ILE* 3.8 17.9 - - - -
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Residues in contact with LEU 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 HIS 2.9 13.2 + - - +
111A SER* 3.1 12.1 + - - +
113A CYS* 1.3 77.6 - - - +
115A GLN* 1.3 59.5 + - - +
117A LEU* 3.4 1.4 + - - +
118A LYS* 3.0 48.4 + - + +
130A PHE* 3.5 32.8 - - + -
132A ILE* 4.1 20.9 - - + -
371A LEU* 4.3 11.4 - - + +
57X T 3.4 51.4 - - + +
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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
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111A SER* 3.0 22.0 + - - +
112A PHE* 3.1 16.1 + - + +
114A LEU* 1.3 80.9 - - - +
116A VAL* 1.3 62.3 + - - +
118A LYS* 3.5 24.2 + - - +
119A LYS* 3.1 25.3 + - - +
397A TYR* 4.0 6.8 + - + +
617B ARG* 5.1 16.8 + - - +
619B ASP* 4.4 13.3 + - - -
621B ASN* 4.5 5.9 - - - +
58X T 6.1 1.6 - - - -
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Residues in contact with VAL 116 (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 PHE* 2.9 49.5 + - + +
113A CYS 3.1 7.6 + - - +
115A GLN* 1.3 74.5 - - - +
117A LEU* 1.3 60.1 + - - +
119A LYS* 3.2 0.7 + - - -
120A TYR* 2.8 35.6 + - + +
375A CYS* 3.8 23.3 - - - +
378A ILE* 3.8 31.6 - - + +
379A LEU* 4.8 4.3 - - + -
397A TYR* 3.6 22.2 - - + +
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Residues in contact with LEU 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 CYS 2.9 23.6 + - - +
114A LEU 3.9 0.9 - - - +
116A VAL* 1.3 75.4 - - - +
118A LYS* 1.3 58.5 + - - +
121A TYR* 3.0 35.2 + - - +
124A ILE* 4.9 0.4 - - + -
126A LEU* 3.8 13.5 - - + +
130A PHE* 3.6 15.3 - - + -
366A ILE* 3.6 31.0 - - + -
371A LEU* 3.7 13.9 - - + -
374A TYR* 3.7 22.0 - - + -
375A CYS* 3.5 32.1 - - + +
378A ILE* 3.7 17.9 - - + -
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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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114A LEU* 3.0 37.4 + - - +
115A GLN* 3.7 17.0 - - - +
116A VAL 3.2 0.2 - - - -
117A LEU* 1.3 78.2 - - - +
119A LYS* 1.3 57.9 + - - +
121A TYR* 3.5 16.7 - - - -
128A PRO* 5.3 7.0 - - - +
130A PHE* 3.9 22.0 - - + -
122B GLN* 5.6 0.5 - - - +
619B ASP* 3.5 13.7 + - - +
621B ASN* 3.2 39.5 - - + +
57X T 3.2 15.4 + - - +
58X T 3.0 44.9 + - - -
59X T 5.1 1.4 + - - -
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Residues in contact with LYS 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 3.1 16.7 + - - +
116A VAL 4.0 1.8 - - - +
118A LYS* 1.3 80.4 - - - +
120A TYR* 1.3 105.4 + - + +
121A TYR* 3.5 5.2 + - - -
122A TYR* 3.3 18.4 - - - -
396A PHE* 3.4 32.1 - - + -
397A TYR* 4.4 7.4 - - - +
161B LYS* 5.8 2.8 + - - +
620B GLU* 4.0 13.5 - - + +
621B ASN* 3.8 16.6 - - - +
622B GLY 5.5 2.7 - - - +
625B SER* 3.6 31.8 + - - -
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Residues in contact with TYR 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 VAL* 2.8 15.4 + - + +
117A LEU 3.8 1.8 - - - -
119A LYS* 1.3 117.6 + - + +
121A TYR* 1.3 62.4 + - - +
122A TYR* 3.0 36.0 + + - -
123A LEU* 3.1 20.3 + - + +
378A ILE* 3.4 32.8 - - + +
392A GLU* 4.6 3.1 + - + -
393A ALA* 3.6 30.4 - - + -
396A PHE* 3.3 24.3 - - - +
397A TYR* 3.4 30.7 - + - -
157B VAL* 6.2 0.4 - - + -
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Residues in contact with TYR 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 LEU 3.0 17.1 + - - +
118A LYS 3.5 19.7 - - - +
119A LYS 4.1 5.4 - - - -
120A TYR* 1.3 76.8 - - - +
122A TYR* 1.3 87.6 + + + +
123A LEU 3.2 0.7 + - - -
124A ILE* 3.2 25.9 + - - +
126A LEU* 3.6 34.4 - - + +
128A PRO* 3.5 44.0 - - + -
130A PHE* 5.4 0.2 - - + -
378A ILE* 4.8 0.4 - - - -
110B TYR* 4.2 9.7 + - - -
113B ALA* 3.8 21.3 - - + -
119B PHE* 3.9 12.7 - + - -
122B GLN* 2.4 35.7 + - - -
622B GLY 5.1 8.7 + - - -
623B VAL* 5.1 1.9 - - - +
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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