Contacts of the helix formed by residues 93 - 108 (chain D) in PDB entry 7CE1
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 PHE 93 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90C LEU* 3.0 46.9 - - + -
91C MET* 3.8 24.2 - - + -
93C PHE* 6.0 4.5 - + - -
90D LEU 4.9 1.2 + - - -
91D MET* 3.0 45.7 - - + +
92D GLY* 1.3 77.8 - - - +
94D THR* 1.3 63.7 + - - +
95D SER* 3.3 6.5 - - - +
96D GLN* 3.2 32.6 + - + +
97D MET* 3.9 2.9 + - - +
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Residues in contact with THR 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95C SER* 3.6 24.9 + - - -
99C PHE* 5.3 1.1 - - + -
84D LEU* 3.4 34.3 - - + -
88D GLU* 2.9 23.9 + - - +
92D GLY* 3.9 9.2 + - - -
93D PHE* 1.3 70.7 - - - +
95D SER* 1.3 65.9 + - - +
97D MET* 3.0 22.7 + - + +
98D VAL* 3.2 16.4 + - + +
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Residues in contact with SER 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84C LEU* 5.8 0.9 - - - -
88C GLU* 2.5 30.0 + - - -
93C PHE* 5.7 0.3 + - - -
94C THR* 3.6 28.3 + - - -
95C SER* 4.5 8.5 - - - +
93D PHE* 4.6 5.9 - - - +
94D THR* 1.3 78.1 - - - +
96D GLN* 1.3 66.1 + - - +
98D VAL* 3.3 12.6 + - - +
99D PHE* 3.1 34.2 + - - -
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Residues in contact with GLN 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86C VAL* 4.8 8.1 + - - +
88C GLU* 5.0 5.6 + - - +
90C LEU* 6.3 3.1 - - + -
93D PHE* 3.2 28.2 + - + +
94D THR 3.1 0.6 - - - -
95D SER* 1.3 84.9 + - - +
97D MET* 1.3 55.0 + - - +
99D PHE* 3.3 25.3 + - - +
100D GLY* 3.0 22.9 + - - -
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Residues in contact with MET 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82D LEU* 5.0 8.1 - - + -
84D LEU* 5.0 13.5 - - - -
93D PHE 3.9 1.5 + - - +
94D THR* 3.0 18.8 + - + +
96D GLN* 1.3 76.0 - - - +
98D VAL* 1.3 68.4 + - + +
100D GLY* 3.1 4.4 + - - +
101D ILE* 2.8 46.9 + - + +
140D ILE* 5.7 6.3 - - + -
142D SER* 6.2 2.9 - - - -
164D HIS* 4.1 37.2 - - + +
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Residues in contact with VAL 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C LEU* 6.4 0.7 - - + -
98C VAL* 6.4 2.9 - - + -
114C VAL* 4.3 23.8 - - + -
82D LEU* 4.4 15.5 - - + -
84D LEU* 5.3 3.6 - - + -
94D THR* 3.2 24.7 + - + +
95D SER* 3.3 12.5 + - - +
97D MET* 1.3 78.5 - - + +
99D PHE* 1.3 62.9 + - + +
101D ILE* 2.8 24.6 + - - +
102D THR* 2.9 21.0 + - + +
112D LEU* 3.9 22.2 - - + -
114D VAL* 5.5 2.9 - - + -
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Residues in contact with PHE 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C LEU* 4.3 28.7 - - + -
85C SER 3.7 16.6 - - - -
86C VAL* 3.9 43.1 - - + -
88C GLU* 3.7 31.9 - - - -
114C VAL* 5.7 2.0 - - + -
116C PRO* 4.4 14.6 - - + -
95D SER* 3.1 22.6 + - - -
96D GLN* 3.6 24.7 - - - +
97D MET 3.2 0.2 - - - -
98D VAL* 1.3 76.3 - - + +
100D GLY* 1.3 69.3 + - - +
101D ILE 3.0 1.3 - - - -
102D THR* 2.9 19.7 + - + -
103D GLU* 3.3 10.7 + - - +
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Residues in contact with GLY 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96D GLN 3.0 13.8 + - - -
97D MET* 3.1 6.0 + - - -
99D PHE* 1.3 76.8 - - - +
101D ILE* 1.3 63.0 + - - +
103D GLU* 3.4 16.8 - - - +
104D VAL* 4.2 8.3 + - - +
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Residues in contact with ILE 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80D ILE* 5.6 0.4 - - + -
82D LEU* 3.9 25.8 - - + -
97D MET* 2.8 32.3 + - + +
98D VAL* 2.8 14.2 + - - +
100D GLY* 1.3 76.1 - - - +
102D THR* 1.3 55.0 + - - +
103D GLU 3.3 0.3 + - - -
104D VAL* 3.7 3.5 + - - +
105D LEU* 2.7 44.2 - - + +
112D LEU* 3.9 25.6 - - + -
140D ILE* 3.3 35.4 - - + -
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Residues in contact with THR 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86C VAL* 5.7 0.9 - - - +
114C VAL* 5.1 5.4 - - + +
116C PRO* 3.5 40.8 - - + +
98D VAL* 2.9 27.2 + - + +
99D PHE* 2.9 13.4 + - + +
101D ILE* 1.3 72.3 - - - +
103D GLU* 1.3 64.9 + - - +
105D LEU* 2.6 34.7 + - - +
106D ALA* 2.7 19.0 + - - -
112D LEU* 4.5 12.3 - - + -
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Residues in contact with GLU 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118C THR* 4.5 18.5 - - - +
99D PHE 3.3 7.7 + - - +
100D GLY* 3.4 15.9 - - - +
102D THR* 1.3 84.9 + - - +
104D VAL* 1.3 65.0 + - + +
106D ALA* 3.8 15.9 + - - +
107D THR* 3.9 9.7 - - - +
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Residues in contact with VAL 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D GLY 4.6 9.2 - - - +
101D ILE* 3.7 2.5 + - - +
102D THR 2.9 1.2 + - - -
103D GLU* 1.3 78.5 - - + +
105D LEU* 1.3 71.5 + - + +
107D THR* 2.7 35.0 + - + +
108D THR* 3.6 8.6 + - + +
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Residues in contact with LEU 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80D ILE* 3.8 32.8 - - + -
101D ILE* 2.7 36.8 - - + +
102D THR* 2.6 17.7 + - - +
104D VAL* 1.3 79.9 - - + +
106D ALA* 1.3 56.4 + - - -
108D THR* 2.5 41.6 + - + +
110D TYR* 4.0 24.7 - - + +
111D HIS 4.2 10.5 - - - +
112D LEU* 4.6 10.5 - - + -
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Residues in contact with ALA 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D THR* 2.7 18.1 + - - +
103D GLU* 3.9 15.0 - - - +
104D VAL 3.2 0.2 - - - -
105D LEU* 1.3 73.7 - - - +
107D THR* 1.3 62.6 + - + +
108D THR 3.4 5.4 + - - +
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Residues in contact with THR 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103D GLU 3.9 11.7 - - - +
104D VAL* 2.7 21.0 + - + +
106D ALA* 1.3 77.1 - - + +
108D THR* 1.3 78.5 + - - +
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Residues in contact with THR 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104D VAL* 3.6 11.7 - - + +
105D LEU* 2.5 34.6 + - + +
106D ALA* 3.5 5.5 - - - +
107D THR* 1.3 97.7 + - - +
109D GLN* 1.3 65.0 + - - +
110D TYR* 3.2 29.1 + - + +
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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