Contacts of the helix formed by residues 93 - 106 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90C LEU 4.9 1.4 + - - -
91C MET* 3.0 51.1 - - + -
92C GLY* 1.3 75.8 - - - +
94C THR* 1.3 64.4 + - - +
95C SER* 3.2 8.3 - - - +
96C GLN* 3.2 32.8 + - + +
294C SER* 3.8 10.3 - - - +
295C ALA* 3.5 34.3 - - + -
297C PHE* 3.7 24.2 - + - -
312C ILE* 3.9 6.6 - - - +
88D GLU* 5.8 2.2 - - - -
90D LEU* 3.1 40.6 - - + -
91D MET* 4.2 7.0 - - - -
93D PHE* 6.0 4.7 - + - -
95D SER* 5.7 0.2 - - - -
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Residues in contact with THR 94 (chain C).
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* 3.6 33.4 - - + -
88C GLU* 2.7 27.6 + - - +
92C GLY* 3.7 10.9 + - - -
93C PHE* 1.3 71.4 - - - +
95C SER* 1.3 66.3 + - - +
97C MET* 2.9 33.2 + - + +
98C VAL* 3.3 12.8 + - + +
312C ILE* 5.0 1.3 - - - -
95D SER* 3.6 22.8 + - - -
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Residues in contact with SER 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93C PHE* 4.3 7.6 - - - +
94C THR* 1.3 78.7 - - - +
96C GLN* 1.3 57.5 + - - +
98C VAL* 3.2 13.0 + - - +
99C PHE* 3.0 39.6 + - - -
88D GLU* 2.4 39.0 + - - -
94D THR* 3.6 26.0 + - - -
95D SER* 4.5 7.4 - - - +
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Residues in contact with GLN 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93C PHE* 3.2 26.9 + - + +
94C THR 3.1 0.4 - - - -
95C SER* 1.3 78.8 + - - +
97C MET* 1.3 56.3 + - - +
99C PHE* 3.4 14.5 + - - +
100C GLY 2.8 22.7 + - - -
294C SER 5.4 3.1 - - - +
295C ALA* 5.7 3.6 - - + -
312C ILE* 4.4 4.7 - - + -
313C LYS* 3.4 48.0 - - + +
86D VAL* 4.5 5.1 + - - +
88D GLU* 3.4 28.1 + - - +
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Residues in contact with MET 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C LEU* 4.3 17.3 - - + -
84C LEU* 4.0 26.9 - - + -
94C THR* 2.9 20.4 + - + +
96C GLN* 1.3 76.5 - - - +
98C VAL* 1.3 60.5 + - - +
100C GLY* 3.1 1.3 + - - +
101C ILE* 2.8 48.7 + - + +
140C ILE* 5.5 1.1 - - - -
142C SER* 5.7 4.9 - - - -
164C HIS* 3.9 30.5 - - + +
312C ILE* 3.5 27.3 - - + +
316C GLY* 3.6 12.9 - - - +
319C LEU* 4.2 14.4 - - + -
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Residues in contact with VAL 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C LEU* 4.2 17.0 - - + -
84C LEU* 5.3 2.9 - - + -
94C THR* 3.7 20.4 - - + +
95C SER* 3.2 13.4 + - - +
97C MET* 1.3 76.0 - - + +
99C PHE* 1.3 66.7 + - + +
101C ILE* 3.2 10.0 + - - +
102C THR* 2.9 36.0 + - + +
112C LEU* 3.8 8.5 - - + -
114C VAL* 5.6 4.7 - - + -
84D LEU* 5.5 3.6 - - + -
114D VAL* 3.6 33.4 - - + -
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Residues in contact with PHE 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C SER* 3.0 30.4 + - - +
96C GLN* 3.7 17.3 - - - +
98C VAL* 1.3 82.4 - - + +
100C GLY* 1.3 63.2 + - - +
102C THR* 3.0 15.4 + - - -
103C GLU* 3.0 23.2 + - - +
313C LYS* 4.4 6.7 - - - -
84D LEU* 3.9 34.8 - - + -
85D SER 3.4 21.3 - - - -
86D VAL* 3.9 40.6 - - + -
88D GLU* 3.1 34.1 - - - -
94D THR* 5.3 0.4 - - + -
116D PRO* 4.4 9.9 - - + -
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Residues in contact with GLY 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96C GLN 2.8 13.8 + - - -
97C MET 3.1 3.8 + - - -
99C PHE* 1.3 77.3 - - - +
101C ILE* 1.3 61.0 + - - +
103C GLU* 3.7 5.2 + - - +
104C VAL 3.7 2.6 + - - -
313C LYS* 3.4 31.1 - - - +
316C GLY* 3.4 7.2 - - - -
317C ARG* 3.2 26.7 - - - +
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Residues in contact with ILE 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80C ILE* 5.1 1.6 - - + -
82C LEU* 3.7 32.5 - - + -
97C MET* 2.8 33.2 + - + +
98C VAL* 3.6 5.2 - - - +
100C GLY* 1.3 71.4 - - - +
102C THR* 1.3 65.5 + - - +
104C VAL* 3.1 9.0 + - - +
105C LEU* 3.1 39.0 + - + +
112C LEU* 4.1 13.9 - - + -
140C ILE* 3.7 26.9 - - + -
316C GLY* 3.3 22.0 - - - +
319C LEU* 5.2 2.2 - - + -
320C ALA* 4.0 11.2 - - + +
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Residues in contact with THR 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98C VAL* 2.9 22.7 + - + +
99C PHE* 3.0 16.3 + - - -
101C ILE* 1.3 74.4 - - - +
103C GLU* 1.3 55.6 + - - +
105C LEU* 3.5 9.8 - - + +
106C ALA* 2.8 32.6 + - - +
112C LEU* 3.7 25.6 - - + -
86D VAL* 5.7 0.5 - - - +
114D VAL* 4.2 13.0 - - + +
116D PRO* 3.1 43.5 - - + +
118D THR* 5.9 0.7 - - - -
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Residues in contact with GLU 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99C PHE 3.0 18.6 + - - +
100C GLY* 3.7 6.1 - - - +
101C ILE 3.2 0.2 - - - -
102C THR* 1.3 78.9 + - - +
104C VAL* 1.3 63.6 + - - +
106C ALA* 3.6 14.5 + - - +
107C THR* 4.6 5.4 + - - +
313C LYS* 2.6 42.1 + - - -
317C ARG* 3.9 19.4 + - + -
86D VAL* 4.2 11.8 - - + +
118D THR* 3.9 25.8 - - + +
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Residues in contact with VAL 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100C GLY 3.7 0.9 + - - +
101C ILE 3.1 2.0 + - - +
103C GLU* 1.3 76.9 - - - +
105C LEU* 1.3 62.7 + - - +
106C ALA 3.4 0.3 + - - -
107C THR* 3.3 20.1 + - - +
108C THR* 4.4 3.3 - - - +
317C ARG* 3.3 48.9 - - + +
320C ALA* 3.5 23.8 - - + +
321C LYS* 3.8 27.6 - - + +
324C LEU* 4.6 12.3 - - + -
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Residues in contact with LEU 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80C ILE* 4.2 11.2 - - + -
101C ILE* 3.1 36.1 + - + +
102C THR* 3.0 13.3 + - + +
104C VAL* 1.3 77.4 - - - +
106C ALA* 1.3 58.5 + - - +
107C THR 3.2 0.2 - - - -
108C THR* 2.7 34.9 + - - +
110C TYR* 3.7 37.6 - - + +
111C HIS 4.6 0.4 - - - +
112C LEU* 4.0 28.3 - - + +
320C ALA* 4.9 2.9 - - + -
324C LEU* 3.7 28.7 - - + -
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Residues in contact with ALA 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102C THR 2.8 18.0 + - - +
103C GLU* 3.8 10.5 - - - +
104C VAL 3.3 1.0 - - - -
105C LEU* 1.3 72.9 - - - +
107C THR* 1.3 63.8 + - + +
108C THR 3.5 6.1 - - - +
116D PRO 6.1 0.9 - - - +
118D THR* 5.8 6.7 - - + -
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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