Contacts of the helix formed by residues 101 - 110 (chain C) in PDB entry 3EXF
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 SER 101 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96C PHE* 5.0 2.2 - - - -
99C GLY 3.7 1.3 + - - -
100C LEU* 1.3 75.6 - - - +
102C VAL* 1.3 62.2 + - - +
103C ARG* 4.1 8.7 + - - +
104C GLU* 2.9 39.7 + - - +
105C ILE* 2.9 31.1 + - - +
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Residues in contact with VAL 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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41C THR* 3.8 15.9 - - + -
45C MET* 3.9 15.9 - - - -
96C PHE* 3.6 31.5 - - + -
101C SER* 1.3 69.6 - - - +
103C ARG* 1.3 68.2 + - - +
105C ILE* 4.4 5.6 - - - -
106C LEU* 2.8 38.5 + - + +
316C GLU* 4.9 11.9 - - + +
317C ILE* 4.1 20.0 - - + -
320C ALA* 3.5 22.4 - - + -
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Residues in contact with ARG 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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101C SER* 3.3 9.0 + - - +
102C VAL* 1.3 77.1 - - - +
104C GLU* 1.3 64.1 + - + +
106C LEU* 3.8 0.7 - - - +
107C ALA* 2.8 28.6 + - - +
319C ASP* 3.5 38.0 + - - +
320C ALA* 4.0 18.5 - - + +
322C GLN* 5.7 1.2 - - - +
323C PHE* 3.2 56.4 - - + +
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Residues in contact with GLU 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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99C GLY 5.4 0.2 - - - +
100C LEU* 3.2 30.8 - - + +
101C SER* 2.9 35.1 + - - +
103C ARG* 1.3 79.2 - - + +
105C ILE* 1.3 62.4 + - - +
108C GLU* 3.2 4.3 + - - +
114C GLY 4.4 13.2 - - - +
115C GLY* 3.2 27.9 - - - -
116C CYS* 3.3 22.6 + - + +
323C PHE* 5.6 0.4 - - - -
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Residues in contact with ILE 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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45C MET* 4.2 26.2 - - + -
92C HIS* 4.4 10.3 - - + +
95C THR* 3.1 27.8 - - - +
96C PHE* 3.6 27.4 - - + +
100C LEU* 4.0 10.8 - - + -
101C SER 2.9 25.1 + - - +
102C VAL 3.9 3.4 - - - +
104C GLU* 1.3 74.2 - - + +
106C LEU* 1.3 66.3 + - + +
108C GLU* 3.1 3.5 + - - +
109C LEU* 3.0 34.0 + - + +
116C CYS* 5.0 2.2 - - - -
126C MET* 4.2 24.1 - - + +
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Residues in contact with LEU 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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45C MET* 4.5 17.9 - - + +
48C LYS* 4.1 8.3 - - + -
49C ALA* 4.5 16.2 - - + +
52C LEU* 4.4 16.6 - - + -
102C VAL* 2.8 28.4 + - + +
103C ARG 4.2 0.7 - - - +
105C ILE* 1.3 74.1 - - + +
107C ALA* 1.3 57.1 + - - +
109C LEU* 3.6 18.3 - - + +
110C THR* 3.1 31.9 + - - +
317C ILE* 4.2 6.3 - - + +
320C ALA* 3.9 14.1 - - + +
321C ALA* 3.8 35.4 - - + +
324C ALA* 3.5 12.3 - - + -
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Residues in contact with ALA 107 (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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103C ARG 2.8 19.5 + - - +
106C LEU* 1.3 76.4 - - - +
108C GLU* 1.3 58.8 + - - +
110C THR* 3.0 14.6 + - - +
111C GLY 3.0 2.6 + - - -
112C ARG* 2.9 33.8 + - + -
114C GLY 3.9 4.0 - - - -
115C GLY* 3.3 25.1 - - - +
323C PHE* 4.0 11.9 - - + -
324C ALA* 3.5 12.2 - - + +
327C ASP* 4.5 0.2 - - - +
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Residues in contact with GLU 108 (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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304B TYR* 3.1 15.4 - - - -
104C GLU 3.2 15.2 + - - +
105C ILE 3.1 5.6 + - - +
107C ALA* 1.3 73.3 - - - +
109C LEU* 1.3 67.2 + - - +
111C GLY* 3.0 12.3 + - - +
112C ARG 4.7 0.4 - - - +
115C GLY* 3.5 3.8 - - - -
116C CYS* 3.8 11.9 - - - +
117C ALA* 2.7 30.6 + - + -
118C LYS 3.2 0.5 + - - -
119C GLY* 2.8 22.1 + - - -
120C LYS 3.3 3.8 + - - -
121C GLY* 2.6 32.9 + - - -
122C GLY* 3.0 24.4 + - - +
126C MET* 3.9 16.2 - - + -
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Residues in contact with LEU 109 (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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304B TYR* 2.5 29.3 + - - +
45C MET* 6.4 0.7 - - + -
49C ALA* 4.1 14.1 - - + -
58C ILE* 3.8 41.1 - - + +
62C CYS* 4.7 1.6 - - - -
92C HIS* 3.6 25.8 - - + +
105C ILE* 3.0 23.5 + - + +
106C LEU* 3.6 15.9 - - + +
108C GLU* 1.3 77.4 - - - +
110C THR* 1.3 57.1 + - - +
111C GLY 3.2 0.3 + - - -
122C GLY 4.8 0.4 - - - +
123C SER* 3.3 41.7 - - - +
126C MET* 5.2 2.0 - - - -
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Residues in contact with THR 110 (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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304B TYR* 4.5 1.8 - - - -
52C LEU* 4.3 18.4 - - + -
57C ILE* 3.5 39.2 - - + +
58C ILE* 4.4 3.6 - - + -
106C LEU 3.1 18.6 + - - +
107C ALA* 3.0 13.9 + - - -
108C GLU 3.2 0.4 - - - -
109C LEU* 1.3 75.5 - - - +
111C GLY* 1.3 57.7 + - - +
112C ARG* 3.1 23.4 + - - +
324C ALA* 3.2 30.9 + - + +
325C THR* 5.1 0.2 - - + -
329C GLU* 5.6 0.2 - - - +
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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