Contacts of the helix formed by residues 102 - 112 (chain C) in PDB entry 3EU9
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 ARG 102 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65C THR 3.5 15.9 - - - +
66C GLN 2.7 28.5 + - - -
67C TYR* 3.3 16.7 + - - +
68C GLY* 3.3 21.8 - - - +
97C ALA* 2.8 25.2 + - - +
100C ASN* 3.4 23.1 + - + +
101C ASN* 1.3 70.3 + - - +
103C ILE* 1.3 64.6 + - - +
104C ASP 3.4 2.5 - - - -
105C LEU* 3.2 22.5 + - + +
106C VAL* 3.0 23.6 + - - +
139C MET* 3.4 2.9 - - - +
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Residues in contact with ILE 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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208A ARG* 5.0 10.5 - - + -
212A THR* 4.4 17.9 - - + +
101C ASN* 3.1 29.1 + - - +
102C ARG* 1.3 71.1 - - - +
104C ASP* 1.3 69.8 + - - +
106C VAL* 3.2 11.0 + - - +
107C LYS* 3.2 19.9 + - - +
138C SER* 3.7 30.7 - - - +
139C MET* 3.8 13.9 - - + -
142C GLN* 3.0 34.5 - - + +
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Residues in contact with ASP 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A GLU* 5.7 6.1 - - - +
70C TYR* 3.7 25.4 + - + +
102C ARG 3.4 0.6 - - - -
103C ILE* 1.3 82.7 - - - +
105C LEU* 1.3 61.7 + - - +
107C LYS* 3.3 16.5 + - - +
108C TYR* 3.0 23.2 + - - +
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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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65C THR* 3.9 37.9 - - + +
68C GLY* 4.2 13.5 - - - +
70C TYR* 3.4 31.2 - - + +
73C CYS* 3.8 30.1 - - + -
97C ALA* 4.2 2.5 - - + -
102C ARG* 3.2 24.9 + - + +
104C ASP* 1.3 79.3 - - + +
106C VAL* 1.3 57.6 + - - +
108C TYR* 3.6 5.1 - - + +
109C TYR* 2.8 53.6 + - + +
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Residues in contact with VAL 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C LEU* 3.9 15.1 - - + +
97C ALA* 3.9 15.7 - - + -
98C ALA* 4.2 4.5 - - - +
102C ARG 3.0 17.6 + - - +
103C ILE 3.5 8.1 - - - +
105C LEU* 1.3 77.7 - - - +
107C LYS* 1.3 63.9 + - - +
109C TYR 3.4 0.2 + - - -
110C ILE* 3.0 45.0 + - + +
139C MET* 3.5 27.1 - - + -
142C GLN* 4.0 16.2 - - + -
143C LEU* 3.7 17.9 - - + -
146C TYR* 5.0 0.9 - - + -
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Residues in contact with LYS 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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211A LEU 5.1 8.1 + - - -
212A THR* 5.3 4.7 + - - +
103C ILE* 3.2 14.4 + - - +
104C ASP* 3.6 16.5 + - - +
106C VAL* 1.3 77.5 - - - +
108C TYR* 1.3 58.5 + - - +
110C ILE* 3.4 2.6 + - - +
111C SER* 3.0 29.9 + - - -
142C GLN* 2.9 41.3 - - - +
146C TYR* 3.2 31.8 + - - +
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Residues in contact with TYR 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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70C TYR* 3.6 26.0 - + + +
74C ARG* 3.6 45.7 + - + +
77C VAL* 3.5 36.9 - - + +
78C GLU* 3.8 8.9 - - + +
104C ASP 3.0 17.7 + - - +
105C LEU* 3.6 11.2 - - + +
107C LYS* 1.3 77.8 - - - +
109C TYR* 1.3 76.4 + + - +
111C SER* 2.5 28.3 + - - -
112C LYS* 3.1 32.4 + - + +
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Residues in contact with TYR 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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61C ILE* 4.0 5.7 - - - +
65C THR* 2.7 31.0 + - + -
73C CYS* 3.2 21.1 - - + +
77C VAL* 3.9 17.3 - - + -
83C VAL* 3.9 16.8 - - + +
93C LEU* 3.8 43.3 - - + -
94C LEU* 4.0 9.6 - - + +
97C ALA* 4.3 5.4 - - + -
105C LEU* 2.8 38.0 + - + +
108C TYR* 1.3 94.8 - + - +
110C ILE* 1.3 61.6 + - - +
112C LYS* 3.1 12.2 + - - +
113C GLY 3.3 0.9 + - - -
114C ALA* 2.9 35.5 + - + +
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Residues in contact with ILE 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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94C LEU* 4.1 21.1 - - + -
106C VAL* 3.0 37.7 + - + +
107C LYS 3.8 3.1 - - - +
109C TYR* 1.3 73.4 - - - +
111C SER* 1.3 66.4 + - - +
113C GLY* 3.1 14.0 + - - -
114C ALA* 3.9 10.6 + - - +
116C VAL* 4.0 22.0 - - + -
143C LEU* 4.6 3.8 - - + -
146C TYR* 3.6 50.9 - - + -
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Residues in contact with SER 111 (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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107C LYS 3.0 14.5 + - - -
108C TYR* 2.5 27.4 + - - -
110C ILE* 1.3 77.5 - - - +
112C LYS* 1.3 68.1 + - - +
113C GLY 3.2 2.5 + - - -
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Residues in contact with LYS 112 (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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77C VAL* 4.1 20.0 - - + -
78C GLU* 5.9 5.7 - - - +
83C VAL* 3.4 26.9 - - + +
108C TYR* 3.1 42.4 + - + +
109C TYR 3.1 8.5 + - - +
110C ILE 3.1 0.8 - - - -
111C SER* 1.3 89.4 - - - +
113C GLY* 1.3 56.1 + - - +
114C ALA 3.6 0.4 - - - -
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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