Contacts of the helix formed by residues 105 - 111 (chain C) in PDB entry 1IVH
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 ILE 105 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61C LEU 3.7 20.4 - - - +
62C GLY* 4.5 0.7 - - - -
64C THR* 5.7 2.0 - - - +
65C ALA* 4.3 15.3 - - + +
100C HIS* 3.0 36.6 + - + +
101C SER 3.4 13.5 - - - +
104C CYS* 1.3 76.4 - - - +
106C ASN* 1.3 58.4 + - - +
108C LEU* 2.7 30.7 + - - +
109C VAL* 3.0 27.2 + - + +
121C LEU* 4.3 7.0 - - + -
124C LEU* 3.6 38.1 - - + +
125C ILE* 4.0 9.2 - - + +
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Residues in contact with ASN 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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64C THR* 3.6 23.1 + - - +
76C TYR* 3.4 18.5 + - - -
101C SER 3.3 3.9 + - - +
102C ASN* 3.1 39.7 + - - +
105C ILE* 1.3 79.4 - - - +
107C GLN* 1.3 60.5 + - - +
109C VAL* 2.9 36.8 - - - +
110C ARG* 3.1 19.0 + - - +
253C LEU* 3.2 29.5 - - - +
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Residues in contact with GLN 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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102C ASN 3.5 3.4 + - - +
103C LEU* 3.2 22.7 + - - +
104C CYS 3.2 3.1 + - - +
105C ILE 3.1 1.0 - - - -
106C ASN* 1.3 79.5 - - - +
108C LEU* 1.3 56.4 + - - +
110C ARG* 3.2 16.5 + - - -
111C ASN* 2.9 48.7 + - - +
133C LEU* 5.2 6.1 - - + +
177C ILE* 4.0 8.3 - - + -
179C TYR* 3.7 16.1 + - - +
237C LEU* 4.1 16.6 - - + +
246C VAL* 3.0 27.3 + - + +
247C LEU 4.5 0.6 + - - -
249C SER* 4.7 0.3 + - - -
250C GLY* 3.1 26.1 + - - -
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Residues in contact with LEU 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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104C CYS* 3.0 31.3 + - - +
105C ILE* 2.7 14.8 + - - +
107C GLN* 1.3 72.7 - - - +
109C VAL* 1.3 56.8 + - - +
112C GLY* 2.8 30.5 + - - +
116C GLN* 4.8 10.8 - - + +
117C LYS* 3.6 8.8 - - + +
120C TYR* 4.1 29.8 - - + -
121C LEU* 3.8 20.2 - - + -
124C LEU* 4.7 7.9 - - + -
175C VAL* 4.9 6.3 - - + -
177C ILE* 4.0 9.9 - - + -
197C ILE* 4.0 27.8 - - + -
237C LEU* 4.4 10.8 - - + -
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Residues in contact with VAL 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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64C THR 4.7 8.5 - - - +
65C ALA* 4.1 4.9 - - + -
66C PRO* 4.1 23.5 - - + +
105C ILE* 3.0 22.1 + - + +
106C ASN* 2.9 34.5 - - - +
108C LEU* 1.3 75.9 - - - +
110C ARG* 1.3 63.8 + - + +
112C GLY 4.8 0.5 - - - +
117C LYS* 4.1 21.7 + - - +
121C LEU* 3.7 26.5 - - + -
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Residues in contact with ARG 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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76C TYR* 4.4 4.3 + - - +
106C ASN* 3.1 40.4 + - - +
107C GLN* 3.7 18.4 + - - +
108C LEU 3.2 0.2 - - - -
109C VAL* 1.3 88.0 - - + +
111C ASN* 1.3 72.8 + - - +
112C GLY 5.1 0.7 - - - -
245C TYR* 5.9 1.0 + - - -
249C SER* 3.9 26.9 + - - -
253C LEU* 3.7 20.5 - - - +
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Residues in contact with ASN 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 GLN* 2.9 34.0 + - - +
110C ARG* 1.3 88.4 + - - +
112C GLY* 1.3 65.8 + - - +
113C ASN 3.8 1.0 + - - -
116C GLN* 4.4 0.3 - - - +
237C LEU* 3.5 18.6 - - + -
238C GLY* 3.5 24.6 + - - +
245C TYR* 5.6 6.1 - - - -
246C VAL* 3.4 35.3 - - + +
249C SER* 4.9 3.6 + - - -
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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