Contacts of the helix formed by residues 102 - 112 (chain C) in PDB entry 1HJV
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 GLY 102 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98C GLY 4.7 1.2 + - - -
99C TRP 4.0 8.2 + - - -
100C ASN 2.8 8.2 + - - -
101C PHE* 1.3 95.3 - - - +
103C SER* 1.3 65.3 + - - +
104C GLN 3.5 2.5 - - - -
105C ARG* 3.7 6.8 + - - -
106C PHE* 3.8 6.1 + - - +
139C TRP* 5.5 0.3 - - - -
140C LEU 4.9 4.5 + - - -
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Residues in contact with SER 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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102C GLY* 1.3 72.7 - - - +
104C GLN* 1.3 67.2 + - - +
106C PHE 3.6 0.5 + - - -
107C SER* 3.4 19.8 + - - -
139C TRP* 3.9 10.9 + - - +
140C LEU 3.4 20.2 + - - -
141C TYR 3.9 17.2 + - - +
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Residues in contact with GLN 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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102C GLY 3.5 0.2 - - - -
103C SER* 1.3 80.0 - - - +
105C ARG* 1.3 67.3 + - - +
106C PHE 3.0 2.3 + - - -
107C SER* 3.0 9.7 + - - -
108C LYS* 2.8 35.4 + - + +
145C ARG* 3.8 24.1 + - - +
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Residues in contact with ARG 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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60C ASN* 2.6 31.6 + - - +
61C ILE* 2.6 24.9 + - - +
63C ASN* 5.3 6.1 + - - +
69C TRP* 6.2 0.2 - - - -
101C PHE* 3.1 52.6 + - + +
102C GLY* 3.7 2.5 + - - +
103C SER 3.5 0.8 - - - -
104C GLN* 1.3 76.2 - - - +
106C PHE* 1.3 59.4 + - - +
108C LYS* 4.2 3.4 - - - +
109C ILE* 3.0 42.6 + - - +
1384C NAG 4.0 16.8 + - - -
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Residues in contact with PHE 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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61C ILE* 4.6 12.1 - - + -
96C VAL* 3.3 42.2 - - + -
97C GLY* 3.7 7.0 - - - -
101C PHE* 3.7 24.0 - + + -
102C GLY 3.8 6.1 + - - +
103C SER 3.6 3.3 + - - +
104C GLN 3.1 0.6 - - - -
105C ARG* 1.3 77.9 - - - +
107C SER* 1.3 59.8 + - - +
109C ILE* 3.2 6.5 + - + +
110C ALA* 2.9 33.6 + - + +
119C PHE* 4.7 8.3 - + - -
137C LEU* 5.1 6.1 - - + -
138C ALA 3.6 15.5 - - - -
139C TRP* 3.6 57.2 - + + +
140C LEU 5.2 0.4 - - - -
153C LEU* 4.5 14.8 - - + -
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Residues in contact with SER 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 SER 3.4 10.5 + - - -
104C GLN* 3.0 16.0 + - - -
106C PHE* 1.3 79.1 - - - +
108C LYS* 1.3 50.5 + - - +
110C ALA* 4.2 0.2 - - - +
111C SER* 2.6 42.3 + - - -
139C TRP* 3.6 14.0 - - - -
145C ARG* 2.5 28.3 + - - -
146C ASP* 2.5 32.9 + - - +
149C HIS* 5.1 0.3 - - - -
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Residues in contact with LYS 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 GLN* 2.8 26.3 + - + +
105C ARG* 4.3 3.8 - - - +
107C SER* 1.3 74.3 - - - +
109C ILE* 1.3 62.6 + - + +
111C SER* 3.1 16.7 + - - +
112C ASN* 3.8 20.9 + - + +
115C SER* 4.6 1.4 + - - -
145C ARG* 4.9 1.8 - - - +
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Residues in contact with ILE 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* 4.1 36.6 - - + +
63C ASN* 4.2 15.7 - - - +
64C ASP* 3.9 37.9 - - - +
101C PHE* 4.8 0.9 - - + -
105C ARG* 3.0 36.2 + - - +
106C PHE* 3.2 8.2 + - + +
107C SER 3.2 0.6 - - - -
108C LYS* 1.3 81.2 - - + +
110C ALA* 1.3 58.5 + - + +
111C SER 3.5 0.2 - - - -
115C SER* 3.3 23.3 - - - +
116C ARG* 3.4 9.4 + - - -
119C PHE* 4.9 10.3 - - + -
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Residues in contact with ALA 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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106C PHE* 2.9 17.2 + - + +
107C SER 4.2 0.2 - - - +
109C ILE* 1.3 77.5 - - + +
111C SER* 1.3 64.4 + - - +
112C ASN* 3.4 2.0 + - - -
116C ARG* 3.9 32.1 + - - +
119C PHE* 6.5 0.4 - - + -
139C TRP* 4.1 25.6 - - + -
149C HIS* 4.2 10.2 - - + +
153C LEU* 4.1 22.9 - - + -
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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 SER 2.6 23.1 + - - -
108C LYS* 3.1 19.6 + - - +
110C ALA* 1.3 80.6 - - - +
112C ASN* 1.3 58.4 + - - +
113C THR* 3.2 10.4 + - - -
116C ARG* 5.1 1.9 + - - -
145C ARG* 4.4 12.2 + - - -
149C HIS* 3.3 32.4 + - - -
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Residues in contact with ASN 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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108C LYS* 3.8 17.2 + - + +
109C ILE 4.3 0.2 + - - -
110C ALA 3.4 1.9 - - - -
111C SER* 1.3 77.7 + - - +
113C THR* 1.3 66.6 + - - +
114C GLN* 2.6 51.9 + - - +
115C SER* 2.8 43.1 + - - +
116C ARG* 2.8 13.0 + - - +
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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