Contacts of the helix formed by residues 104 - 110 (chain A) in PDB entry 2HU4
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 ASN 104 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A LYS* 2.6 38.1 + - - +
103A ASP* 1.3 79.0 + - - +
105A SER* 1.3 64.9 + - - +
106A ILE 3.0 4.6 + - - -
107A ARG* 3.2 24.6 + - - +
108A ILE* 3.1 29.5 + - + +
442A SER* 3.8 7.3 + - - -
443A SER 4.8 0.4 + - - -
460A ASP* 3.9 1.7 + - - -
137C GLY* 3.6 19.9 - - - +
155C HIS* 3.0 28.1 - - - +
157C THR* 4.0 12.8 + - - +
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Residues in contact with SER 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A ASP* 2.7 18.1 + - - -
104A ASN* 1.3 71.7 - - - +
106A ILE* 1.3 62.5 + - - +
108A ILE* 3.8 0.6 - - - -
109A GLY* 2.8 25.1 + - - -
114A VAL* 3.5 17.3 - - - +
115A PHE 5.5 0.3 + - - -
117A ILE* 5.6 0.2 - - - +
140A LEU* 4.0 0.7 - - - +
166A ALA* 3.9 9.4 - - - -
167A PRO* 3.7 32.0 - - - +
440A SER* 5.5 0.7 + - - -
441A GLY 3.3 22.3 + - - -
442A SER* 3.3 7.7 + - - -
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Residues in contact with ILE 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A ASN 3.0 0.8 + - - -
105A SER* 1.3 82.9 + - - +
107A ARG* 1.3 67.2 + - - +
108A ILE 3.1 1.1 - - - -
109A GLY* 3.1 8.5 + - - -
110A SER 3.2 9.7 + - - -
140A LEU* 3.9 15.0 - - + -
428A ARG* 3.7 22.4 - - + -
438A TRP* 4.1 13.2 - - + -
440A SER* 3.9 8.3 - - - +
441A GLY* 3.8 31.0 - - - +
442A SER* 3.6 2.5 + - - +
460A ASP* 3.3 24.7 - - - +
462A ALA* 3.5 20.2 - - + -
466A PHE* 3.5 22.2 - - + -
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Residues in contact with ARG 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A ASN* 3.2 23.4 + - - +
106A ILE* 1.3 76.8 - - - +
108A ILE* 1.3 62.5 + - - +
110A SER* 3.2 6.8 - - - -
460A ASP* 3.2 22.6 + - - +
461A GLY 3.1 36.0 + - - +
462A ALA* 3.7 3.1 - - - +
136C GLN* 2.7 26.2 + - - -
137C GLY 2.7 26.1 + - - +
138C ALA* 3.9 1.8 - - - +
142C ASP* 3.6 3.6 - - - +
144C HIS* 3.1 63.4 + - + +
148C THR* 5.6 1.4 - - - +
150C LYS* 5.8 5.9 - - - +
155C HIS* 3.6 26.6 + - - +
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Residues in contact with ILE 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A ASP 3.6 22.9 - - - +
104A ASN* 3.3 14.8 - - + +
105A SER* 3.8 3.8 - - - +
107A ARG* 1.3 73.7 - - - +
109A GLY* 1.3 57.0 + - - +
110A SER 3.0 8.5 + - - -
111A LYS 3.1 3.3 + - - -
112A GLY* 2.9 24.1 + - - -
114A VAL* 4.0 14.8 - - + -
166A ALA* 4.2 9.6 - - + +
115C PHE* 3.6 33.2 - - + -
137C GLY 4.1 14.8 - - - +
138C ALA* 4.6 3.8 - - - +
139C LEU* 3.5 30.2 - - + +
169C PRO* 4.4 13.7 - - + -
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Residues in contact with GLY 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A SER 2.8 19.8 + - - -
106A ILE 3.1 4.6 + - - -
108A ILE* 1.3 70.6 - - - +
110A SER* 1.3 64.7 + - - +
111A LYS 2.9 4.0 + - - -
112A GLY 3.8 3.4 - - - -
114A VAL* 3.5 21.2 - - - +
140A LEU* 3.8 20.7 - - - +
141A ASN* 4.3 1.4 - - - +
466A PHE* 4.4 0.7 - - - -
111D LYS* 3.2 19.1 + - - -
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Residues in contact with SER 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A ILE 3.2 5.3 + - - -
107A ARG 3.2 1.3 - - - -
108A ILE 3.0 1.2 + - - -
109A GLY* 1.3 76.2 - - - +
111A LYS* 1.3 56.9 + - - +
141A ASN* 2.8 28.5 + - - +
466A PHE* 3.7 15.8 - - - -
142C ASP* 2.6 39.3 + - - +
143C LYS* 4.1 11.3 - - - +
144C HIS* 3.1 27.0 + - - -
111D LYS* 4.3 0.9 + - - -
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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