Contacts of the helix formed by residues 130 - 139 (chain A) in PDB entry 1HXK
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 GLU 130 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89A SER 4.4 4.7 - - - +
90A HIS* 4.0 14.4 + - - -
91A ASN* 3.1 50.0 + - - +
93A PRO* 4.1 10.8 - - + -
128A TRP* 2.8 29.2 + - - +
129A ALA* 1.3 87.6 + - + +
131A ILE* 1.3 64.7 + - - +
132A SER* 3.3 3.1 - - - +
133A TYR* 3.4 17.2 + - + +
134A PHE 3.3 7.1 + - - -
164A GLY 4.1 0.7 - - - -
165A TRP 4.0 11.2 - - - +
166A VAL* 4.7 0.7 - - - +
167A MET* 4.1 21.4 - - + +
471A HIS* 5.8 0.2 - - - -
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Residues in contact with ILE 131 (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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128A TRP* 4.6 1.1 - - + -
129A ALA 3.9 6.1 - - - +
130A GLU* 1.3 72.2 - - - +
132A SER* 1.3 65.6 + - - +
134A PHE* 4.1 5.2 - - + -
135A ALA* 2.8 25.7 + - - +
160A PHE* 3.6 32.5 - - + -
163A GLY* 3.4 22.4 - - - +
164A GLY 3.1 21.4 + - - +
165A TRP* 3.5 11.0 + - + -
185A GLY* 3.7 24.7 - - - +
188A TRP* 3.9 22.4 - - + -
189A LEU* 3.8 16.8 - - + -
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Residues in contact with SER 132 (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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93A PRO* 3.8 15.9 - - - +
99A PHE* 3.5 24.9 - - - -
130A GLU* 4.3 1.4 - - - +
131A ILE* 1.3 78.1 - - - +
133A TYR* 1.3 67.1 + - - +
135A ALA* 4.1 1.9 - - - +
136A ARG* 3.2 21.0 + - - +
165A TRP* 2.9 60.6 + - - -
166A VAL* 4.3 0.2 - - - +
467A LEU* 4.4 5.2 - - - -
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Residues in contact with TYR 133 (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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91A ASN* 3.7 27.8 - - + -
92A ASP 2.7 33.3 + - - -
93A PRO* 3.5 21.1 - - + +
94A GLY 3.7 0.5 + - - -
99A PHE* 3.4 40.2 + + - -
102A TYR* 3.0 20.5 - - + +
103A TYR* 4.0 17.2 - + + -
107A THR* 3.7 34.3 - - + -
111A LEU* 4.1 2.8 - - - +
128A TRP* 4.1 4.9 - - + -
130A GLU* 3.4 16.3 + - + +
131A ILE 3.1 0.4 - - - -
132A SER* 1.3 79.7 + - - +
134A PHE* 1.3 64.6 + - - +
136A ARG* 3.3 3.8 + - - +
137A PHE* 3.0 23.2 + - - +
342A PHE* 4.8 0.4 - + - -
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Residues in contact with PHE 134 (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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111A LEU* 4.0 28.9 - - + -
128A TRP* 3.9 17.0 - + + +
130A GLU 3.3 4.4 + - - +
131A ILE* 3.1 12.4 + - + +
133A TYR* 1.3 79.6 - - - +
135A ALA* 1.3 57.2 + - - +
137A PHE* 3.3 4.1 + + - +
138A TYR* 2.8 43.5 + + + +
149A MET* 3.6 44.6 - - + -
158A LEU* 4.9 4.7 - - + -
160A PHE* 3.5 39.3 - + + -
188A TRP* 3.5 31.6 - + - -
189A LEU* 5.1 0.2 - - + -
193A MET* 4.2 5.6 - - - -
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Residues in contact with ALA 135 (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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131A ILE* 2.8 19.9 + - - +
132A SER 4.1 0.4 - - - +
134A PHE* 1.3 69.8 - - - +
136A ARG* 1.3 64.8 + - - +
139A HIS* 3.0 36.7 + - + -
165A TRP* 4.0 19.7 - - + -
188A TRP* 3.6 42.4 - - + +
463A ARG* 5.5 1.8 - - - +
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Residues in contact with ARG 136 (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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99A PHE* 4.1 17.3 - - + -
100A GLU* 2.9 41.1 + - - -
103A TYR* 3.5 29.2 + - + -
104A GLN* 3.5 12.5 - - - +
132A SER 3.2 13.1 + - - +
133A TYR 3.3 9.4 + - - +
135A ALA* 1.3 79.7 - - - +
137A PHE* 1.3 62.2 + - - +
139A HIS* 4.1 2.9 + - - +
140A ASP* 3.1 40.8 + - - +
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Residues in contact with PHE 137 (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 TYR* 3.3 21.1 - - + -
108A LYS* 3.4 31.4 - - + -
111A LEU* 3.6 29.2 - - + -
112A SER* 3.5 27.1 - - - -
115A LEU* 5.1 2.2 - - + -
133A TYR 3.0 13.3 + - - +
134A PHE* 3.5 10.8 - + - +
136A ARG* 1.3 74.9 - - - +
138A TYR* 1.3 68.9 + - + +
140A ASP* 2.9 16.7 + - + +
141A LEU* 3.4 49.3 + - + +
149A MET* 3.8 18.8 - - + -
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Residues in contact with TYR 138 (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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134A PHE* 2.8 29.4 + + + +
137A PHE* 1.3 74.8 - - - +
139A HIS* 1.3 65.2 + - - +
140A ASP 3.1 0.2 - - - -
141A LEU* 3.0 40.2 + - + +
146A LYS* 3.3 61.6 - - + +
149A MET* 4.4 6.5 - - + -
150A LYS* 3.4 26.0 - - - +
188A TRP* 3.6 27.8 - + + -
192A PHE* 4.1 23.8 + + + -
193A MET* 3.3 26.5 - - + +
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Residues in contact with HIS 139 (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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135A ALA* 3.0 28.3 + - + +
136A ARG* 4.6 4.0 - - - +
138A TYR* 1.3 77.8 - + - +
140A ASP* 1.3 63.5 + - - +
141A LEU 3.4 4.1 + - - +
146A LYS* 4.5 14.0 + - - +
188A TRP* 2.9 36.0 + + - -
192A PHE* 3.7 28.9 - + - -
463A ARG* 5.5 7.0 + - - -
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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