Contacts of the strand formed by residues 117 - 124 (chain A) in PDB entry 3HMX
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 117 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111A ALA* 3.8 15.1 - - - +
112A LYS* 4.6 27.0 + - - +
113A ASN* 4.8 3.6 - - - +
115A SER* 3.2 17.0 + - - +
116A GLY* 1.3 79.0 + - - +
118A PHE* 1.3 60.4 + - - +
170A GLU* 3.3 29.1 + - + +
171A CYS 3.2 9.9 - - - +
172A GLN* 3.1 28.7 + - + +
207A ILE* 5.5 0.3 - - - +
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Residues in contact with PHE 118 (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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109A CYS* 4.8 1.1 - - - -
110A GLU 3.4 15.7 - - - +
111A ALA* 4.0 11.4 - - + +
116A GLY 3.5 15.0 - - - -
117A ARG* 1.3 74.1 - - - +
119A THR* 1.3 65.2 + - - +
120A CYS* 4.0 23.3 - - - -
136A SER* 4.4 9.2 - - - -
146A VAL* 4.5 7.4 - - + -
170A GLU* 3.7 3.3 - - - +
171A CYS* 2.8 65.9 + - + +
173A GLU 5.1 0.2 - - - -
186A ILE* 3.6 36.6 - - + -
188A VAL* 4.4 3.8 - - + -
205A PHE* 3.9 25.1 - + - -
207A ILE* 4.8 4.5 - - + -
210A ILE* 4.6 4.3 - - + -
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Residues in contact with THR 119 (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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109A CYS* 3.6 0.7 - - - -
110A GLU* 2.9 36.8 + - + +
118A PHE* 1.3 71.3 - - - +
120A CYS* 1.3 70.5 + - - +
121A TRP* 3.6 15.7 + - + +
168A SER* 4.4 10.1 - - - +
169A VAL 3.2 13.0 + - - +
170A GLU* 3.6 22.3 - - - +
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Residues in contact with CYS 120 (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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107A LEU* 5.6 3.6 - - + -
108A ARG 3.1 6.7 - - - +
109A CYS* 2.0 46.0 - - - -
118A PHE* 4.0 19.4 - - - -
119A THR* 1.3 72.0 - - - +
121A TRP* 1.3 63.6 + - - +
122A TRP* 4.5 7.6 - - + -
168A SER* 3.1 5.2 - - - -
169A VAL* 2.7 53.7 + - + +
171A CYS* 6.0 0.2 - - - -
188A VAL* 4.1 16.6 - - + -
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Residues in contact with TRP 121 (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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98A GLN* 3.8 21.0 - - - +
108A ARG* 3.0 72.9 + - + -
109A CYS 4.6 1.4 - - - +
110A GLU* 4.6 21.3 - - + +
119A THR* 3.6 22.2 + - + -
120A CYS* 1.3 82.1 - - - +
122A TRP* 1.3 64.4 + - - +
123A LEU* 4.5 10.1 - - + -
166A GLU* 4.1 29.6 - - + +
167A TYR 3.0 15.3 - - - +
168A SER* 3.8 9.4 - - - -
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Residues in contact with TRP 122 (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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95A LEU* 3.3 35.0 - - + -
98A GLN* 4.2 0.9 - - - -
106A PHE 3.7 17.7 - - - +
107A LEU* 4.3 11.7 - - + -
120A CYS* 4.5 7.2 - - + -
121A TRP* 1.3 79.1 - - - +
123A LEU* 1.3 71.7 + - - +
124A THR* 4.7 1.1 - - + -
132A PHE* 3.6 29.7 - + - -
134A VAL* 3.8 23.8 - - + -
151A ALA* 3.4 26.7 - - + -
165A TYR 4.2 0.2 - - - +
166A GLU* 4.0 0.2 - - - +
167A TYR* 2.9 53.6 + + + +
169A VAL* 3.7 26.9 - - + -
188A VAL* 5.8 0.4 - - + -
190A VAL* 3.8 27.6 - - + -
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Residues in contact with LEU 123 (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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95A LEU* 3.3 8.5 - - - +
96A LYS* 2.7 41.9 + - + +
98A GLN* 4.1 31.7 + - + +
106A PHE 4.4 1.8 + - - -
121A TRP* 4.5 11.9 - - + -
122A TRP* 1.3 86.0 - - - +
124A THR* 1.3 60.2 + - - +
157A ARG* 5.8 3.8 - - - +
164A GLU* 3.4 40.2 - - + +
165A TYR 3.7 2.9 - - - +
166A GLU* 3.5 34.8 - - + +
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Residues in contact with THR 124 (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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94A ILE* 3.2 23.2 + - - +
95A LEU* 4.3 10.8 - - + -
96A LYS* 4.5 3.8 - - - +
122A TRP* 4.7 1.6 - - + -
123A LEU* 1.3 76.4 - - - +
125A THR* 1.3 62.0 + - - +
126A ILE* 2.9 28.3 + - - +
130A LEU* 4.2 8.3 - - + +
132A PHE* 4.9 3.1 - - + -
164A GLU* 4.8 3.1 - - - +
165A TYR* 2.9 43.2 + - - +
167A TYR* 3.7 28.0 - - + -
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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