Contacts of the strand formed by residues 104 - 111 (chain A) in PDB entry 5MR4
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 104 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102A PRO 3.3 1.4 + - - -
103A CYS* 1.3 77.1 - - - +
105A LEU* 1.3 63.5 + - - -
106A ARG* 3.5 12.9 + - - +
130A CYS* 3.5 2.3 - - - -
131A ALA 2.8 31.4 + - - +
194A CYS* 3.5 17.9 - - - -
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Residues in contact with LEU 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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101A ARG* 4.6 4.5 + - - -
104A GLY* 1.3 71.4 - - - -
106A ARG* 1.3 69.5 + - - +
107A GLU* 5.8 0.4 - - + +
128A ARG* 4.3 22.4 - - + -
129A TYR 3.4 9.2 - - - +
191A ALA* 3.9 30.1 - - + +
192A ARG 3.4 24.2 - - - +
193A GLU* 4.6 3.4 - - - -
194A CYS* 3.6 21.0 - - + +
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Residues in contact with ARG 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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101A ARG* 3.5 52.6 + - - +
102A PRO 3.1 21.6 + - - -
104A GLY* 3.5 32.8 - - - +
105A LEU* 1.3 77.3 + - - +
107A GLU* 1.3 63.0 + - - +
128A ARG* 3.1 10.2 - - - +
129A TYR* 2.8 67.1 + - + +
131A ALA* 3.2 16.7 + - + -
155B ARG* 3.7 11.2 - - - +
157B GLU* 2.7 37.8 + - - +
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Residues in contact with GLU 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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105A LEU* 5.8 0.9 - - + +
106A ARG* 1.3 78.4 - - - +
108A LEU* 1.3 62.5 + - - +
126A LEU* 3.8 22.9 - - + +
127A PHE 3.5 4.0 - - - -
128A ARG* 3.0 41.3 + - + +
129A TYR* 4.6 1.6 - - - -
155B ARG* 3.7 21.6 + - - +
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Residues in contact with LEU 108 (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 GLU* 1.3 77.5 - - - +
109A GLU* 1.3 65.4 - - - +
110A VAL* 3.6 24.0 - - + -
126A LEU* 3.8 4.1 - - - +
127A PHE* 2.9 38.8 + - + +
129A TYR* 4.3 9.2 - - + +
148B LEU* 3.9 17.5 - - + -
153B ARG* 3.3 55.2 - - + +
154B LEU* 4.1 9.2 - - + -
155B ARG* 4.8 10.3 - - - +
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Residues in contact with GLU 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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108A LEU* 1.3 74.7 - - - +
110A VAL* 1.3 59.4 + - - +
124A THR* 4.1 8.5 - - + +
125A VAL 3.6 4.7 - - - -
126A LEU* 4.1 10.6 - - + +
153B ARG* 3.3 23.6 + - - -
166C LYS* 3.7 23.8 + - - -
170C LEU* 3.7 35.1 - - + +
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Residues in contact with VAL 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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108A LEU* 3.6 31.6 - - + +
109A GLU* 1.3 79.1 - - - +
111A ARG* 1.3 63.2 + - - +
114A GLU* 4.0 6.3 - - - +
115A LEU* 4.2 22.0 - - + -
124A THR* 3.2 7.7 - - - +
125A VAL* 2.9 59.6 + - + +
127A PHE* 4.0 11.2 - - + -
148B LEU* 4.0 16.2 - - + -
153B ARG* 4.0 8.3 - - - +
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Residues in contact with ARG 111 (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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110A VAL* 1.3 76.6 - - - +
112A VAL* 1.3 65.4 + - - +
113A SER* 3.1 15.7 - - - +
114A GLU* 3.0 46.0 + - + +
115A LEU 4.0 1.6 + - - -
122A ASP* 3.6 52.2 + - - +
123A GLU 3.4 4.9 - - - +
124A THR* 4.4 10.8 + - - +
162C LEU* 4.1 12.9 - - - +
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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