Contacts of the strand formed by residues 124 - 131 (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 THR 124 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A GLU* 4.1 14.6 - - + -
110A VAL 3.2 21.0 + - - +
111A ARG* 4.6 10.7 + - - -
122A ASP 4.3 4.2 + - - -
123A GLU* 1.3 76.8 + - - +
125A VAL* 1.3 73.7 + - - +
166C LYS* 3.9 41.9 + - + +
169C ASN* 3.3 28.8 + - - +
170C LEU* 4.3 11.0 - - + -
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Residues in contact with VAL 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A GLU* 3.6 3.5 - - - -
110A VAL* 2.9 53.6 + - + +
112A VAL* 3.8 22.9 - - + +
115A LEU* 4.7 1.1 - - + -
124A THR* 1.3 81.9 - - - +
126A LEU* 1.3 63.0 + - - +
127A PHE* 3.4 7.8 + - + +
174A VAL* 3.6 36.8 - - + -
176A PHE* 4.7 3.6 - - + -
189A LEU* 4.3 18.8 - - + -
190A SER* 6.1 0.2 - - - +
169C ASN* 3.9 9.9 - - - +
170C LEU* 4.2 1.3 - - - -
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Residues in contact with LEU 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A GLU* 3.8 37.9 - - + +
108A LEU* 3.8 6.3 - - - +
109A GLU* 4.1 22.7 - - + +
125A VAL* 1.3 73.3 - - - +
127A PHE* 1.3 61.7 + - - +
128A ARG* 3.3 39.8 + - + +
171A GLU* 4.8 6.9 - - - +
190A SER* 3.3 11.6 + - - -
169C ASN 4.5 10.0 + - - +
170C LEU* 3.8 29.8 - - + +
175C LYS* 6.5 0.7 - - + -
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Residues in contact with PHE 127 (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 ARG 3.9 0.5 - - - +
107A GLU* 3.5 2.1 - - - -
108A LEU* 2.9 45.1 + - + +
110A VAL* 4.0 18.4 - - + -
115A LEU* 5.0 5.4 - - + -
125A VAL* 3.4 3.4 + - + -
126A LEU* 1.3 72.8 - - - +
128A ARG* 1.3 59.4 + - - +
129A TYR* 3.8 18.6 - + + -
189A LEU* 3.3 42.8 - - + -
190A SER* 3.3 10.8 - - - -
141B TYR* 4.0 28.3 - + - -
144B GLY* 5.0 3.1 - - - -
145B LEU* 3.7 31.6 - - + -
148B LEU* 3.6 27.8 - - + -
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Residues in contact with ARG 128 (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* 4.3 22.2 - - + -
106A ARG 3.1 7.0 - - - +
107A GLU* 3.0 34.8 + - + +
126A LEU* 3.3 32.4 + - + +
127A PHE* 1.3 78.6 - - - +
129A TYR* 1.3 59.2 + - - +
171A GLU* 5.6 2.4 + - - +
190A SER* 2.9 15.6 + - - +
191A ALA* 2.8 49.1 + - - +
192A ARG* 5.8 6.0 - - - +
141B TYR* 3.6 3.5 - - - -
172C ASP* 3.5 36.1 + - - -
175C LYS* 5.3 4.9 - - - +
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Residues in contact with TYR 129 (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 GLY 3.6 0.3 - - - +
105A LEU* 3.4 4.8 - - - -
106A ARG* 2.8 64.2 + - + +
107A GLU 4.4 0.9 - - - -
108A LEU* 4.3 16.4 - - + +
127A PHE* 3.8 19.7 - + + -
128A ARG* 1.3 75.0 - - - +
130A CYS* 1.3 72.9 + - - +
131A ALA* 3.8 16.4 - - + -
191A ALA* 4.0 2.5 - - - -
141B TYR* 3.5 17.9 - - + +
145B LEU* 3.6 25.6 - - + -
154B LEU* 3.7 45.0 + - + +
155B ARG* 4.1 13.2 + - - -
157B GLU* 5.1 2.6 + - + -
159B VAL* 4.1 6.3 - - + -
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Residues in contact with CYS 130 (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 GLY 3.5 4.3 - - - -
129A TYR* 1.3 71.0 - - - +
131A ALA* 1.3 62.9 + - - +
165A CYS* 4.0 17.4 - - - +
166A ARG* 4.1 11.4 - - - -
167A PRO* 3.6 26.2 - - + -
191A ALA* 3.9 6.1 - - - -
193A GLU 3.8 2.9 - - - -
194A CYS* 2.1 51.8 - - + -
141B TYR* 3.0 14.1 + - - +
159B VAL* 3.5 18.2 - - - +
160B ARG 4.7 2.4 + - - +
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Residues in contact with ALA 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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103A CYS* 3.2 0.2 - - - -
104A GLY 2.8 30.3 + - - +
106A ARG* 3.2 13.4 + - + -
129A TYR* 3.8 21.9 + - + -
130A CYS* 1.3 76.0 - - - +
132A GLY* 1.3 60.7 + - - +
165A CYS* 3.8 7.0 - - - -
157B GLU* 3.8 20.0 - - + +
158B ARG 3.4 15.9 - - - +
159B VAL* 4.3 4.9 - - + +
160B ARG 5.8 0.2 - - - +
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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