Contacts of the strand formed by residues 138 - 146 (chain A) in PDB entry 2MGZ
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 SER 138 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107A ILE* 4.3 2.8 - - - +
108A PRO 3.0 25.3 + - - -
109A PHE* 3.0 15.4 + - - -
110A LYS* 5.2 0.6 - - - +
111A TYR* 4.9 7.6 - - - -
131A ILE* 4.5 10.1 - - - -
132A ILE 3.4 12.8 - - - -
133A PHE* 3.8 15.8 - - - -
134A ASN 4.6 0.4 - - - -
137A GLY* 1.3 72.2 - - - -
139A LYS* 1.3 57.5 + - - +
140A GLY* 3.1 15.5 + - - -
141A PHE 5.3 0.4 - - - -
1C U 3.0 23.4 + - - +
3C C 3.2 4.8 + - - -
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Residues in contact with LYS 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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132A ILE* 2.8 47.9 + - + +
133A PHE* 4.0 1.6 - - - +
134A ASN* 3.7 21.5 - - + +
138A SER* 1.3 69.2 - - - +
140A GLY* 1.3 55.9 + - - +
141A PHE* 3.3 38.8 - - + +
3C C 2.9 73.1 + - + +
4C A 4.7 4.1 - - - +
6C G 5.1 7.9 - - - +
7C G 5.9 4.5 - - - -
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Residues in contact with GLY 140 (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 ILE* 3.3 25.3 + - - +
108A PRO 4.7 0.2 - - - -
109A PHE* 4.9 4.7 - - - -
138A SER* 3.0 19.3 + - - -
139A LYS* 1.3 75.2 - - - +
141A PHE* 1.3 57.0 + - - +
2C G 3.0 35.0 + - - -
3C C 4.7 0.6 - - - -
4C A 3.3 8.9 - - - -
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Residues in contact with PHE 141 (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 HIS* 3.7 19.1 - + - +
104A VAL 3.5 14.4 - - - +
105A SER* 4.5 1.1 - - - -
107A ILE* 3.9 12.7 - - - +
131A ILE* 4.2 5.2 - - - +
132A ILE* 3.6 31.7 + - + +
138A SER* 5.6 0.3 - - - -
139A LYS* 3.3 57.2 - - + -
140A GLY* 1.3 77.8 - - - +
142A GLY* 1.3 62.4 + - - +
143A PHE* 4.5 2.9 - + - -
3C C 3.8 4.5 - - - -
4C A 3.5 43.1 - + + +
5C U 4.2 11.0 - - - -
6C G 3.9 34.5 - - - -
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Residues in contact with GLY 142 (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 HIS* 3.4 10.7 - - - -
104A VAL* 2.8 38.2 + - - +
107A ILE* 3.9 9.8 - - - +
116A LEU* 5.0 0.2 - - - -
130A GLU 3.1 15.5 - - - -
131A ILE* 4.5 1.1 - - - -
132A ILE* 5.1 1.8 - - - -
141A PHE* 1.3 78.6 - - - +
143A PHE* 1.3 64.1 + - - -
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Residues in contact with PHE 143 (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* 3.6 30.1 - - - +
102A LEU 3.2 15.7 - - - +
103A HIS* 3.7 18.2 - + + +
104A VAL* 4.5 1.6 - - - +
116A LEU* 3.8 9.1 - - - +
129A VAL* 3.7 0.7 - - - -
130A GLU* 2.9 32.3 + - + +
132A ILE* 5.5 1.1 - - + -
141A PHE* 4.5 5.2 - + - -
142A GLY* 1.3 78.9 - - - -
144A VAL* 1.3 65.3 + - - +
174A ALA* 4.0 7.6 - - + -
175A THR 4.4 1.3 - - - -
5C U 3.2 42.0 - - - -
6C G 3.3 66.2 - + - -
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Residues in contact with VAL 144 (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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100A ARG 4.0 0.9 - - - +
101A ARG* 3.5 4.5 - - - +
102A LEU* 2.8 45.4 + - + +
104A VAL* 4.4 4.3 - - + -
116A LEU* 4.6 7.2 - - + +
120A PHE* 3.8 53.2 - - + -
126A VAL* 3.7 18.6 - - + -
128A ASP 3.4 14.1 - - - +
129A VAL* 4.1 12.3 - - + +
143A PHE* 1.3 76.5 - - - +
145A THR* 1.3 65.5 + - - +
146A MET* 4.6 4.9 - - + -
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Residues in contact with THR 145 (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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100A ARG* 3.5 34.1 - - + +
101A ARG* 2.9 35.2 + - + +
126A VAL* 3.7 2.9 - - - +
127A VAL* 2.8 32.0 + - + -
128A ASP* 2.8 31.1 + - + +
144A VAL* 1.3 70.5 - - - +
146A MET* 1.3 65.8 + - - +
176A GLN* 6.6 0.4 - - + -
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Residues in contact with MET 146 (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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100A ARG* 2.9 42.7 + - - +
102A LEU* 5.1 2.2 - - + -
120A PHE* 3.7 29.4 - - + +
123A VAL* 4.3 3.4 - - + -
124A GLY* 3.4 30.5 - - - +
125A PRO 3.8 9.2 - - - +
126A VAL* 3.8 21.5 - - + -
127A VAL* 3.8 3.6 - - - -
144A VAL* 4.6 5.6 - - + +
145A THR* 1.3 77.5 - - - +
147A GLN* 1.3 61.0 + - - +
148A ASN 3.3 18.1 + - - +
151A ASP* 4.0 18.4 - - + +
152A ALA* 3.5 23.8 - - + -
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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