Contacts of the strand formed by residues 207 - 213 (chain A) in PDB entry 5MGS
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 207 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109A SER* 3.2 24.1 + - - +
110A HIS* 3.8 19.6 + - - +
111A THR 3.4 17.3 - - - +
112A VAL* 4.1 15.1 - - + +
150A ILE* 3.7 42.2 - - - +
151A LEU 3.6 5.8 + - - +
152A PHE* 3.3 23.2 - - + -
153A TRP* 2.7 27.2 + - - -
206A ILE* 1.3 85.7 - - - +
208A TRP* 1.3 55.5 + - - +
174H ASN* 3.1 35.8 + - - +
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Residues in contact with TRP 208 (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* 3.7 0.7 - - - +
109A SER* 2.9 54.3 + - - -
111A THR* 3.2 39.5 - - + -
112A VAL 3.7 4.0 - - - -
113A ASN* 3.3 28.0 - - + -
118A SER* 3.5 35.9 - - - +
121A ASP* 2.9 47.7 + - + +
122A CYS* 3.6 24.2 - - - -
125A LYS* 5.4 1.1 - - - -
129A LEU* 4.1 2.0 - - + -
152A PHE* 3.9 1.8 - - - -
153A TRP* 3.7 16.8 - - + +
206A ILE 3.7 7.0 - - - -
207A ARG* 1.3 76.8 - - - +
209A ILE* 1.3 64.8 + - - +
210A CYS* 3.6 7.7 - - - -
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Residues in contact with ILE 209 (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 LEU* 4.4 13.2 - - + -
107A LEU 3.3 8.5 - - - +
108A PHE* 3.4 38.4 - - + -
122A CYS* 4.2 0.4 - - - -
129A LEU* 3.5 10.4 - - - +
130A LEU* 3.0 53.2 + - + +
141A THR* 4.6 0.7 - - + -
152A PHE* 3.6 26.5 - - + -
153A TRP 3.2 6.1 + - - +
154A ILE* 4.9 1.8 - - + -
192A ILE* 4.0 22.0 - - + -
208A TRP* 1.3 78.8 - - - +
210A CYS* 1.3 72.7 + - - +
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Residues in contact with CYS 210 (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 TRP* 3.7 13.6 - - + -
106A LEU* 3.3 5.4 - - - -
107A LEU* 2.9 39.6 + - + +
121A ASP* 3.9 5.6 - - - -
122A CYS* 2.1 50.0 - - - -
125A LYS* 4.7 5.6 - - - -
127A SER* 3.3 13.5 - - - +
128A SER 3.1 5.8 - - - -
130A LEU 4.8 0.4 - - - -
208A TRP* 3.6 16.6 - - - -
209A ILE* 1.3 79.0 - - - +
211A GLN* 1.3 60.0 + - - +
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Residues in contact with GLN 211 (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 TRP* 4.0 2.2 - - - -
104A LYS* 2.9 41.4 + - + +
105A CYS 3.2 5.2 - - - +
106A LEU* 3.7 16.6 - - + -
127A SER* 3.4 6.1 - - - -
128A SER* 2.7 51.4 + - - +
129A LEU 4.1 2.2 - - - +
130A LEU* 3.4 6.3 - - + +
131A LEU* 2.9 39.7 + - - +
210A CYS* 1.3 74.9 - - - +
212A LYS* 1.3 62.8 + - - +
213A GLU* 3.9 22.4 + - - +
126B GLU* 4.4 4.5 + - - +
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Residues in contact with LYS 212 (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 PRO* 4.5 19.9 - - + +
98A TRP* 3.5 40.1 - - + -
104A LYS* 3.4 3.1 - - - -
105A CYS* 2.8 49.2 + - + +
125A LYS 3.2 14.4 + - - -
126A GLU* 3.1 29.1 + - - +
127A SER* 4.1 0.2 - - - -
211A GLN* 1.3 81.0 - - - +
213A GLU* 1.3 65.3 + - - +
126B GLU* 3.5 17.9 - - - +
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Residues in contact with GLU 213 (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 GLU 3.9 4.9 - - - +
104A LYS* 4.6 14.0 - - + +
131A LEU* 5.2 5.2 - - - +
211A GLN* 3.9 21.9 + - - +
212A LYS* 1.3 75.2 - - - +
214A LEU* 1.3 67.0 + - - +
126B GLU* 2.9 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