Contacts of the strand formed by residues 207 - 213 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109E SER* 3.2 27.6 + - - +
110E HIS* 3.9 19.6 + - - -
111E THR 3.5 16.4 - - - +
112E VAL* 4.0 17.1 - - + +
150E ILE* 3.6 43.0 - - - +
151E LEU 3.5 4.7 + - - +
152E PHE* 3.2 23.8 - - + -
153E TRP* 2.8 21.3 + - - -
206E ILE* 1.3 81.9 - - - +
208E TRP* 1.3 62.1 + - - +
91H LEU* 3.8 16.2 - - - +
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Residues in contact with TRP 208 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107E LEU* 3.8 1.1 - - - +
108E PHE* 3.8 0.2 - - - -
109E SER* 2.9 55.8 + - - -
111E THR* 3.1 39.9 - - - -
112E VAL 3.7 1.1 - - - -
113E ASN* 3.3 31.0 - - + -
118E SER* 3.5 34.5 - - - +
121E ASP* 2.9 47.3 + - + +
122E CYS* 3.8 8.5 - - - -
129E LEU* 4.1 2.2 - - + -
152E PHE* 3.8 2.0 - - - +
153E TRP* 3.6 17.0 - - + +
206E ILE 3.7 4.0 - - - -
207E ARG* 1.3 80.2 - - - +
209E ILE* 1.3 64.5 + - - +
210E CYS* 3.7 22.2 - - - -
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Residues in contact with ILE 209 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106E LEU* 4.4 13.5 - - + -
107E LEU 3.3 8.3 - - - +
108E PHE* 3.6 38.8 - - + -
122E CYS* 4.3 0.4 - - - -
129E LEU* 3.6 10.0 - - - +
130E LEU* 2.9 55.4 + - + +
141E THR* 4.7 0.7 - - + -
145E ILE* 5.3 0.2 - - + -
152E PHE* 3.5 25.6 - - + -
153E TRP 3.2 8.1 + - - +
154E ILE* 4.9 0.4 - - + -
192E ILE* 4.1 22.0 - - + -
208E TRP* 1.3 79.0 - - - +
210E CYS* 1.3 75.1 + - - +
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Residues in contact with CYS 210 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98E TRP* 3.7 12.1 - - + -
106E LEU* 3.3 5.5 - - - -
107E LEU* 2.9 37.2 + - + +
121E ASP* 3.8 6.1 - - - -
122E CYS* 2.1 49.6 - - - -
125E LYS* 4.8 5.6 - - - -
127E SER* 3.3 13.5 - - - +
128E SER 3.2 5.6 - - - -
130E LEU 4.8 0.2 - - - -
208E TRP* 3.7 17.0 - - - -
209E ILE* 1.3 78.5 - - - +
211E GLN* 1.3 61.3 + - - +
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Residues in contact with GLN 211 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98E TRP* 4.0 1.8 - - - -
104E LYS* 2.8 42.8 + - + +
105E CYS 3.2 9.4 - - - +
106E LEU* 3.9 12.3 - - + -
127E SER* 3.2 6.8 - - - -
128E SER* 2.8 50.9 + - - +
129E LEU 4.0 3.1 - - - +
130E LEU* 3.6 5.8 - - + +
131E LEU* 2.9 42.2 + - - +
210E CYS* 1.3 75.4 - - - +
212E LYS* 1.3 63.4 + - - +
213E GLU* 4.0 20.8 + - - +
126F GLU* 4.3 3.9 + - - +
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Residues in contact with LYS 212 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95E PRO* 4.7 18.4 - - + -
98E TRP* 3.6 33.2 - - + -
104E LYS* 3.3 3.9 - - - +
105E CYS* 2.8 45.4 + - + +
125E LYS 3.0 19.8 + - - -
126E GLU* 2.9 35.8 + - - +
127E SER* 3.9 2.0 - - - -
211E GLN* 1.3 81.2 - - - +
213E GLU* 1.3 63.9 + - - +
214E LEU 3.8 0.2 + - - -
126F GLU* 3.5 13.2 + - - +
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Residues in contact with GLU 213 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103E GLU 3.7 8.3 - - - +
104E LYS* 4.5 11.4 - - + +
131E LEU* 5.2 4.3 - - - +
211E GLN* 4.0 23.3 + - - +
212E LYS* 1.3 74.2 - - - +
214E LEU* 1.3 66.7 + - - +
126F GLU* 2.9 22.5 + - - +
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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