Contacts of the strand formed by residues 188 - 192 (chain C) 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 SER 188 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158C PHE* 3.1 26.7 + - - +
165C TRP* 3.8 13.5 - - - -
183C ASP 3.6 2.6 + - - -
185C LYS* 3.1 39.3 + - - +
186C GLU 4.1 0.2 + - - -
187C ASN* 1.3 77.2 - - - +
189C CYS* 1.3 59.3 + - - +
199C SER* 3.4 22.8 + - - -
200C GLU 3.4 8.0 + - - -
201C TYR* 4.9 2.6 - - - -
202C CYS* 3.3 10.2 - - - -
502C NAG 5.5 0.5 - - - +
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Residues in contact with CYS 189 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115C TRP* 3.4 30.1 - - + +
153C TRP* 3.3 24.7 - - + -
156C LEU 3.7 4.9 - - - -
157C ASN* 3.6 17.3 - - - +
165C TRP* 4.5 0.2 - - - -
188C SER* 1.3 71.1 - - - +
190C ILE* 1.3 66.4 + - - +
199C SER* 3.4 4.0 - - - -
200C GLU 2.8 29.1 + - - +
202C CYS* 2.0 45.8 - - - -
502C NAG 3.9 1.8 - - - -
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Residues in contact with ILE 190 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153C TRP* 3.4 8.1 - - - -
154C ILE* 3.0 46.3 + - + +
156C LEU* 2.9 40.7 + - + +
165C TRP* 3.5 40.4 - - + -
180C ILE* 3.8 26.0 - - + -
189C CYS* 1.3 76.8 - - - +
191C SER* 1.3 63.5 + - - +
197C VAL* 3.5 26.7 - - + -
198C TYR 3.6 0.7 - - - +
199C SER* 3.9 5.8 - - - -
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Residues in contact with SER 191 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151C LEU* 3.7 20.6 - - - +
152C PHE 3.0 17.3 - - - -
153C TRP* 4.0 4.5 - - - -
154C ILE 4.5 0.4 - - - +
189C CYS 4.0 0.6 + - - -
190C ILE* 1.3 73.3 - - - +
192C ILE* 1.3 63.7 + - - +
197C VAL* 3.4 8.5 - - - +
198C TYR* 2.8 43.5 + - - +
200C GLU* 4.0 4.0 - - - +
206C ILE* 3.5 26.5 - - - -
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Residues in contact with ILE 192 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130C LEU* 4.2 15.0 - - + -
132C ILE* 4.4 6.3 - - + -
138C LEU* 4.2 15.5 - - + -
141C THR* 4.3 12.6 - - + -
142C GLN* 4.8 4.7 - - + -
145C ILE* 4.6 11.0 - - + -
151C LEU* 3.4 6.8 - - - -
152C PHE* 2.8 39.6 + - + +
154C ILE* 4.0 25.8 - - + -
191C SER* 1.3 79.4 - - - +
193C SER* 1.3 63.4 + - - +
196C SER 3.4 7.6 - - - +
197C VAL* 4.0 18.8 - - + -
198C TYR* 4.9 0.7 - - - +
209C ILE* 4.0 25.1 - - + -
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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