Contacts of the strand formed by residues 197 - 201 (chain F) 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 VAL 197 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138F LEU* 3.9 31.0 - - + -
142F GLN* 4.4 0.4 - - - +
178F LEU* 3.4 33.9 - - + +
179F GLU 4.1 2.6 + - - +
180F ILE* 3.7 18.3 - - + -
181F ARG* 2.9 30.4 + - - +
190F ILE* 3.4 31.2 - - + -
191F SER 3.3 6.5 - - - +
192F ILE* 4.2 6.7 - - + -
196F SER* 1.3 81.5 - - - +
198F TYR* 1.3 58.9 + - - +
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Residues in contact with TYR 198 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151F LEU* 3.5 30.1 - - + -
180F ILE* 4.8 0.2 - - - -
181F ARG* 3.4 50.9 + - + -
190F ILE* 3.7 4.5 - - - -
191F SER* 2.8 41.1 + - - +
193F SER* 4.4 4.7 - - - -
196F SER* 3.7 25.4 + - - -
197F VAL* 1.3 74.0 - - - +
199F SER* 1.3 61.5 + - - +
200F GLU* 3.6 20.1 + - - +
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Residues in contact with SER 199 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165F TRP* 4.0 2.5 - - - -
180F ILE* 4.1 4.6 - - - +
181F ARG 2.9 17.1 + - - +
182F GLY* 4.1 5.2 - - - -
183F ASP* 2.5 38.5 + - - +
188F SER* 3.6 13.7 + - - -
189F CYS 3.4 6.7 - - - -
190F ILE* 3.8 17.2 - - - +
198F TYR* 1.3 70.9 - - - +
200F GLU* 1.3 73.7 + - - +
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Residues in contact with GLU 200 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151F LEU* 3.7 13.8 - - + +
153F TRP* 3.7 16.6 - - + -
188F SER* 3.6 3.5 - - - -
189F CYS 2.9 31.3 + - - +
191F SER* 3.9 18.4 - - - +
198F TYR* 3.6 19.7 + - - +
199F SER* 1.3 84.6 + - - +
201F TYR* 1.3 65.0 + - - +
204F THR* 4.1 7.8 + - + +
206F ILE* 3.9 14.4 - - + -
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Residues in contact with TYR 201 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153F TRP* 3.2 3.5 - - - -
185F LYS* 3.1 41.3 + - - -
186F GLU 5.3 2.2 - - - -
187F ASN* 3.4 17.0 - - + +
188F SER* 4.7 4.7 - - - -
200F GLU* 1.3 74.5 + - - +
202F CYS* 1.3 59.4 + - - +
203F SER* 4.0 13.5 - - - +
204F THR* 2.6 40.6 + - - +
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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