Contacts of the strand formed by residues 186 - 190 (chain E) in PDB entry 6VMS
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 GLN 186 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109E ASP 5.5 1.9 - - - +
110E PHE* 4.9 17.9 - - - +
111E TRP* 5.1 5.4 + - - +
177E PHE* 3.3 11.7 - - - -
178E LEU* 2.8 36.0 + - + +
180E ARG* 4.2 21.8 - - - +
183E GLN* 5.6 4.5 + - - +
184E SER* 3.1 34.5 + - - +
185E PRO* 1.3 78.9 + - - +
187E LEU* 1.3 66.5 + - - +
188E LEU* 3.5 0.4 + - - -
199E VAL* 6.5 0.4 - - + -
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Residues in contact with LEU 187 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107E PRO 4.1 0.2 - - - +
108E PHE 3.2 24.2 - - - +
109E ASP* 3.7 15.7 + - - +
110E PHE* 6.1 0.2 - - - +
111E TRP* 5.0 2.2 - - - -
175E TYR* 3.9 19.1 - - + -
176E TRP 3.7 11.9 - - - +
177E PHE* 3.6 28.2 - - + -
186E GLN* 1.3 77.3 + - - +
188E LEU* 1.3 57.8 + - - +
189E ILE 3.9 10.5 - - - +
190E TYR* 3.1 44.4 - - + -
196E ALA* 3.1 25.5 - - + +
199E VAL* 4.1 5.9 - - - +
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Residues in contact with LEU 188 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176E TRP* 2.8 26.0 + - + +
177E PHE* 4.5 3.6 - - - +
178E LEU* 4.8 12.8 - - + +
186E GLN* 3.5 2.6 + - - +
187E LEU* 1.3 74.5 - - - +
189E ILE* 1.3 70.0 + - + +
195E LEU* 3.8 3.8 - - - +
196E ALA* 3.1 22.2 + - - +
199E VAL* 3.6 37.2 - - + +
203E PHE* 3.7 37.5 - - + -
214E LEU* 4.1 16.4 - - + -
227E TYR* 4.0 22.7 - - + -
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Residues in contact with ILE 189 (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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174E LEU 4.9 0.2 - - - -
175E TYR* 3.6 7.1 - - - -
176E TRP* 3.4 34.4 + - + -
187E LEU* 4.0 8.9 - - - +
188E LEU* 1.3 93.2 - - + +
190E TYR* 1.3 66.1 + - - +
192E MET* 3.2 34.8 - - - +
193E SER 3.6 3.1 - - - +
194E ASN 3.2 13.7 - - - +
195E LEU* 4.1 9.9 - - + -
203E PHE* 4.4 2.9 - - + -
204E SER* 3.8 26.7 - - - +
205E GLY 4.2 0.7 - - - +
214E LEU* 3.5 32.1 - - + -
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Residues in contact with TYR 190 (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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105E SER 5.1 5.6 - - - +
106E SER* 2.2 50.1 + - - -
107E PRO* 3.8 14.8 - - + -
109E ASP* 3.8 4.9 + - - +
175E TYR* 4.3 12.8 - + + -
187E LEU* 3.1 26.2 - - + -
189E ILE 1.3 66.2 - - - -
191E ARG* 1.3 79.3 + - + +
192E MET 2.9 3.9 + - - -
193E SER 3.2 0.5 + - - -
194E ASN* 2.4 67.8 + - + +
195E LEU 3.4 20.9 - - - -
196E ALA* 3.5 17.2 - - - +
197E SER* 4.3 5.6 + - - -
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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