Contacts of the strand formed by residues 199 - 204 (chain E) in PDB entry 6XOX
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 ALA 199 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146E SER* 5.7 0.4 - - - -
147E CYS 4.0 3.4 - - - -
148E ARG* 5.2 7.0 - - - +
195E GLY* 3.1 5.5 - - - -
196E SER* 2.9 42.6 + - - +
197E GLY 4.3 1.8 - - - +
198E THR* 1.3 81.5 - - - +
200E PHE* 1.3 62.5 + - - +
201E THR* 5.1 1.1 - - - -
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Residues in contact with PHE 200 (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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128E MET* 4.8 1.6 - - + -
146E SER* 3.0 10.2 + - - -
147E CYS* 2.9 49.6 + - + +
148E ARG 4.8 0.7 - - - -
149E SER* 4.0 7.9 - - - -
153E LEU* 3.6 37.2 - - + -
160E THR* 3.5 22.9 - - + -
162E LEU* 3.5 32.5 - - + -
164E TRP* 4.2 1.8 - - + +
180E MET* 3.7 15.9 - - + -
194E SER 3.7 2.7 - - - +
195E GLY* 4.6 0.4 - - - -
196E SER 3.1 21.8 - - - -
197E GLY* 4.1 0.4 - - - -
198E THR* 3.5 25.8 - - - -
199E ALA* 1.3 75.6 - - - +
201E THR* 1.3 65.2 + - - +
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Residues in contact with THR 201 (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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144E SER* 3.3 26.5 - - - +
145E ILE 3.7 5.6 - - - +
146E SER* 4.4 6.5 + - - +
164E TRP* 3.9 5.7 + - - -
193E GLY* 3.4 4.2 - - - -
194E SER* 2.9 50.6 + - - +
195E GLY* 5.3 2.1 - - - -
199E ALA 5.1 0.9 + - - -
200E PHE* 1.3 79.7 + - - +
202E LEU* 1.3 59.9 + - - +
203E THR* 3.3 15.0 + - - +
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Residues in contact with LEU 202 (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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143E VAL 4.0 0.6 - - - +
144E SER* 3.3 1.7 + - - -
145E ILE* 2.9 48.9 + - + +
164E TRP* 3.5 42.3 - - + -
176E LEU* 4.1 15.7 - - + -
177E ILE* 3.7 20.4 - - + -
191E PHE* 4.4 14.1 - - + -
192E SER 3.3 21.8 - - - +
193E GLY* 4.7 0.2 - - - -
201E THR* 1.3 70.4 - - - +
203E THR* 1.3 68.8 + - - +
204E ILE* 4.3 7.0 - - + -
215E TYR* 3.8 24.2 - - + -
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Residues in contact with THR 203 (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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142E SER* 4.7 9.0 - - - -
143E VAL 3.6 3.1 - - - +
144E SER* 3.4 15.1 + - - -
190E ARG 3.5 1.2 - - - +
192E SER* 2.9 49.4 + - - -
194E SER* 6.0 0.9 - - - -
201E THR* 3.3 18.5 + - - +
202E LEU* 1.3 78.2 + - - +
204E ILE* 1.3 63.6 + - - +
205E SER* 3.4 21.8 + - - +
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Residues in contact with ILE 204 (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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141E GLU 3.3 4.0 - - - +
142E SER* 3.1 2.8 - - - -
143E VAL* 2.9 50.1 + - + +
145E ILE* 5.1 2.2 - - + -
190E ARG* 3.4 32.3 - - + +
191E PHE* 3.6 24.9 - - + -
202E LEU* 4.3 13.0 - - + -
203E THR* 1.3 70.8 - - - +
205E SER* 1.3 65.5 + - - +
207E LEU* 3.7 29.0 + - + +
211E ASP* 4.4 8.1 - - - +
215E TYR* 3.6 31.0 - - + +
233E LEU* 4.7 1.8 - - + -
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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