Contacts of the strand formed by residues 230 - 238 (chain D) in PDB entry 6E7P
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 ASN 230 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166D CYS 3.9 0.5 - - - +
167D GLN 3.7 0.3 - - - -
168D ARG* 3.1 48.3 + - - +
228D LEU* 4.2 1.7 - - - +
229D VAL* 1.3 90.0 - - - +
231D VAL* 1.3 67.5 + - - +
232D THR* 4.2 13.6 + - + +
261D THR* 5.2 4.5 - - + +
262D PHE 3.4 15.7 - - - +
263D ASP* 4.0 21.2 + - + +
265D LYS* 6.2 0.6 - - - +
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Residues in contact with VAL 231 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125D LEU* 5.8 1.8 - - + -
129D ILE* 4.5 15.5 - - + -
165D LEU* 5.1 11.9 - - + -
166D CYS 3.6 13.0 - - - +
167D GLN* 4.5 13.7 - - + -
223D LEU* 4.7 11.9 - - + -
228D LEU* 3.8 28.9 - - + -
230D ASN* 1.3 76.9 - - - +
232D THR* 1.3 68.9 + - - +
233D ILE* 5.3 2.0 - - + -
262D PHE* 2.8 58.5 + - + +
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Residues in contact with THR 232 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164D ALA 3.7 0.8 - - - +
165D LEU* 3.4 1.4 - - - +
166D CYS* 3.1 36.7 + - - +
168D ARG* 4.0 22.4 + - - +
230D ASN* 4.6 19.3 - - - +
231D VAL* 1.3 78.5 - - - +
233D ILE* 1.3 68.1 + - - +
234D HIS* 3.4 17.7 + - - +
259D LEU* 3.9 20.9 - - + -
260D ILE 3.5 4.9 - - - -
261D THR* 4.9 11.0 - - + -
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Residues in contact with ILE 233 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129D ILE* 4.6 14.4 - - + +
132D ALA* 4.3 22.0 - - + +
133D VAL* 4.8 6.5 - - + -
163D LEU* 3.7 25.1 - - + -
164D ALA 3.6 4.3 - - - +
165D LEU* 3.8 20.0 - - + -
231D VAL* 5.3 2.2 - - + -
232D THR* 1.3 82.5 - - - +
234D HIS* 1.3 62.4 + - - +
235D PHE* 4.3 10.8 - - + -
258D VAL 3.5 1.4 - - - +
259D LEU* 3.4 8.0 - - - +
260D ILE* 3.0 44.9 + - + +
262D PHE* 4.2 22.9 - - + -
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Residues in contact with HIS 234 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156D PRO* 4.7 22.9 - - + +
157D TRP* 3.4 25.6 + + + +
162D GLY 3.3 10.4 - - - +
163D LEU* 3.4 1.7 - - - +
164D ALA* 3.4 28.2 + - + +
166D CYS* 5.3 5.4 - - - -
168D ARG* 5.1 6.1 + - - -
232D THR* 3.4 26.5 + - - +
233D ILE* 1.3 75.7 - - - +
235D PHE* 1.3 65.1 + - - +
257D SER* 5.9 0.6 + - - -
258D VAL 3.6 6.1 + - - +
259D LEU* 3.5 29.6 - - + +
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Residues in contact with PHE 235 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105D PHE* 3.4 31.6 - + - -
132D ALA 5.8 2.7 - - - -
136D TYR* 3.7 34.8 - + + +
157D TRP* 4.0 4.2 - - - -
162D GLY 3.5 15.0 - - - +
163D LEU* 3.6 23.8 - - + -
233D ILE* 4.3 6.1 - - + -
234D HIS* 1.3 77.3 - - - +
236D ARG* 1.3 70.4 + - - +
237D LEU* 3.7 27.1 - - + -
257D SER* 3.7 1.4 + - - -
258D VAL* 2.9 64.0 + - + +
260D ILE* 4.5 12.6 - - + -
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Residues in contact with ARG 236 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136D TYR* 5.0 2.4 + - - -
149D TYR* 4.3 0.5 - - - -
150D VAL* 3.7 51.2 + - + +
152D GLY* 3.3 28.5 - - - -
153D GLY 3.7 6.1 - - - +
154D GLY* 3.9 7.7 - - - +
157D TRP* 3.3 50.7 - - + -
235D PHE* 1.3 83.8 - - - +
237D LEU* 1.3 74.3 + - - +
255D THR* 4.7 11.0 - - + -
256D PHE 3.3 15.5 - - - +
257D SER* 4.2 13.5 - - - +
258D VAL* 5.7 0.4 - - - -
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Residues in contact with LEU 237 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D PHE* 4.1 25.1 - - + -
105D PHE* 5.1 2.2 - - + -
136D TYR* 4.8 1.6 - - + -
139D LEU* 4.2 24.0 - - + -
147D TYR* 4.1 18.6 - - + -
148D ALA 3.4 24.0 - - - +
149D TYR* 4.2 12.8 - - + -
235D PHE* 3.7 28.5 - - + -
236D ARG* 1.3 82.1 - - - +
238D LYS* 1.3 65.1 + - - +
255D THR* 3.4 2.1 - - - -
256D PHE* 2.8 43.9 + - + +
258D VAL* 5.3 1.6 - - + -
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Residues in contact with LYS 238 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177C PRO* 4.4 13.0 - - + +
178C ALA* 5.0 18.4 - - + +
147D TYR* 3.9 4.2 - - - +
148D ALA* 3.2 31.5 + - + +
149D TYR 4.9 8.6 + - - +
150D VAL* 5.6 14.7 - - + +
237D LEU* 1.3 75.8 - - - +
239D THR* 1.3 64.3 - - - +
253D CYS 6.0 0.2 + - - -
254D TYR 3.4 6.3 - - - +
255D THR* 3.1 31.8 + - + +
282D GLN* 3.7 19.4 - - - +
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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