Contacts of the strand formed by residues 322 - 330 (chain C) in PDB entry 3OEH
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 322 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163C ARG* 3.5 35.5 - - - +
164C GLY* 4.3 0.2 - - - -
260C ARG* 3.7 12.0 + - - +
264C LYS 3.2 6.7 + - - +
265C HIS* 2.9 29.6 + - - +
266C ALA* 3.1 26.3 + - - +
312C ALA 3.3 9.6 - - - -
313C LYS* 4.4 5.6 - - - -
321C GLY* 1.3 74.4 - - - -
323C LEU* 1.3 59.9 + - - +
324C THR* 3.8 6.9 + - - -
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Residues in contact with LEU 323 (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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164C GLY* 3.6 5.5 - - - -
253C ALA* 4.0 13.9 - - - +
256C GLY* 4.1 9.0 - - - +
257C GLU* 3.8 30.3 - - + +
260C ARG* 3.9 12.6 - - + +
266C ALA* 3.5 27.8 - - + +
268C ILE* 3.6 34.5 - - + -
270C TYR* 4.9 2.9 - - - +
310C ARG* 4.2 13.0 - - + +
311C ALA* 3.3 21.4 - - + +
312C ALA 2.9 33.2 + - - +
322C SER* 1.3 73.2 - - - +
324C THR* 1.3 58.5 + - - +
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Residues in contact with THR 324 (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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148C VAL* 3.7 17.0 - - + +
161C ILE* 4.0 14.8 - - + -
162C GLY 3.6 16.4 - - - +
163C ARG* 3.4 10.0 - - - +
164C GLY 3.2 15.6 + - - +
165C GLN 3.4 16.6 - - - +
201C LEU* 4.7 0.9 - - - +
266C ALA 3.1 11.1 + - - -
267C LEU* 3.3 16.8 - - + +
268C ILE* 2.7 34.7 + - - +
322C SER* 3.8 5.4 + - - -
323C LEU* 1.3 71.0 - - - +
325C ALA* 1.3 59.4 + - - +
326C LEU* 4.8 0.7 - - + -
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Residues in contact with ALA 325 (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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165C GLN 3.0 7.9 + - - +
166C ARG* 3.4 4.7 - - + -
167C GLU 3.0 24.9 + - - -
268C ILE* 3.3 5.6 - - + -
270C TYR* 3.7 25.8 - - + -
308C LEU* 3.8 17.3 - - + -
311C ALA* 3.7 21.7 - - + +
324C THR* 1.3 73.2 - - - +
326C LEU* 1.3 66.7 + - - +
327C PRO* 3.6 1.1 - - - -
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Residues in contact with LEU 326 (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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148C VAL* 6.1 0.7 - - + -
161C ILE* 4.2 26.5 - - + -
167C GLU* 3.3 28.7 - - + +
169C ILE* 4.2 22.0 - - + -
180C VAL* 5.5 2.2 - - + +
181C ALA* 4.4 15.7 - - - -
184C THR* 4.6 14.4 - - + +
267C LEU* 3.5 26.9 - - + -
268C ILE 2.8 12.8 + - - +
269C VAL* 3.4 15.9 - - + +
270C TYR* 3.2 16.1 + - - -
324C THR* 4.8 0.9 - - + -
325C ALA* 1.3 82.4 - - - +
327C PRO* 1.3 66.8 - - - +
328C VAL* 4.3 1.6 - - - +
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Residues in contact with PRO 327 (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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166C ARG 4.8 0.2 - - - -
167C GLU 3.2 16.8 - - - +
168C LEU* 3.6 11.8 - - + +
169C ILE* 2.9 25.6 + - - -
270C TYR* 3.6 12.9 - - + +
273C LEU* 3.8 28.0 - - + -
308C LEU* 3.7 25.8 - - + -
325C ALA* 3.6 6.3 - - + +
326C LEU* 1.3 90.2 - - - +
328C VAL* 1.3 60.2 + - - +
344C VAL* 4.6 0.4 - - + -
348C THR* 3.9 19.7 - - + -
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Residues in contact with VAL 328 (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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169C ILE* 3.3 22.2 - - + +
177C LYS* 3.5 44.4 - - + +
181C ALA* 5.4 1.1 - - + -
269C VAL* 4.4 5.6 - - + -
270C TYR 2.8 15.1 + - - +
271C ASP* 3.9 25.6 - - + +
272C ASP* 3.3 18.2 - - + +
273C LEU* 2.9 27.2 + - - +
326C LEU 4.3 5.6 - - - +
327C PRO* 1.3 76.5 - - - +
329C ILE* 1.3 67.3 + - - +
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Residues in contact with ILE 329 (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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168C LEU* 3.6 23.8 - - + +
169C ILE 2.9 7.1 + - - -
170C ILE* 3.5 11.4 - - + -
171C GLY 3.3 22.3 + - - -
177C LYS* 3.3 8.3 - - - +
272C ASP* 4.8 0.4 - - - -
273C LEU* 3.6 22.4 - - + -
274C SER* 3.5 17.7 - - - +
328C VAL* 1.3 83.3 - - - +
330C GLU* 1.3 68.1 + - - +
340C ILE* 4.1 10.3 - - + -
341C PRO* 3.9 34.1 - - + -
344C VAL* 4.0 24.5 - - + -
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Residues in contact with GLU 330 (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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171C GLY 3.3 7.4 - - - +
173C ARG* 3.7 29.8 - - - +
177C LYS* 4.2 10.9 + - - -
272C ASP* 5.1 8.3 - - - +
274C SER* 2.9 27.9 + - - +
275C LYS* 3.8 22.4 + - - -
329C ILE* 1.3 80.7 - - - +
331C THR* 1.3 72.3 + - - +
332C GLN* 3.7 20.2 + - - +
341C PRO* 4.7 3.3 - - - +
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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