Contacts of the strand formed by residues 322 - 330 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163B ARG* 3.6 35.3 - - - +
164B GLY 4.4 0.2 + - - -
201B LEU* 5.4 0.2 - - - +
260B ARG* 3.7 6.0 - - - +
264B LYS 2.9 11.0 + - - +
265B HIS* 3.1 26.8 + - - +
266B ALA 3.0 26.5 + - - +
312B ALA 3.3 8.5 - - - -
313B LYS* 4.0 11.7 - - - -
321B GLY* 1.3 75.1 - - - -
323B LEU* 1.3 59.3 + - - +
324B THR* 4.4 1.9 + - - -
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Residues in contact with LEU 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164B GLY* 3.1 20.4 - - - +
253B ALA* 4.3 11.2 - - + +
256B GLY* 3.6 32.3 - - - +
257B GLU* 4.1 17.5 - - + -
260B ARG* 3.5 14.6 - - + +
266B ALA* 3.5 19.7 - - + +
268B ILE* 4.2 23.8 - - + -
270B TYR* 5.3 1.3 - - - +
310B ARG* 3.2 34.8 - - + +
311B ALA* 3.7 5.2 - - - +
312B ALA 2.9 15.4 + - - +
322B SER* 1.3 73.0 - - - +
324B THR* 1.3 63.0 + - - +
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Residues in contact with THR 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148B VAL* 4.3 9.2 - - + +
161B ILE* 4.4 9.6 - - + -
162B GLY 3.6 17.3 - - - +
163B ARG* 3.4 8.7 - - - +
164B GLY 2.7 21.7 + - - -
165B GLN 3.3 17.9 - - - +
201B LEU* 5.2 2.2 - - - +
266B ALA 3.1 13.0 + - - -
267B LEU* 3.5 20.4 - - + +
268B ILE* 2.6 36.3 + - - +
322B SER* 4.4 2.4 + - - -
323B LEU* 1.3 74.2 - - - +
325B ALA* 1.3 60.6 + - - +
326B LEU* 4.6 0.9 - - + -
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Residues in contact with ALA 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165B GLN 3.2 7.7 + - - +
166B ARG* 3.2 6.6 - - + -
167B GLU 3.0 25.5 + - - -
268B ILE* 3.4 17.7 - - + -
270B TYR* 4.1 4.7 - - + -
308B LEU* 3.9 28.3 - - + -
311B ALA* 4.0 16.0 - - + +
324B THR* 1.3 73.2 - - - +
326B LEU* 1.3 65.1 + - - +
327B PRO* 3.4 2.0 - - + +
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Residues in contact with LEU 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148B VAL* 5.9 0.2 - - + -
161B ILE* 4.1 29.2 - - + -
167B GLU* 3.2 27.1 - - + +
169B ILE* 4.4 22.7 - - + -
180B VAL* 5.6 1.8 - - + -
181B ALA* 4.6 4.0 - - - -
184B THR* 4.4 22.0 - - + +
267B LEU* 3.7 26.9 - - + -
268B ILE 2.8 10.1 + - - -
269B VAL* 3.6 24.2 - - + +
270B TYR* 3.4 15.3 + - - -
324B THR* 4.6 1.8 - - + -
325B ALA* 1.3 83.3 - - - +
327B PRO* 1.3 65.0 - - - +
328B VAL* 4.2 2.3 - - - +
352B ILE* 6.2 0.9 - - + -
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Residues in contact with PRO 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166B ARG* 5.0 0.4 - - - -
167B GLU 3.4 10.5 - - - +
168B LEU* 3.3 13.2 - - + +
169B ILE* 2.9 25.8 + - - +
270B TYR* 3.7 11.9 - - + +
273B LEU* 3.4 29.2 - - + -
308B LEU* 3.8 23.6 - - + -
325B ALA* 3.4 10.8 - - + +
326B LEU* 1.3 88.4 - - - +
328B VAL* 1.3 59.9 + - - +
344B VAL* 4.4 0.2 - - + -
348B THR* 3.8 21.8 - - + -
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Residues in contact with VAL 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169B ILE* 3.2 19.5 - - + +
177B LYS* 3.5 46.4 - - + +
181B ALA* 5.3 1.1 - - + -
269B VAL* 4.5 6.3 - - + -
270B TYR 2.8 19.0 + - - +
271B ASP* 3.3 32.5 - - + +
272B ASP* 2.9 26.2 - - + +
273B LEU* 3.0 12.4 + - - +
326B LEU 4.2 6.5 - - - +
327B PRO* 1.3 76.5 - - - +
329B ILE* 1.3 65.4 + - - +
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Residues in contact with ILE 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168B LEU* 3.6 20.8 - - + +
169B ILE 3.0 6.8 + - - +
170B ILE* 3.5 24.2 - - + -
171B GLY 3.4 22.3 + - - +
177B LYS* 3.5 5.9 - - - +
273B LEU* 3.9 10.8 - - + -
274B SER* 3.4 28.5 - - - +
328B VAL* 1.3 78.1 - - - +
330B GLU* 1.3 71.6 + - - +
340B ILE* 3.8 26.9 - - + +
341B PRO* 4.1 19.3 - - + -
344B VAL* 4.2 19.1 - - + -
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Residues in contact with GLU 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171B GLY 3.3 3.1 - - - -
173B ARG* 3.9 32.1 - - - +
177B LYS* 3.9 17.6 + - - +
272B ASP* 4.0 10.5 + - - +
274B SER* 2.7 24.1 + - - +
275B LYS* 4.3 18.8 + - - -
329B ILE* 1.3 79.6 - - - +
331B THR* 1.3 74.7 + - - +
332B GLN* 3.6 24.6 + - - +
341B PRO* 5.1 2.1 - - - +
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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