Contacts of the strand formed by residues 322 - 331 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163A ARG* 3.5 14.6 - - - +
164A GLY 4.2 11.2 + - - -
260A ARG* 3.4 14.3 - - - +
264A LYS 2.9 6.6 + - - +
265A HIS* 2.7 29.8 + - - +
266A ALA* 3.2 21.1 + - - +
312A ALA 3.2 12.6 - - - -
313A LYS* 4.0 18.2 - - - -
321A GLY* 1.3 75.1 - - - -
323A LEU* 1.3 58.3 + - - +
324A THR* 4.6 1.8 + - - -
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Residues in contact with LEU 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A GLY* 3.2 13.2 - - - -
253A ALA* 4.4 7.6 - - - +
256A GLY* 3.7 32.3 - - - +
257A GLU* 4.4 15.7 - - + +
260A ARG* 3.4 16.4 - - + +
266A ALA* 3.4 18.4 - - + +
268A ILE* 4.0 26.7 - - + -
270A TYR* 5.0 6.1 - - - +
310A ARG* 3.7 21.8 - - + +
311A ALA* 3.6 15.3 - - + +
312A ALA 2.9 24.1 + - - -
322A SER* 1.3 74.5 - - - +
324A THR* 1.3 62.1 + - - +
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Residues in contact with THR 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A VAL* 3.9 19.5 - - + +
161A ILE* 4.1 11.9 - - + -
162A GLY 4.0 7.2 - - - +
163A ARG* 3.3 10.4 - - - +
164A GLY 2.9 19.5 + - - +
165A GLN 3.5 13.9 - - - +
201A LEU* 4.9 2.9 - - - +
266A ALA 3.0 11.6 + - - -
267A LEU* 3.4 23.2 - - + +
268A ILE* 2.7 34.2 + - - +
311A ALA* 4.4 0.4 - - - -
322A SER* 4.6 1.7 + - - -
323A LEU* 1.3 73.3 - - - +
325A ALA* 1.3 61.3 + - - +
326A LEU* 4.3 0.7 - - + -
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Residues in contact with ALA 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A GLN 3.0 8.8 + - - +
166A ARG* 3.3 13.1 - - + -
167A GLU 3.0 26.0 + - - -
268A ILE* 3.3 17.3 - - + +
270A TYR* 4.1 17.0 - - + +
308A LEU* 4.3 7.2 - - + -
311A ALA* 3.9 18.0 - - + +
324A THR* 1.3 74.3 - - - +
326A LEU* 1.3 64.7 + - - +
327A PRO* 3.4 2.1 - - + +
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Residues in contact with LEU 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A ILE* 3.8 32.3 - - + -
167A GLU* 3.4 19.3 - - + +
169A ILE* 4.1 19.5 - - + -
180A VAL* 5.0 1.1 - - + +
181A ALA* 4.1 27.4 - - + -
184A THR* 4.3 16.8 - - + +
267A LEU* 3.8 25.8 - - + -
268A ILE 2.8 11.5 + - - +
269A VAL* 3.4 17.6 - - + +
270A TYR 3.3 15.9 + - - -
324A THR* 5.4 0.2 - - + -
325A ALA* 1.3 74.8 - - - +
327A PRO* 1.4 68.1 - - - +
328A VAL* 4.1 0.9 - - - +
352A ILE* 5.5 0.7 - - + -
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Residues in contact with PRO 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A ARG* 4.9 0.4 - - + -
167A GLU 3.3 18.6 - - - +
168A LEU* 3.5 11.8 - - + +
169A ILE* 2.9 26.5 + - - +
270A TYR* 3.8 12.1 - - + +
273A LEU* 4.1 19.3 - - + -
308A LEU* 3.8 30.1 - - + -
325A ALA* 3.4 10.8 - - + +
326A LEU* 1.4 84.8 - - - +
328A VAL* 1.3 60.6 + - - +
344A VAL* 4.5 2.5 - - + -
348A THR* 3.9 20.4 - - + -
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Residues in contact with VAL 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A ILE* 3.3 22.9 - - + +
177A LYS* 3.7 40.2 - - + +
181A ALA* 5.5 0.4 - - + -
269A VAL* 4.4 6.5 - - + -
270A TYR 2.7 20.4 + - - +
271A ASP* 3.8 25.1 - - + +
272A ASP* 3.0 16.2 - - + +
273A LEU* 2.8 30.8 + - - +
326A LEU 4.1 6.7 - - - +
327A PRO* 1.3 78.6 - - - +
329A ILE* 1.3 67.0 + - - +
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Residues in contact with ILE 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A LEU* 3.5 24.2 - - + -
169A ILE 3.0 6.3 + - - -
170A ILE* 3.5 23.4 - - + -
171A GLY 3.3 23.7 + - - +
177A LYS* 3.5 4.2 - - - +
273A LEU* 3.7 20.0 - - + -
274A SER* 3.6 13.2 - - - +
327A PRO 5.4 0.2 - - - -
328A VAL* 1.3 80.1 - - - +
330A GLU* 1.3 71.1 + - - +
340A ILE* 4.0 10.8 - - + +
341A PRO* 4.0 18.4 - - + -
344A VAL* 3.5 34.8 - - + -
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Residues in contact with GLU 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A GLY 3.3 3.4 - - - +
173A ARG* 3.4 38.1 - - - +
177A LYS* 4.0 11.1 + - - +
272A ASP* 4.7 8.3 + - - +
274A SER* 2.8 28.2 + - - +
275A LYS* 4.6 13.9 + - - +
329A ILE* 1.3 78.6 - - - +
331A THR* 1.3 70.6 + - - +
332A GLN* 3.4 23.4 + - - +
341A PRO* 4.6 5.0 - - - +
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Residues in contact with THR 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A ILE* 3.5 36.6 - - + -
171A GLY* 2.9 19.2 + - - -
172A ASP* 2.6 37.2 + - - +
173A ARG 4.3 1.0 + - - -
330A GLU* 1.3 79.9 - - - +
332A GLN* 1.3 72.5 + - - +
334A GLY* 4.0 5.1 - - - -
335A ASP 4.2 14.6 - - - +
336A VAL* 4.6 11.2 - - + -
341A PRO* 4.5 15.9 - - + -
353A PHE* 5.1 3.1 - - + -
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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