Contacts of the strand formed by residues 317 - 326 (chain A) in PDB entry 2OLO
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 ARG 317 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A GLU* 4.7 17.5 + - - +
229A ALA* 3.3 1.7 - - - +
230A ALA* 2.8 36.9 + - + +
272A ARG* 5.5 11.1 - - - +
315A PRO 3.3 1.9 - - - -
316A VAL* 1.3 91.3 - - + +
318A THR* 1.3 75.3 + - - +
319A SER* 3.3 33.4 + - - -
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Residues in contact with THR 318 (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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228A ILE 3.3 9.0 - - - -
229A ALA* 4.0 1.1 - - + -
292A ALA* 3.8 12.9 + - - +
297A MET* 3.9 29.7 - - + +
315A PRO* 3.8 26.7 - - + -
317A ARG* 1.3 88.2 + - - +
319A SER* 1.3 66.4 + - - +
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Residues in contact with SER 319 (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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46A SER* 5.9 2.6 - - - -
228A ILE* 2.9 40.5 + - - +
290A GLY 4.5 8.7 - - - -
292A ALA* 3.6 8.1 - - - +
317A ARG* 3.3 36.9 + - - -
318A THR* 1.3 77.3 - - - +
320A THR* 1.3 77.0 + - - +
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Residues in contact with THR 320 (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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41A GLU 4.5 11.4 - - - +
42A ASN 6.2 0.2 - - - -
46A SER* 4.6 4.7 + - - -
225A GLU* 2.6 40.1 + - + +
226A MET 3.0 12.6 - - - +
227A ALA* 4.5 2.0 - - + -
228A ILE* 4.7 2.5 - - - +
290A GLY* 3.3 14.5 + - - -
291A VAL 3.7 5.8 - - - +
292A ALA* 3.5 28.7 - - - +
319A SER* 1.3 88.1 + - - +
321A CYS* 1.3 62.6 + - - +
322A LEU* 5.3 1.2 - - - +
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Residues in contact with CYS 321 (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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43A GLY 3.9 6.3 - - - +
44A GLY 3.2 22.9 - - - -
46A SER* 3.5 15.0 - - - +
50A ARG* 3.5 7.6 - - - -
224A TYR 3.6 0.2 - - - +
225A GLU* 3.7 0.5 - - - -
226A MET* 2.8 33.7 + - - +
228A ILE* 5.0 3.8 - - + -
320A THR* 1.3 75.3 - - - +
322A LEU* 1.3 66.4 + - - +
1001A FAD 1.7 73.6 - - + -
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Residues in contact with LEU 322 (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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42A ASN 3.9 19.1 - - - +
43A GLY* 3.2 18.9 + - - +
44A GLY* 3.2 20.5 - - - +
206A PRO* 4.2 24.2 - - + -
207A TYR* 5.6 4.0 - - + +
223A VAL* 4.5 9.4 - - + -
224A TYR 3.4 2.2 - - - +
225A GLU* 3.8 32.5 - - + +
282A LEU* 4.2 7.0 - - + -
285A PRO* 4.7 10.1 - - + +
288A ALA* 3.9 22.7 - - + -
320A THR* 5.3 1.1 - - - +
321A CYS* 1.3 74.8 - - - +
323A ALA* 1.3 62.8 + - - +
324A VAL* 4.2 6.0 + - + +
1001A FAD 3.4 7.7 - - - +
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Residues in contact with ALA 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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222A SER 3.7 0.6 - - - +
223A VAL* 3.2 6.2 - - - +
224A TYR* 2.9 40.5 + - + +
226A MET* 3.7 28.3 - - + -
321A CYS 3.9 0.6 + - - -
322A LEU* 1.3 74.6 - - - +
324A VAL* 1.3 62.5 + - - +
325A LEU* 4.1 12.3 - - + -
355A TRP* 4.0 18.8 - - + -
1001A FAD 4.4 4.3 - - + -
3002A MPD 5.1 0.2 - - + -
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Residues in contact with VAL 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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44A GLY* 6.1 1.1 - - - -
205A GLY* 4.1 7.6 - - - +
206A PRO* 3.6 39.5 - - + -
221A TYR* 3.5 35.0 - - + -
222A SER 3.4 3.4 - - - +
223A VAL* 4.5 0.9 - - + +
322A LEU 4.2 7.2 + - - +
323A ALA* 1.3 80.8 - - - +
325A LEU* 1.3 61.2 + - - +
352A GLY 3.6 18.6 - - - +
353A ALA* 4.1 2.9 - - - -
354A GLY 2.9 33.0 + - - +
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Residues in contact with LEU 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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221A TYR* 3.1 5.4 - - - -
222A SER* 2.7 41.6 + - - +
224A TYR* 4.4 8.7 - - + -
323A ALA* 4.5 7.0 - - + -
324A VAL* 1.3 88.4 - - - +
326A PRO* 1.3 76.2 - - + +
332A GLN 5.3 0.7 - - - +
353A ALA* 3.9 1.1 - - - -
354A GLY* 3.9 3.8 - - - +
355A TRP* 3.8 38.8 - - + +
3001A MPD 4.2 15.5 - - + -
3002A MPD 4.1 45.5 - - + -
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Residues in contact with PRO 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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220A ALA 3.6 7.4 - - - +
221A TYR* 4.0 2.2 - - + -
222A SER* 5.6 0.2 - - - -
224A TYR* 5.6 0.7 + - - -
325A LEU* 1.3 93.0 - - + +
327A THR* 1.3 65.8 + - - +
328A ASP* 3.3 7.0 + - + +
329A PRO* 4.5 2.1 - - - +
331A ARG* 3.4 40.1 - - + +
332A GLN* 3.5 29.2 - - - +
333A PHE 3.9 2.5 - - - +
334A PHE* 3.8 22.4 - - + -
353A ALA* 3.8 10.3 - - + -
354A GLY 4.5 0.9 - - - +
3002A MPD 6.0 1.9 - - - +
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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