Contacts of the helix formed by residues 369 - 383 (chain A) in PDB entry 2O1S
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 ALA 369 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A THR* 4.8 3.8 - - + -
344A PRO* 4.2 1.2 - - - +
366A VAL* 3.6 26.1 - - + +
367A ALA 2.7 8.7 + - - -
368A ILE* 1.3 72.6 - - - +
370A GLU* 1.3 65.0 + - - +
371A GLN 3.1 3.8 + - - -
372A HIS* 3.2 3.2 + - + -
373A ALA* 3.0 20.3 + - - +
162B GLU* 3.2 42.8 - - + +
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Residues in contact with GLU 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A PRO* 3.8 22.9 - - + +
368A ILE* 4.1 9.6 - - - +
369A ALA* 1.3 73.8 - - - +
371A GLN* 1.3 63.8 + - - +
373A ALA* 3.3 5.2 + - - +
374A VAL* 3.3 17.5 + - - +
391A ILE* 3.4 28.7 - - + +
395A PHE* 3.5 24.8 - - + +
398A ARG* 3.8 18.9 + - + +
399A ALA* 3.5 15.6 - - + +
3001A TPP 2.8 47.6 + - - +
162B GLU* 4.7 0.6 + - - -
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Residues in contact with GLN 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A ALA 3.1 0.8 + - - -
370A GLU* 1.3 78.5 - - - +
372A HIS* 1.3 61.9 + - - +
374A VAL* 3.4 1.0 + - - +
375A THR* 3.3 17.4 + - - -
398A ARG* 3.1 32.7 - - + +
402A GLN* 3.4 40.1 + - - +
158B GLY 4.8 0.2 - - - -
159B MSE 3.6 28.6 - - + +
162B GLU* 3.5 12.9 + - - +
371B GLN* 3.3 38.2 - - - +
398B ARG* 3.4 25.2 - - - +
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Residues in contact with HIS 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A VAL* 3.6 19.6 - - + +
369A ALA* 3.2 4.2 + - + +
371A GLN* 1.3 73.5 - - - +
373A ALA* 1.3 59.9 + - - +
376A PHE* 2.8 47.0 + - + +
128B SER* 2.8 37.3 + - - +
131B ILE* 3.6 14.9 - - + +
159B MSE 4.5 4.9 - - - +
162B GLU* 3.0 32.7 + - + +
163B ALA* 3.5 23.1 - - + +
166B HIS* 3.0 45.5 - + + +
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Residues in contact with ALA 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A ILE* 3.9 23.4 - - + +
344A PRO* 4.1 15.5 - - + -
366A VAL* 3.8 20.0 - - + -
369A ALA 3.0 12.3 + - - +
370A GLU 3.4 10.5 - - - +
371A GLN 3.2 0.2 - - - -
372A HIS* 1.3 77.3 + - - +
374A VAL* 1.3 61.4 + - - +
376A PHE* 3.6 4.6 - - - +
377A ALA* 3.2 21.1 + - - +
389A VAL* 4.0 10.6 - - + +
391A ILE* 5.8 0.4 - - + -
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Residues in contact with VAL 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A GLU 3.3 12.6 + - - +
371A GLN 3.4 1.5 + - - +
372A HIS 3.3 0.2 - - - -
373A ALA* 1.3 75.8 - - - +
375A THR* 1.3 65.8 + - - +
377A ALA* 3.1 14.0 + - - +
378A ALA* 3.1 10.6 + - - +
389A VAL* 4.3 15.9 - - + -
391A ILE* 5.2 1.3 - - + -
396A LEU* 4.6 3.8 - - + -
399A ALA* 3.6 15.7 - - + -
402A GLN* 3.7 30.1 - - + -
403A VAL* 3.8 8.5 - - + +
407A VAL* 3.7 22.9 - - + +
416A PHE* 3.9 25.1 - - + -
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Residues in contact with THR 375 (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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371A GLN 3.3 3.8 + - - -
374A VAL* 1.3 75.1 - - - +
376A PHE* 1.3 64.7 + - - +
378A ALA* 3.2 8.1 + - + +
379A GLY 3.1 16.6 + - - -
402A GLN* 2.9 28.8 - - - +
406A ASP* 3.1 14.7 + - + +
125B THR* 3.4 31.6 - - + -
128B SER* 3.2 30.1 - - - -
129B ALA* 3.5 12.7 - - + +
159B MSE 3.2 4.7 - - + +
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Residues in contact with PHE 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A ILE* 3.5 23.6 - - + -
364A PHE* 3.7 44.0 - + + -
366A VAL* 4.8 0.9 - - + -
372A HIS* 2.8 31.9 + + + +
373A ALA* 3.6 3.6 - - - +
375A THR* 1.3 76.7 - - - +
377A ALA* 1.3 62.4 + - - +
379A GLY* 3.3 2.3 + - - -
380A LEU* 3.1 47.4 + - + +
128B SER* 3.8 8.0 + - - -
131B ILE* 3.3 43.7 - - + -
132B GLY* 3.4 20.0 - - - -
135B VAL* 4.1 5.2 - - + -
166B HIS* 4.0 6.5 - + - -
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Residues in contact with ALA 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A ILE* 3.8 7.2 - - + -
373A ALA 3.2 4.0 + - - +
374A VAL 3.1 11.3 + - - +
376A PHE* 1.3 79.0 - - - +
378A ALA* 1.3 60.2 + - - +
380A LEU* 3.2 1.0 + - - -
381A ALA* 2.8 26.2 + - - +
387A PRO* 3.1 31.8 - - + +
389A VAL* 3.5 29.2 - - + -
414A VAL* 3.9 10.5 - - + -
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Residues in contact with ALA 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A VAL 3.1 10.2 + - - +
375A THR* 3.3 20.9 - - + +
376A PHE 3.2 0.2 - - - -
377A ALA* 1.3 76.1 - - - +
379A GLY* 1.3 51.2 + - - +
381A ALA* 3.1 5.9 + - - +
382A ILE* 2.7 41.6 + - + +
406A ASP* 3.6 12.8 - - + +
407A VAL* 4.2 4.7 - - + -
410A GLN* 5.0 2.5 - - - +
412A LEU* 3.6 24.9 - - + +
414A VAL* 4.2 4.7 - - - +
118B LEU* 5.4 0.4 - - + -
129B ALA* 5.1 3.4 - - + -
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Residues in contact with GLY 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A THR 3.1 8.3 + - - -
376A PHE 3.3 2.7 + - - -
377A ALA 3.3 0.2 - - - -
378A ALA* 1.3 78.6 - - - +
380A LEU* 1.3 50.3 + - - +
382A ILE* 3.0 5.7 + - - +
383A GLY* 2.8 31.9 + - - -
129B ALA* 3.2 31.3 - - - +
132B GLY 3.7 7.2 - - - -
133B ILE* 3.6 12.3 + - - +
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Residues in contact with LEU 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A MSE 3.7 35.9 - - + -
342A ILE* 3.9 15.9 - - + -
364A PHE* 4.9 2.2 - - + -
376A PHE* 3.1 41.6 + - + +
377A ALA 3.5 5.6 - - - +
379A GLY* 1.3 74.0 - - - +
381A ALA* 1.3 64.3 + - - +
383A GLY* 3.1 8.7 + - - -
384A GLY 3.3 0.2 + - - -
385A TYR* 3.0 30.2 + - + +
387A PRO* 4.0 10.1 - - + -
132B GLY 3.5 18.0 + - - +
135B VAL* 4.0 23.6 - - + -
136B ALA* 4.4 9.0 - - + +
139B LYS* 6.1 0.2 - - + -
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Residues in contact with ALA 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A ALA 2.8 16.9 + - - +
378A ALA* 3.4 12.3 - - - +
380A LEU* 1.3 72.2 - - - +
382A ILE* 1.3 64.8 + - - +
384A GLY* 2.9 15.4 + - - -
385A TYR 3.5 12.9 + - - +
387A PRO* 3.9 13.8 - - + +
412A LEU* 4.3 18.2 - - + +
413A PRO* 4.7 13.5 - - + +
414A VAL* 4.2 8.1 - - + -
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Residues in contact with ILE 382 (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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378A ALA 2.7 23.8 + - - +
379A GLY* 3.3 11.4 - - - +
381A ALA* 1.3 73.5 - - - +
383A GLY* 1.3 57.7 + - - +
384A GLY* 3.0 5.7 + - - -
410A GLN* 4.3 1.6 - - - +
412A LEU* 3.9 20.4 - - + -
73B GLN* 4.5 8.5 + - - +
110B ARG* 4.0 28.8 + - - +
117B VAL* 3.7 22.0 - - + +
118B LEU* 3.3 35.0 - - + -
133B ILE* 4.0 20.9 - - + -
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Residues in contact with GLY 383 (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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379A GLY 2.8 15.2 + - - -
380A LEU 3.1 4.8 + - - -
382A ILE* 1.3 73.2 - - - +
384A GLY* 1.3 58.7 + - - +
385A TYR* 3.4 16.6 - - - -
73B GLN* 6.1 1.3 - - - -
133B ILE* 5.1 6.7 - - - -
136B ALA* 3.6 23.2 - - - +
140B GLU* 5.9 1.7 - - - +
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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