Contacts of the helix formed by residues 369 - 383 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A GLU* 3.1 43.7 - - + +
156B THR 4.4 4.0 - - - +
344B PRO* 4.0 4.1 - - - +
366B VAL* 3.5 21.0 - - + +
367B ALA 2.8 8.3 + - - -
368B ILE* 1.3 73.5 - - - +
370B GLU* 1.3 59.6 + - - +
371B GLN 3.3 2.2 - - - -
372B HIS* 4.1 4.9 - - + +
373B ALA* 3.0 27.0 + - - +
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Residues in contact with GLU 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A GLU* 4.3 1.2 + - - +
344B PRO* 4.0 19.3 - - + +
368B ILE* 4.1 22.3 - - - +
369B ALA* 1.3 71.4 - - - +
371B GLN* 1.3 68.5 + - - +
373B ALA* 3.2 15.7 + - - +
374B VAL* 3.2 18.0 + - - +
391B ILE* 3.6 17.7 - - + +
395B PHE* 3.3 50.2 - - + +
398B ARG* 3.5 28.9 - - + +
399B ALA* 3.8 11.7 - - + -
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Residues in contact with GLN 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A GLY* 4.5 3.6 - - - -
159A MSE 3.4 32.9 - - + +
162A GLU* 3.4 17.1 + - - +
371A GLN* 3.3 31.3 - - - +
398A ARG* 3.4 20.1 - - - +
158B GLY* 4.6 2.4 - - - -
162B GLU* 5.1 1.6 + - - -
369B ALA 3.3 0.6 - - - -
370B GLU* 1.3 79.3 - - - +
372B HIS* 1.3 64.8 + - - +
374B VAL* 3.2 7.6 + - - -
375B THR* 3.2 10.4 + - - -
398B ARG* 3.5 22.8 - - + +
399B ALA* 4.2 0.4 - - - -
402B GLN* 3.1 45.0 - - - +
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Residues in contact with HIS 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A SER* 3.0 38.5 - - - +
131A ILE* 3.8 15.2 - - - +
159A MSE 4.6 2.8 - - - +
162A GLU* 3.0 29.2 + - + +
163A ALA* 3.5 14.4 - - - -
166A HIS* 2.8 47.3 + + + +
366B VAL* 3.8 16.4 + - + +
369B ALA* 3.6 4.5 + - + +
370B GLU 3.4 0.2 - - - -
371B GLN* 1.3 79.9 - - - +
373B ALA* 1.3 57.1 + - - +
375B THR* 4.8 0.2 - - - -
376B PHE* 2.8 54.4 + + + +
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Residues in contact with ALA 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B ILE* 4.1 18.4 - - + +
344B PRO* 4.3 12.8 - - + -
366B VAL* 3.7 19.3 - - + -
369B ALA 3.0 15.7 + - - +
370B GLU* 3.2 14.1 - - - +
371B GLN 3.1 0.4 - - - -
372B HIS* 1.3 77.6 + - - +
374B VAL* 1.3 62.2 + - - +
376B PHE* 3.7 4.0 - - - +
377B ALA* 3.1 21.7 + - - +
389B VAL* 4.1 11.8 - - + +
391B ILE* 5.9 0.7 - - + -
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Residues in contact with VAL 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370B GLU 3.2 14.4 + - - +
371B GLN 3.2 0.8 + - - +
373B ALA* 1.3 75.7 - - + +
375B THR* 1.3 60.2 + - - +
377B ALA* 3.0 9.6 + - - +
378B ALA* 2.9 24.3 + - - +
389B VAL* 4.4 12.8 - - + -
391B ILE* 5.4 1.3 - - + -
396B LEU* 4.8 2.9 - - + -
399B ALA* 3.6 18.2 - - + -
402B GLN* 3.9 26.2 - - + -
403B VAL* 3.9 3.6 - - + +
407B VAL* 3.6 26.2 - - + +
416B PHE* 3.9 28.5 - - + -
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Residues in contact with THR 375 (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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118A LEU* 5.5 0.9 - - + -
125A THR* 3.7 12.1 - - - +
128A SER* 3.5 27.4 - - - -
129A ALA* 3.4 20.0 - - + +
159A MSE 3.2 7.8 - - + +
371B GLN 3.2 4.8 + - - -
374B VAL* 1.3 73.7 - - - +
376B PHE* 1.3 64.2 + - - +
378B ALA* 3.4 9.0 + - + +
379B GLY 3.1 15.6 + - - -
402B GLN* 3.1 16.8 - - - +
406B ASP* 2.7 37.4 + - + +
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Residues in contact with PHE 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A SER* 3.8 8.7 - - - -
131A ILE* 3.7 22.7 - - + -
132A GLY* 3.5 35.4 - - - -
135A VAL* 4.1 6.7 - - + -
166A HIS* 4.0 7.6 - + - -
342B ILE* 3.8 17.5 - - + -
364B PHE* 3.8 44.4 - + + -
366B VAL* 4.3 11.2 - - + -
372B HIS* 2.8 35.2 + + + +
373B ALA* 3.7 2.0 - - - +
375B THR* 1.3 75.8 - - - +
377B ALA* 1.3 62.1 + - - +
379B GLY* 3.2 2.6 + - - -
380B LEU* 3.0 40.7 + - + +
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Residues in contact with ALA 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B ILE* 3.7 15.5 - - + -
373B ALA 3.1 7.2 + - - +
374B VAL 3.0 11.1 + - - +
376B PHE* 1.3 75.7 - - - +
378B ALA* 1.3 65.4 + - - +
380B LEU* 3.0 2.5 + - - +
381B ALA 2.9 19.1 + - - -
387B PRO* 3.2 23.5 - - + +
389B VAL* 3.6 30.5 - - + -
414B VAL* 3.9 9.9 - - + -
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Residues in contact with ALA 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A LEU* 5.9 2.2 - - + -
129A ALA* 5.4 2.2 - - + -
374B VAL 2.9 12.5 + - - +
375B THR* 3.4 16.2 - - + +
376B PHE 3.2 0.2 - - - -
377B ALA* 1.3 77.7 - - - +
379B GLY* 1.3 56.8 + - - +
381B ALA* 3.3 2.0 + - - +
382B ILE* 3.0 35.2 + - + +
406B ASP* 3.4 29.8 - - + +
407B VAL* 4.4 3.1 - - + -
412B LEU* 3.5 15.0 - - + +
414B VAL* 4.1 7.8 - - - +
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Residues in contact with GLY 379 (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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129A ALA* 3.5 26.6 - - - +
132A GLY 3.6 9.6 - - - +
133A ILE* 3.6 13.0 - - - +
375B THR 3.1 12.2 + - - -
376B PHE 3.2 3.6 + - - -
377B ALA 3.1 0.4 - - - -
378B ALA* 1.3 74.6 - - - +
380B LEU* 1.3 62.9 + - - +
382B ILE* 3.3 7.7 + - - +
383B GLY* 3.0 17.5 + - - -
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Residues in contact with LEU 380 (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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132A GLY* 3.6 17.9 - - - +
135A VAL* 3.9 24.7 - - + -
136A ALA* 4.5 6.7 - - + +
139A LYS* 6.1 0.4 - - + -
340B MSE 3.9 30.3 - - + -
342B ILE* 3.7 30.7 - - + -
364B PHE* 4.9 3.1 - - + -
376B PHE* 3.0 29.2 + - + +
377B ALA 3.0 7.2 + - - +
379B GLY* 1.3 77.4 - - - +
381B ALA* 1.3 63.5 + - - +
383B GLY* 3.1 8.0 + - - -
384B GLY 3.3 0.3 + - - -
385B TYR* 3.0 31.6 + - + +
387B PRO* 4.0 9.9 - - + -
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Residues in contact with ALA 381 (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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377B ALA 2.9 12.5 + - - +
378B ALA 3.6 7.6 - - - +
380B LEU* 1.3 73.6 - - - +
382B ILE* 1.3 66.9 + - - +
384B GLY* 2.9 14.6 + - - -
385B TYR 3.4 12.8 - - - +
387B PRO* 3.9 14.7 - - + +
412B LEU* 4.3 23.3 - - + +
413B PRO* 4.6 13.0 - - + -
414B VAL* 4.4 4.3 - - + -
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Residues in contact with ILE 382 (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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73A GLN* 4.3 8.1 - - - +
110A ARG* 4.2 20.7 + - - +
117A VAL* 3.5 39.0 - - + +
118A LEU* 4.3 20.0 - - + -
129A ALA* 5.0 1.3 - - + -
133A ILE* 4.1 18.4 - - + -
378B ALA* 3.0 23.4 + - + +
379B GLY* 3.3 9.2 + - - +
381B ALA* 1.3 76.3 - - - +
383B GLY* 1.3 61.0 + - - +
384B GLY 3.4 0.7 + - - -
412B LEU* 3.7 28.2 - - + +
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Residues in contact with GLY 383 (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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133A ILE* 5.3 5.6 - - - -
136A ALA* 3.7 27.0 - - - +
140A GLU* 5.7 3.1 - - - +
379B GLY 3.0 12.3 + - - -
380B LEU 3.5 4.7 - - - -
381B ALA 3.0 0.8 - - - -
382B ILE* 1.3 77.0 - - - +
384B GLY* 1.3 56.4 + - - +
385B TYR* 3.6 8.2 - - - -
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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