Contacts of the helix formed by residues 362 - 380 (chain B) in PDB entry 2H5G
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 THR 362 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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363B VAL* 1.3 67.1 + - - +
364B GLU* 3.5 18.7 + - + +
365B GLN* 3.2 51.8 + - + +
366B GLN* 2.9 35.3 + - - +
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Residues in contact with VAL 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362B THR* 1.3 81.2 + - - +
364B GLU* 1.3 74.6 - - - +
366B GLN* 3.3 13.3 + - + +
367B GLY 2.9 22.3 + - - -
502B LEU* 5.8 1.1 - - + -
536B VAL* 4.3 27.4 - - + -
540B GLU* 3.6 34.7 + - + +
548B LEU* 4.9 14.4 - - + -
551B MSE 3.3 19.1 - - + +
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Residues in contact with GLU 364 (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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362B THR* 3.3 15.1 + - + +
363B VAL* 1.3 93.8 - - - +
365B GLN* 1.3 58.2 + - - +
367B GLY* 3.4 1.4 + - - -
368B GLU* 3.2 25.5 + - - +
548B LEU* 4.7 12.2 - - + +
551B MSE 3.9 19.6 - - - +
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Residues in contact with GLN 365 (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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362B THR* 3.2 40.7 + - + +
364B GLU* 1.3 73.9 - - - +
366B GLN* 1.3 60.8 + - + +
368B GLU* 3.4 7.2 + - + +
369B MSE 3.0 39.6 + - - +
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Residues in contact with GLN 366 (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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362B THR 2.9 19.8 + - - +
363B VAL* 3.5 19.3 + - + +
364B GLU 3.3 0.2 - - - -
365B GLN* 1.3 74.3 - - - +
367B GLY* 1.3 59.2 + - - +
369B MSE 3.3 3.6 + - - -
370B ALA* 2.9 27.2 + - - +
502B LEU* 3.8 12.3 - - + -
534B GLN* 3.0 41.2 + - - +
535B LEU 3.1 25.6 + - - +
536B VAL* 3.8 22.4 - - - +
537B ASN* 4.5 3.3 + - - +
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Residues in contact with GLY 367 (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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363B VAL 2.9 11.1 + - - -
364B GLU 3.4 3.1 + - - -
365B GLN 3.3 0.2 - - - -
366B GLN* 1.3 77.3 - - - +
368B GLU* 1.3 54.6 + - - +
370B ALA* 3.4 2.3 + - - +
371B ARG* 2.9 29.2 + - - +
475B VAL* 4.6 3.7 - - - +
502B LEU* 3.9 10.9 - - - +
551B MSE 3.7 36.1 - - - +
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Residues in contact with GLU 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364B GLU 3.2 16.0 + - - +
365B GLN* 3.9 7.4 - - + +
366B GLN 3.3 0.2 - - - -
367B GLY* 1.3 74.0 - - - +
369B MSE 1.3 58.5 + - + +
371B ARG* 3.4 8.6 + - - +
372B SER* 3.0 29.3 + - - -
551B MSE 4.8 0.8 - - - +
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Residues in contact with MSE 369 (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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365B GLN* 3.0 27.4 + - - +
366B GLN* 3.6 4.9 - - - +
368B GLU* 1.3 75.7 - - + +
370B ALA* 1.3 55.4 + - - +
372B SER* 3.3 6.4 + - - +
373B GLY* 2.8 29.3 + - - -
521B GLN* 5.9 0.9 - - - +
531B GLU* 3.2 48.8 - - + +
534B GLN* 3.0 43.1 - - - +
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Residues in contact with ALA 370 (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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366B GLN 2.9 17.2 + - - +
367B GLY 3.7 4.3 - - - +
369B MSE 1.3 73.2 - - - +
371B ARG* 1.3 59.8 + - - +
373B GLY 3.7 0.2 - - - -
374B GLY 2.8 24.8 + - - -
475B VAL* 4.0 11.2 - - + -
500B GLY* 3.3 11.1 - - - -
501B LEU 4.0 20.6 - - - +
502B LEU* 4.0 11.0 - - + -
531B GLU 3.5 10.9 + - - -
532B ALA* 4.1 2.4 - - - +
534B GLN* 4.0 11.4 - - + -
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Residues in contact with ARG 371 (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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367B GLY 2.9 17.5 + - - +
368B GLU* 3.7 8.7 - - - +
369B MSE 3.3 0.2 - - - -
370B ALA* 1.3 76.8 - - - +
372B SER* 1.3 56.9 + - - +
374B GLY* 3.3 1.8 + - - -
375B ARG* 3.0 48.7 + - + +
474B GLY* 6.2 0.4 - - - -
475B VAL* 3.5 21.0 - - + +
550B LYS 5.7 5.2 - - - -
551B MSE 5.5 5.8 - - - +
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Residues in contact with SER 372 (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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368B GLU 3.0 15.9 + - - -
369B MSE 3.3 4.2 + - - -
371B ARG* 1.3 73.0 - - - +
373B GLY* 1.3 62.4 + - - +
375B ARG* 3.4 8.8 + - - +
376B MSE 3.0 35.2 + - - +
531B GLU* 3.1 20.8 + - - -
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Residues in contact with GLY 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369B MSE 2.8 18.7 + - - -
372B SER* 1.3 74.5 + - - +
374B GLY* 1.3 58.6 + - - +
376B MSE 3.5 9.5 + - - +
377B LEU* 2.9 28.6 + - - +
529B VAL* 4.2 6.7 - - - +
531B GLU* 4.4 5.6 - - - -
532B ALA* 3.6 25.8 - - - +
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Residues in contact with GLY 374 (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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370B ALA 2.8 21.2 + - - -
371B ARG* 3.7 1.6 - - - -
372B SER 3.2 0.2 - - - -
373B GLY* 1.3 73.4 - - - +
375B ARG* 1.3 56.9 + - - +
377B LEU* 3.1 6.2 + - - +
378B ALA* 2.9 24.4 + - - +
474B GLY 5.1 1.3 - - - -
498B GLY 3.2 11.2 - - - +
499B ASN 3.9 5.2 - - - -
500B GLY* 3.6 23.8 - - - -
532B ALA* 4.1 0.6 - - - +
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Residues in contact with ARG 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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371B ARG* 3.0 31.8 + - + +
372B SER* 3.8 7.2 - - - +
373B GLY 3.4 0.2 - - - -
374B GLY* 1.3 76.4 - - - +
376B MSE 1.3 59.9 + - - +
378B ALA* 3.4 7.6 + - - +
379B THR* 3.2 29.4 + - + +
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Residues in contact with MSE 376 (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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372B SER* 3.0 23.5 + - - +
373B GLY* 3.7 8.1 - - - +
374B GLY 3.3 0.2 - - - -
375B ARG* 1.3 72.1 - - - +
377B LEU* 1.3 66.0 + - - +
379B THR* 3.0 23.2 + - - +
380B LEU* 3.2 15.8 + - + +
527B HIS 5.6 1.1 - - - +
528B GLY 4.1 11.7 - - - +
529B VAL* 3.7 23.6 - - + -
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Residues in contact with LEU 377 (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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373B GLY 2.9 10.9 + - - +
374B GLY 3.2 9.0 - - - +
376B MSE 1.3 76.9 - - - +
378B ALA* 1.3 58.7 + - - +
380B LEU* 3.3 19.7 + - + +
385B ARG* 3.0 26.4 + - + -
388B ILE* 4.0 17.0 - - + -
494B ALA 4.4 1.1 - - - +
495B ILE* 3.8 41.5 - - + +
498B GLY* 4.5 2.0 - - - -
499B ASN 3.5 25.8 - - - +
524B LEU* 4.2 4.5 - - + -
529B VAL* 3.6 29.7 - - + +
532B ALA* 3.9 15.9 - - + -
533B VAL* 6.0 0.2 - - + -
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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
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374B GLY 2.9 15.8 + - - +
375B ARG* 3.7 8.7 - - - +
376B MSE 3.3 0.2 - - - -
377B LEU* 1.3 75.9 - - - +
379B THR* 1.3 60.5 + - + +
380B LEU 3.8 1.2 - - - +
385B ARG* 3.3 16.5 + - - +
451B VAL* 4.7 11.1 - - + +
472B PRO* 3.9 30.1 - - + -
498B GLY* 3.9 6.9 - - - +
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Residues in contact with THR 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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375B ARG* 3.2 15.8 + - + +
376B MSE 3.0 22.1 + - - +
378B ALA* 1.3 77.1 - - + +
380B LEU* 1.3 66.8 + - - +
381B GLU* 3.9 6.9 + - - +
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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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376B MSE 3.2 21.0 + - + +
377B LEU* 3.3 22.2 + - + +
378B ALA 3.8 1.7 - - - +
379B THR* 1.3 83.3 + - - +
381B GLU* 1.3 66.8 + - - +
382B PRO* 3.8 0.9 - - - +
384B GLN* 3.8 24.2 - - + +
385B ARG* 2.9 23.0 + - + +
388B ILE* 4.0 17.0 - - + -
527B HIS* 3.7 39.5 - - + +
529B VAL* 4.4 6.1 - - + -
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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