Contacts of the helix formed by residues 373 - 387 (chain B) in PDB entry 6FF7
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 ILE 373 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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323B PHE* 5.7 9.2 - - + -
369B PHE* 4.0 8.4 + - - +
371B GLU 4.0 0.2 - - - -
372B PHE* 1.3 80.2 - - + +
374B LEU* 1.3 66.2 + - + +
375B GLU 3.7 0.4 - - - -
376B PRO* 4.2 3.7 - - - +
377B LEU* 3.3 22.7 + - - +
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Residues in contact with LEU 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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271B PRO* 5.8 3.6 - - + +
369B PHE 3.4 17.9 + - - +
370B VAL* 4.4 8.5 - - + -
373B ILE* 1.3 77.6 - - + +
375B GLU* 1.3 61.7 + - - +
377B LEU* 3.2 9.4 + - - +
378B TYR* 2.9 23.6 + - - +
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Residues in contact with GLU 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393A LEU* 4.9 1.6 - - - +
271B PRO* 4.9 12.9 - - + +
370B VAL* 4.0 23.3 - - - +
371B GLU* 5.1 4.2 - - - +
373B ILE 4.8 0.4 - - - +
374B LEU* 1.3 76.4 - - - +
376B PRO* 1.4 59.5 - - - +
378B TYR* 3.3 10.7 + - + +
379B LYS* 2.9 26.7 + - - +
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Residues in contact with PRO 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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386A PRO* 5.9 2.0 - - + -
387A PHE* 4.5 24.7 - - + +
388A LEU* 5.6 4.0 - - + +
371B GLU 5.4 3.9 - - - +
372B PHE 4.2 19.4 - - - +
373B ILE* 4.0 5.9 - - - +
374B LEU 3.4 0.8 - - - -
375B GLU* 1.4 72.1 - - - +
377B LEU* 1.3 60.9 + - - +
379B LYS* 3.2 7.3 + - + +
380B ILE* 3.0 30.8 + - - +
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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 ILE 3.3 13.5 + - - +
374B LEU* 3.2 12.7 + - - +
376B PRO* 1.3 77.1 - - - +
378B TYR* 1.3 57.7 + - - +
380B ILE* 4.3 3.3 - - - +
381B LEU* 2.9 34.9 + - - +
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Residues in contact with TYR 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393A LEU* 4.2 15.0 - - + -
374B LEU 2.9 13.5 + - - +
375B GLU* 3.3 15.9 - - + +
377B LEU* 1.3 76.6 - - - +
379B LYS* 1.3 56.6 + - - +
381B LEU* 4.0 3.1 - - - +
382B ALA* 2.8 35.9 + - - +
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Residues in contact with LYS 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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388A LEU* 4.8 17.9 - - + -
391A THR 5.2 3.1 - - - +
392A PRO 4.7 12.4 - - - +
393A LEU* 4.4 14.5 - - + +
375B GLU 2.9 16.5 + - - +
376B PRO* 3.2 7.4 + - + +
378B TYR* 1.3 76.4 - - - +
380B ILE* 1.3 56.4 + - - +
383B GLN* 2.9 34.8 + - - +
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Residues in contact with ILE 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376B PRO 3.0 14.8 + - - +
377B LEU* 4.3 4.0 - - - +
379B LYS* 1.3 75.3 - - - +
381B LEU* 1.3 56.1 + - - +
383B GLN* 3.9 2.7 - - - +
384B VAL* 3.0 33.4 + - - +
395B THR* 6.2 5.4 - - - -
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Residues in contact with LEU 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 LEU 2.9 21.0 + - - +
378B TYR* 4.0 3.6 - - - +
380B ILE* 1.3 76.7 - - - +
382B ALA* 1.3 56.6 + - - +
384B VAL* 3.3 4.2 + - - +
385B VAL* 3.0 30.3 + - - +
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Residues in contact with ALA 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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393A LEU 3.5 25.1 - - - +
398A THR* 4.3 14.9 - - - -
378B TYR* 2.8 22.7 + - + +
379B LYS 4.4 0.7 - - - +
381B LEU* 1.3 74.6 - - - +
383B GLN* 1.3 58.3 + - - +
385B VAL* 3.8 3.5 - - - +
386B GLY* 2.9 26.7 + - - -
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Residues in contact with GLN 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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392A PRO 5.9 2.7 - - - +
379B LYS 2.9 19.9 + - - +
380B ILE* 4.2 2.7 - - - +
382B ALA* 1.3 76.5 - - - +
384B VAL* 1.3 58.1 + - - +
387B ASP* 2.9 41.7 + - + +
391B SER* 5.6 9.4 - - - +
392B LEU* 5.2 2.1 - - - +
395B THR* 5.7 8.3 - - - -
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Residues in contact with VAL 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380B ILE 3.0 18.8 + - - +
381B LEU* 4.1 3.4 - - - +
383B GLN* 1.3 77.9 - - - +
385B VAL* 1.3 59.5 + - - +
386B GLY 3.5 0.2 - - - -
387B ASP 4.7 2.5 - - - -
388B VAL* 4.5 15.0 - - - +
392B LEU* 5.9 4.0 - - + -
412B ILE* 5.8 2.8 - - - +
416B LEU* 5.9 11.8 - - + +
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Residues in contact with VAL 385 (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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232A LEU* 5.4 3.6 - - - +
398A THR 5.8 0.2 - - - -
401A GLY* 3.7 25.2 - - - +
402A ILE* 5.5 5.6 - - + +
405A LEU* 6.0 4.0 - - + -
381B LEU 3.0 16.1 + - - +
382B ALA* 3.8 3.4 - - - +
384B VAL* 1.3 79.6 - - - +
386B GLY* 1.3 55.1 + - - +
387B ASP 5.6 0.2 - - - -
388B VAL* 5.7 1.3 - - - -
412B ILE* 6.0 7.2 - - + -
416B LEU* 6.4 2.0 - - + -
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Residues in contact with GLY 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A LEU* 4.4 14.9 - - - +
397A ASN* 3.0 30.8 - - - +
398A THR* 4.1 12.1 - - - -
401A GLY* 4.8 2.9 - - - -
382B ALA 2.9 15.3 + - - -
385B VAL* 1.3 81.6 - - - +
387B ASP* 1.3 59.7 + - - +
388B VAL* 3.9 3.5 + - - -
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Residues in contact with ASP 387 (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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382B ALA 4.2 0.2 + - - -
383B GLN* 2.9 29.7 + - + +
384B VAL* 4.7 0.6 - - - -
386B GLY* 1.3 76.7 - - - +
388B VAL* 1.3 59.0 + - - +
389B ASP 3.6 0.9 - - - +
390B THR* 2.9 30.7 - - - +
391B SER* 4.6 8.1 - - - -
392B LEU* 3.6 10.6 + - - +
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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