Contacts of the helix formed by residues 368 - 379 (chain A) in PDB entry 5EVZ
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 368 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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258A PHE* 3.8 33.2 - - + -
296A LYS* 5.0 1.3 - - + -
300A SER* 3.7 2.9 - - - +
327A PHE* 4.1 26.7 - - + -
328A GLU* 5.8 1.1 - - + +
335A PHE* 4.1 17.5 - - + -
365A SER* 3.1 22.1 + - - +
367A ARG* 1.3 76.2 - - - +
369A PRO* 1.3 73.9 - - + +
370A LYS* 3.7 13.5 - - + +
371A ILE* 3.0 25.7 + - + +
372A GLN* 3.1 13.0 + - - +
503A ADP 3.6 22.2 - - + +
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Residues in contact with PRO 369 (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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299A LEU 4.4 2.0 - - - +
300A SER* 3.6 31.4 - - - +
324A ARG* 4.1 28.5 - - + +
328A GLU* 5.0 5.8 - - - +
367A ARG 3.2 9.2 - - - +
368A ILE* 1.3 85.6 - - + +
370A LYS* 1.3 58.1 + - - +
372A GLN* 3.2 16.1 + - - +
373A GLN* 2.9 29.7 + - - +
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Residues in contact with LYS 370 (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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328A GLU* 3.7 40.1 + - + +
332A MET* 3.9 21.6 - - + +
335A PHE* 3.8 28.3 - - + -
368A ILE* 3.2 4.9 - - + +
369A PRO* 1.3 79.6 - - - +
371A ILE* 1.3 57.8 + - - +
373A GLN* 2.9 38.9 + - - +
374A LEU* 3.0 49.9 + - + +
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Residues in contact with ILE 371 (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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223A PHE* 3.9 26.7 - - + -
225A LEU* 3.8 19.5 - - + -
335A PHE* 3.6 47.1 - - + +
338A THR* 4.7 4.7 - - + +
339A MET* 6.0 0.9 - - + -
361A LEU* 5.8 0.7 - - + -
365A SER 3.9 9.4 - - - +
366A THR* 4.2 19.1 - - + -
368A ILE* 3.0 29.1 + - + +
370A LYS* 1.3 75.3 - - - +
372A GLN* 1.3 66.8 + - - +
374A LEU* 3.2 5.8 + - + +
375A VAL* 3.1 24.6 + - + +
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Residues in contact with GLN 372 (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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361A LEU* 3.9 25.8 - - + +
366A THR 3.2 26.3 + - - +
367A ARG* 3.2 22.8 + - - +
368A ILE 3.1 7.2 + - - +
369A PRO* 3.4 11.8 - - - +
371A ILE* 1.3 76.6 - - - +
373A GLN* 1.3 61.3 + - - +
375A VAL* 3.5 2.8 + - - +
376A LYS* 3.1 25.3 + - - +
384A PRO* 6.0 4.3 - - + +
386A ARG* 5.9 1.6 + - - -
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Residues in contact with GLN 373 (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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369A PRO 2.9 16.2 + - - +
370A LYS* 2.9 42.0 + - - +
372A GLN* 1.3 76.2 - - - +
374A LEU* 1.3 59.8 + - - +
376A LYS* 3.3 7.4 + - - +
377A GLU* 2.9 63.6 + - + +
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Residues in contact with LEU 374 (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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332A MET* 4.5 2.9 - - - -
335A PHE* 3.6 41.3 - - + +
336A ARG* 3.5 39.5 - - + +
339A MET* 4.0 17.2 - - + +
370A LYS* 3.0 38.7 + - + +
371A ILE* 3.2 6.3 + - + +
373A GLN* 1.3 75.4 - - - +
375A VAL* 1.3 60.9 + - - +
377A GLU* 3.7 19.8 - - - +
378A PHE* 2.9 30.0 + - - +
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Residues in contact with VAL 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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221A LEU* 6.1 0.4 - - + -
223A PHE* 3.8 48.7 - - + -
339A MET* 3.9 10.1 - - + -
359A ILE* 4.0 27.8 - - + -
361A LEU* 4.2 15.5 - - + -
371A ILE 3.1 17.1 + - - +
372A GLN* 3.9 3.8 - - - +
374A LEU* 1.3 75.0 - - - +
376A LYS* 1.3 62.9 + - - +
378A PHE* 3.2 4.3 + - - +
379A PHE* 3.1 34.8 + - + -
384A PRO* 5.9 2.7 - - + -
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Residues in contact with LYS 376 (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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359A ILE* 6.0 0.2 - - - -
372A GLN 3.1 19.0 + - - +
373A GLN* 3.6 7.2 - - - +
375A VAL* 1.3 76.9 - - - +
377A GLU* 1.3 63.0 + - + +
379A PHE* 3.1 10.4 + - - +
381A GLY* 2.9 50.9 + - - -
382A LYS 3.6 21.0 + - - +
383A GLU* 3.3 36.0 + - - +
384A PRO* 5.3 5.8 - - + -
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Residues in contact with GLU 377 (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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336A ARG* 5.3 0.7 + - - -
353A LYS* 5.0 0.3 + - - -
373A GLN* 2.9 51.5 + - + +
374A LEU* 3.7 23.6 - - + +
376A LYS* 1.3 76.1 - - + +
378A PHE* 1.3 65.7 + - - +
380A ASN* 3.1 20.1 + - - +
381A GLY* 4.6 3.4 - - - +
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Residues in contact with PHE 378 (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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339A MET* 3.6 43.7 - - + -
342A VAL* 3.5 28.3 - - + -
343A GLN* 3.7 26.0 - - + -
346A LEU* 4.1 3.4 - - + -
353A LYS* 2.8 63.8 + - + +
374A LEU 2.9 15.1 + - - +
375A VAL* 3.4 8.3 - - - +
377A GLU* 1.3 76.6 - - - +
379A PHE* 1.3 88.3 + + - +
380A ASN* 3.4 2.1 + - - +
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Residues in contact with PHE 379 (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 LEU* 4.1 20.9 - - + -
223A PHE* 6.4 0.4 - + - -
342A VAL* 4.0 17.0 - - + -
346A LEU* 4.6 2.5 - - + -
353A LYS* 4.1 27.6 - - + -
356A ILE* 3.8 26.9 - - + -
359A ILE* 3.5 37.0 - - + -
375A VAL* 3.1 35.1 + - + +
376A LYS 3.9 2.5 - - - +
377A GLU 3.1 0.2 - - - -
378A PHE* 1.3 105.8 - + - +
380A ASN* 1.3 70.4 + - - +
381A GLY 3.1 3.9 + - - -
382A LYS* 3.2 20.3 + - + +
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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