Contacts of the helix formed by residues 399 - 417 (chain A) in PDB entry 1EQR
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 LYS 399 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314A PRO 3.1 26.3 + - - -
315A LYS* 2.7 31.9 + - + +
316A GLY 3.1 21.3 + - - +
317A ARG* 4.2 27.0 - - + +
397A ASP 3.7 1.8 + - - -
398A ASN* 1.3 71.4 + - - +
400A LYS* 1.3 57.5 + - - +
402A VAL* 3.5 1.2 + - - +
403A ALA* 3.0 30.3 + - - +
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Residues in contact with LYS 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A ASN* 3.1 17.1 + - - +
399A LYS* 1.3 76.6 - - - +
401A ILE* 1.3 67.4 + - + +
403A ALA* 4.0 3.8 - - - +
404A ASP* 2.9 64.9 + - - +
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Residues in contact with ILE 401 (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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344A TYR 3.4 16.4 - - - +
345A GLY* 3.3 31.6 - - - +
346A ALA* 3.6 12.3 - - + +
397A ASP* 4.1 15.0 - - + +
398A ASN* 2.9 34.8 + - + +
400A LYS* 1.3 81.8 - - + +
402A VAL* 1.3 57.3 + - - +
404A ASP* 3.5 5.8 - - - +
405A ALA* 2.7 34.7 + - - +
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Residues in contact with VAL 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A ARG* 3.3 42.6 - - + +
319A ALA* 3.6 31.9 - - + -
395A GLY* 3.7 11.2 - - - +
397A ASP* 3.4 23.3 - - + +
398A ASN 2.9 16.2 + - - +
399A LYS 3.9 0.7 - - - +
401A ILE* 1.3 73.4 - - - +
403A ALA* 1.3 59.6 + - - +
405A ALA* 5.0 0.9 - - - -
406A MET* 2.6 49.3 + - + +
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Residues in contact with ALA 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A GLU* 4.1 10.1 - - + +
280A GLY* 3.1 41.5 - - - +
317A ARG* 4.2 12.1 - - - +
399A LYS 3.0 16.2 + - - +
400A LYS* 4.0 4.7 - - - +
402A VAL* 1.3 77.8 - - - +
404A ASP* 1.3 66.6 + - - +
406A MET* 5.0 0.7 - - - -
407A GLY* 2.9 20.3 + - - +
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Residues in contact with ASP 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A GLY 4.6 3.3 - - - +
344A TYR* 3.7 26.1 - - + +
400A LYS* 2.9 53.8 + - - +
401A ILE* 3.5 9.0 - - - +
403A ALA* 1.3 81.4 - - - +
405A ALA* 1.3 61.1 + - - +
407A GLY 4.3 0.2 - - - -
408A ALA* 3.3 19.6 + - - +
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Residues in contact with ALA 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A PHE* 4.5 1.0 - - - -
341A VAL* 3.7 25.1 - - + +
344A TYR* 3.5 25.1 - - + -
346A ALA* 3.9 13.2 - - + -
401A ILE 2.7 20.8 + - - +
402A VAL* 4.4 1.3 - - - +
404A ASP* 1.3 72.4 - - - +
406A MET* 1.3 62.4 + - + +
408A ALA* 3.3 2.3 + - - +
409A LEU* 2.9 29.3 + - - +
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Residues in contact with MET 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A LEU* 3.7 27.3 - - + +
319A ALA* 3.4 12.8 - - + +
321A LEU* 4.1 18.5 - - + +
341A VAL* 4.8 2.5 - - - -
349A LEU* 4.0 18.4 - - + -
393A PHE* 4.1 10.1 - - + +
394A PHE* 3.6 9.6 - - - +
395A GLY* 3.2 36.3 - - - +
402A VAL* 2.6 42.6 + - + +
405A ALA* 1.3 73.9 - - + +
407A GLY* 1.3 58.4 + - - +
408A ALA 3.1 1.6 - - - -
409A LEU* 3.9 7.4 - - + +
410A ARG* 2.9 28.1 + - - +
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Residues in contact with GLY 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A TYR 3.3 28.0 - - - +
280A GLY* 4.4 1.6 - - - -
281A SER* 6.1 0.9 - - - -
292A LEU* 4.5 1.0 - - - +
403A ALA 2.9 17.8 + - - -
404A ASP 4.3 0.9 - - - -
406A MET* 1.3 77.7 - - - +
408A ALA* 1.3 57.1 + - - +
410A ARG* 3.7 7.8 + - - +
411A LEU* 3.3 28.8 + - - +
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Residues in contact with ALA 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A PHE* 3.4 11.1 - - + -
344A TYR* 3.5 36.6 - - + +
404A ASP 3.3 19.6 + - - +
405A ALA 3.3 5.1 + - - +
406A MET 3.1 0.2 - - - -
407A GLY* 1.3 76.4 - - - +
409A LEU* 1.3 60.6 + - - +
410A ARG 3.0 1.1 - - - -
411A LEU* 3.1 11.0 + - - +
412A LYS* 2.9 25.3 + - - +
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Residues in contact with LEU 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A LEU* 3.4 23.6 - - + -
337A TYR* 3.5 45.1 - - + -
340A PHE* 3.3 18.3 - - + -
341A VAL* 3.9 17.9 - - + -
349A LEU* 4.4 8.3 - - + -
393A PHE* 4.3 16.6 - - + -
405A ALA 2.9 16.2 + - - +
406A MET* 4.1 8.1 - - - +
408A ALA* 1.3 75.2 - - - +
410A ARG* 1.3 58.2 + - - +
412A LYS* 3.9 1.8 - - + +
413A VAL* 3.0 35.6 + - + +
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Residues in contact with ARG 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A ARG 4.6 2.5 - - - -
279A TYR* 3.5 46.1 + - - +
285A ASP* 3.4 14.9 + - - +
288A ASN* 2.5 66.6 + - - +
290A MET* 2.9 46.0 + - + +
291A GLU* 4.6 2.2 - - - +
292A LEU* 4.8 5.2 - - + -
321A LEU* 3.5 21.8 - - + -
406A MET 2.9 20.0 + - - +
407A GLY* 3.7 6.0 + - - +
408A ALA 3.0 0.2 - - - -
409A LEU* 1.3 79.3 - - - +
411A LEU* 1.3 87.2 + - - +
414A GLY 3.5 0.3 + - - -
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Residues in contact with LEU 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A ASP* 3.9 28.5 - - + +
288A ASN* 3.7 9.5 + - + +
407A GLY 3.3 16.8 + - - +
408A ALA* 3.1 10.4 + - - +
410A ARG* 1.3 102.5 - - - +
412A LYS* 1.3 66.1 + - - +
414A GLY* 2.9 11.3 + - - -
415A LYS* 3.3 27.1 + - - +
420A THR* 4.7 1.3 + - + -
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Residues in contact with LYS 412 (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 GLU* 5.3 12.8 + - - +
337A TYR* 5.0 8.7 - - + -
340A PHE* 3.8 48.7 - - + +
408A ALA 2.9 15.8 + - - +
409A LEU* 4.2 2.0 - - - +
411A LEU* 1.3 77.0 - - - +
413A VAL* 1.3 62.0 + - - +
414A GLY 3.0 1.0 + - - -
415A LYS* 3.1 17.4 + - + +
416A ASP* 3.1 44.7 + - - +
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Residues in contact with VAL 413 (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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290A MET* 3.6 17.7 - - + -
321A LEU* 5.2 0.9 - - + -
323A VAL* 3.6 32.5 - - + -
337A TYR* 3.8 29.2 - - + +
393A PHE* 4.8 4.0 - - + -
409A LEU* 3.0 52.9 + - + +
412A LYS* 1.3 75.0 - - - +
414A GLY* 1.3 61.5 + - - +
416A ASP* 4.1 1.3 - - - -
417A LEU* 3.2 30.2 + - + +
419A LEU* 4.2 1.3 - - + +
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Residues in contact with GLY 414 (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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288A ASN* 3.7 10.3 - - - -
290A MET* 3.9 5.6 - - - -
410A ARG 3.5 4.4 + - - -
411A LEU 2.9 8.8 + - - -
412A LYS 2.9 1.4 - - - -
413A VAL* 1.3 78.2 - - - +
415A LYS* 1.3 60.9 + - - +
418A GLY* 3.4 0.5 + - - -
419A LEU* 2.7 34.9 + - - -
420A THR* 3.1 23.5 + - - -
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Residues in contact with LYS 415 (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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411A LEU* 3.7 24.4 + - - +
412A LYS* 3.1 17.8 + - + +
414A GLY* 1.3 74.0 - - - +
416A ASP* 1.3 73.2 - - - +
418A GLY* 2.8 15.3 + - - -
420A THR* 4.7 9.2 - - + +
422A GLU* 3.9 24.2 - - - +
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Residues in contact with ASP 416 (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 GLU* 3.7 8.7 - - - +
337A TYR* 3.2 37.6 + - - +
412A LYS* 3.1 30.6 + - - +
413A VAL 4.1 1.6 - - - +
415A LYS* 1.3 79.1 - - - +
417A LEU* 1.3 63.4 + - + +
418A GLY 2.8 6.6 + - - -
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Residues in contact with LEU 417 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A VAL* 3.5 24.7 - - + -
324A PRO 3.6 15.9 - - - +
325A GLY 4.4 3.8 - - - +
326A GLY* 4.3 2.9 - - - -
329A LEU* 4.3 22.4 - - + -
333A GLN* 6.3 0.9 - - + -
337A TYR* 3.7 21.5 - - + +
413A VAL* 3.2 25.1 + - + +
416A ASP* 1.3 80.9 - - + +
418A GLY* 1.3 65.2 + - - +
419A LEU* 3.3 16.3 + - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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