Contacts of the helix formed by residues 334 - 351 (chain B) in PDB entry 4EGA
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 ASN 334 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305B TYR* 5.9 1.3 - - - -
328B TYR* 4.1 7.1 + - - +
330B ILE* 5.5 2.9 - - + -
331B ARG* 2.9 25.9 + - + +
332B THR 4.0 0.2 - - - +
333B THR* 1.3 82.7 + - - +
335B GLU* 1.3 64.4 + - - +
336B GLN* 2.7 42.4 + - - +
337B HIS* 3.3 16.5 + - + +
338B LYS* 3.4 12.6 + - - +
483B THR* 5.4 0.4 - - - +
487B LEU* 5.3 1.5 - - - +
495B GLU* 3.2 37.5 + - - +
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Residues in contact with GLU 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B THR 3.5 4.5 + - - +
334B ASN* 1.3 72.2 + - - +
336B GLN* 1.3 70.2 + - + +
338B LYS* 3.1 44.3 + - - +
339B ALA* 2.9 21.3 + - - +
807B GOL 4.1 4.2 - - - -
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Residues in contact with GLN 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B ASN* 2.7 31.0 + - - +
335B GLU* 1.3 76.6 - - + +
337B HIS* 1.3 59.8 + - - +
339B ALA* 3.2 10.6 + - - +
340B VAL* 3.1 25.5 + - - +
483B THR* 4.2 2.9 - - + -
487B LEU* 3.9 24.0 - - + +
495B GLU* 4.0 16.8 - - + +
496B VAL 4.3 5.5 + - - -
497B SER* 4.0 8.1 - - - +
498B LEU* 3.7 38.1 - - + +
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Residues in contact with HIS 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B ILE* 4.3 4.5 - - + +
331B ARG 4.2 10.5 - - - +
332B THR* 3.6 29.4 - - + +
334B ASN* 3.3 12.9 + - + +
335B GLU 3.2 0.2 - - - -
336B GLN* 1.3 79.8 - - - +
338B LYS* 1.3 55.7 + - - +
340B VAL 3.3 1.0 + - - -
341B VAL* 2.9 49.5 + - + +
461B ILE* 4.3 3.4 - - + -
476B ASP* 3.0 44.4 + - - -
479B THR 3.7 0.4 - - - -
480B ASN* 3.3 28.0 - - + -
483B THR* 2.8 38.1 + - + +
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Residues in contact with LYS 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B THR 4.4 4.0 - - - +
333B THR 3.7 9.0 - - - -
334B ASN 3.5 9.4 - - - +
335B GLU* 3.1 36.2 + - - +
337B HIS* 1.3 75.6 - - - +
339B ALA* 1.3 64.5 + - - +
341B VAL* 3.4 6.3 + - - +
342B LYS* 2.9 51.9 + - - +
460B ALA 5.2 0.4 + - - -
461B ILE* 3.9 27.7 - - + +
462B PRO* 5.6 4.2 - - - +
807B GOL 2.9 56.8 + - - -
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Residues in contact with ALA 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335B GLU 2.9 11.9 + - - +
336B GLN* 3.3 12.3 - - - +
338B LYS* 1.3 76.2 - - - +
340B VAL* 1.3 58.2 + - - +
342B LYS* 3.2 10.8 + - - +
343B GLU* 2.9 38.8 + - - +
498B LEU* 3.8 17.7 - - + -
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Residues in contact with VAL 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B GLN 3.1 7.8 + - - +
337B HIS 3.8 0.4 - - - +
339B ALA* 1.3 75.2 - - - +
341B VAL* 1.3 57.5 - - - +
343B GLU* 3.1 8.6 + - - +
344B LEU* 2.8 28.9 + - - +
479B THR* 3.8 14.4 - - + -
482B LEU* 3.8 20.9 - - + -
483B THR* 3.5 28.9 - - - +
486B ARG* 3.7 22.9 - - - +
498B LEU* 3.4 38.6 - - + -
802B GOL 4.4 0.4 - - - +
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Residues in contact with VAL 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B HIS* 2.9 53.5 + - + +
338B LYS 3.8 3.8 - - - +
339B ALA 3.3 0.2 - - - -
340B VAL* 1.3 76.5 - - - +
342B LYS* 1.3 58.0 + - - +
344B LEU* 4.0 1.8 - - - +
345B TRP* 2.9 27.9 + - + +
461B ILE* 4.1 21.5 - - + -
471B VAL* 4.1 26.0 - - + -
475B LEU* 3.6 26.0 - - + +
476B ASP 4.2 0.9 - - - +
479B THR* 3.9 10.1 - - + -
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Residues in contact with LYS 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B LYS* 2.9 38.6 + - - +
339B ALA* 3.5 7.9 - - - +
341B VAL* 1.3 75.1 - - - +
343B GLU* 1.3 59.6 + - + +
345B TRP* 3.4 2.1 - - - +
346B THR* 2.9 34.9 + - - -
461B ILE* 3.9 21.7 - - + +
462B PRO* 4.2 24.0 - - - +
464B PRO* 3.9 31.5 - - + +
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Residues in contact with GLU 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B ALA* 2.9 29.2 + - - +
340B VAL 3.1 6.0 + - - +
342B LYS* 1.3 73.7 - - + +
344B LEU* 1.3 64.8 + - - +
346B THR* 3.2 5.7 + - - -
347B LYS* 3.0 24.4 + - - +
486B ARG* 3.1 38.7 + - - -
498B LEU* 4.7 2.3 - - - +
500B ASP* 5.2 2.3 - - - +
802B GOL 3.9 13.9 + - - +
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Residues in contact with LEU 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B VAL 2.8 19.7 + - - +
341B VAL* 4.0 4.7 - - - +
343B GLU* 1.3 72.9 - - - +
345B TRP* 1.3 64.5 + - - +
347B LYS* 3.3 1.8 + - + +
348B LEU* 3.1 41.6 + - + +
475B LEU* 4.1 15.5 - - + +
479B THR* 3.6 31.2 - - + +
482B LEU* 4.4 8.1 - - + -
527B TRP* 5.0 9.4 - - + -
530B PHE* 4.6 11.2 - - + +
531B LEU* 5.8 1.3 - - + -
534B ALA* 3.6 31.0 - - + -
536B LEU* 4.5 11.4 - - + -
802B GOL 4.1 13.1 + - - +
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Residues in contact with TRP 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B VAL* 2.9 20.5 + - + +
342B LYS* 3.4 7.4 - - - +
344B LEU* 1.3 79.0 - - - +
346B THR* 1.3 67.4 + - - +
348B LEU* 3.4 4.3 + - - +
349B GLU* 3.1 32.8 + - + +
354B ILE* 3.9 14.6 - - + +
405B TYR* 3.5 35.5 - + + -
449B VAL* 3.6 45.8 - - + -
450B SER* 4.3 0.7 - - - -
463B VAL* 3.6 30.6 - - + +
464B PRO* 3.7 22.5 + - + +
471B VAL* 3.7 27.8 - - + -
475B LEU* 3.6 25.5 - - + +
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Residues in contact with THR 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B LYS* 2.9 19.4 + - - +
343B GLU* 3.8 6.7 - - - -
344B LEU 3.2 0.2 - - - -
345B TRP* 1.3 78.0 - - - +
347B LYS* 1.3 61.4 + - - +
349B GLU* 3.2 6.6 + - + +
350B GLN* 2.9 54.4 + - + +
464B PRO* 4.0 17.5 - - - +
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Residues in contact with LYS 347 (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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343B GLU 3.0 16.2 + - - +
344B LEU* 3.3 5.4 + - - +
346B THR* 1.3 77.1 - - - +
348B LEU* 1.3 63.1 + - + +
350B GLN* 3.3 17.1 + - + +
351B LYS* 3.2 52.8 + - + +
534B ALA* 3.8 35.2 - - + +
802B GOL 3.9 18.6 - - - +
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Residues in contact with LEU 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B LEU* 3.1 34.0 + - + +
345B TRP 3.6 2.7 - - - +
347B LYS* 1.3 78.6 - - + +
349B GLU* 1.3 58.0 + - - +
351B LYS* 3.5 4.2 + - - +
353B ASP* 3.1 28.1 + - - +
354B ILE* 3.3 30.0 + - + +
407B PHE* 4.2 7.2 - - + -
475B LEU* 3.8 30.1 - - + -
530B PHE* 4.0 22.7 - - + +
533B SER* 3.5 25.8 - - - +
534B ALA* 4.0 12.6 - - + +
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Residues in contact with GLU 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345B TRP* 3.1 28.6 + - + +
346B THR* 3.2 13.3 + - + +
348B LEU* 1.3 74.9 - - - +
350B GLN* 1.3 72.0 + - - +
352B GLY* 3.2 13.5 + - - -
354B ILE* 4.0 28.9 - - + +
355B TYR* 5.6 1.2 - - - -
356B LEU 5.9 0.3 + - - -
405B TYR* 5.4 9.9 - - + -
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Residues in contact with GLN 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B THR* 2.9 39.9 + - + +
347B LYS* 3.3 19.2 + - + +
349B GLU* 1.3 82.8 - - - +
351B LYS* 1.3 60.8 + - + +
352B GLY* 3.1 1.3 + - - -
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Residues in contact with LYS 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347B LYS* 3.2 44.0 + - + +
348B LEU 3.5 3.1 + - - +
349B GLU 3.3 0.4 - - - -
350B GLN* 1.3 75.5 - - + +
352B GLY* 1.3 61.1 + - - +
353B ASP* 3.2 23.7 + - - +
408B ARG* 5.0 0.7 + - - -
533B SER* 3.7 24.5 - - - +
534B ALA 5.0 2.7 - - - -
535B GLY* 5.8 2.4 - - - -
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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