Contacts of the helix formed by residues 334 - 351 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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328A TYR* 4.0 13.1 + - - -
330A ILE* 5.3 2.7 - - + -
331A ARG* 3.0 25.5 + - + +
333A THR* 1.3 82.3 + - - +
335A GLU* 1.3 59.2 + - - +
336A GLN* 3.0 39.7 + - - +
337A HIS* 3.4 9.0 + - + +
338A LYS* 3.1 26.7 + - - +
483A THR* 6.3 0.4 - - - -
487A LEU* 5.3 4.2 - - - +
495A GLU* 3.3 24.1 + - - +
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Residues in contact with GLU 335 (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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333A THR 3.6 3.9 + - - +
334A ASN* 1.3 74.1 + - - +
336A GLN* 1.3 79.6 + - - +
338A LYS* 3.4 27.6 + - - +
339A ALA* 3.2 18.7 + - - +
342A LYS* 5.1 6.4 + - - -
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Residues in contact with GLN 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A ASN* 3.0 14.4 + - - +
335A GLU* 1.3 88.2 + - - +
337A HIS* 1.3 64.8 + - - +
339A ALA* 3.1 17.8 + - - +
340A VAL* 3.1 17.0 + - - +
483A THR* 4.4 2.5 - - - -
487A LEU* 4.1 12.3 - - + -
495A GLU* 3.0 32.8 - - - +
497A SER* 5.9 0.9 - - - -
498A LEU* 3.6 35.1 - - + +
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Residues in contact with HIS 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A ILE* 4.4 4.6 - - + +
331A ARG 4.0 12.1 - - - +
332A THR* 3.3 31.8 - - + -
334A ASN* 3.4 14.6 + - + +
335A GLU 3.4 0.4 - - - -
336A GLN* 1.3 78.6 - - - +
338A LYS* 1.3 64.3 + - - +
340A VAL* 3.0 12.8 + - - +
341A VAL* 3.1 24.7 + - + +
461A ILE* 4.2 2.0 - - + -
476A ASP* 2.8 43.4 + - - -
479A THR 3.7 3.8 - - - -
480A ASN* 3.4 27.7 - - + +
483A THR* 3.2 35.3 + - + +
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Residues in contact with LYS 338 (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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289A HIS* 3.7 26.5 + - - -
332A THR 4.1 4.5 - - - +
333A THR* 4.4 11.7 - - - +
334A ASN 3.1 14.6 + - - +
335A GLU* 3.5 31.5 + - - +
336A GLN 3.2 0.2 - - - -
337A HIS* 1.3 78.1 - - - +
339A ALA* 1.3 62.0 + - - +
341A VAL* 3.4 3.8 + - - +
342A LYS* 3.2 40.8 + - - +
460A ALA 4.5 10.7 + - - -
461A ILE* 4.0 29.4 - - + +
462A PRO* 5.2 5.6 - - + +
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Residues in contact with ALA 339 (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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335A GLU 3.2 13.0 + - - +
336A GLN* 3.1 12.4 + - - +
338A LYS* 1.3 75.7 - - - +
340A VAL* 1.3 62.6 + - - +
342A LYS* 3.3 11.2 + - - +
343A GLU* 3.0 32.4 + - + +
498A LEU* 4.2 14.8 - - + -
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Residues in contact with VAL 340 (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 GLN 3.1 10.5 + - - +
337A HIS 3.0 2.9 + - - +
339A ALA* 1.3 71.8 - - - +
341A VAL* 1.3 60.0 + - - +
343A GLU* 3.1 5.8 + - - +
344A LEU* 2.8 28.9 + - - +
479A THR* 3.4 15.5 - - + -
482A LEU* 3.8 16.2 - - + -
483A THR* 3.2 32.8 - - - +
486A ARG* 3.9 11.9 - - - +
498A LEU* 3.7 29.2 - - + -
806A GOL 3.2 20.6 - - - +
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Residues in contact with VAL 341 (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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337A HIS* 3.1 40.8 + - + +
338A LYS 3.6 6.7 - - - +
340A VAL* 1.3 75.0 - - - +
342A LYS* 1.3 59.1 + - - +
344A LEU* 3.2 2.3 + - - +
345A TRP* 2.8 30.6 + - + +
461A ILE* 3.7 24.0 - - + -
471A VAL* 4.0 35.0 - - + -
475A LEU* 5.2 2.9 - - + +
476A ASP* 4.1 8.7 - - - +
479A THR* 3.9 19.5 - - + +
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Residues in contact with LYS 342 (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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335A GLU* 5.1 7.1 + - - -
338A LYS* 3.2 25.6 + - - +
339A ALA* 3.6 10.9 - - - +
340A VAL 3.2 0.2 - - - -
341A VAL* 1.3 78.1 - - + +
343A GLU* 1.3 59.2 + - + +
345A TRP* 3.7 2.9 - - - +
346A THR* 2.9 29.8 + - - -
461A ILE* 4.0 26.0 - - + -
462A PRO* 4.2 18.5 - - - +
464A PRO* 4.0 26.9 - - + +
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Residues in contact with GLU 343 (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 ALA* 3.0 25.6 + - - +
340A VAL* 3.1 8.5 + - - +
342A LYS* 1.3 73.0 - - + +
344A LEU* 1.3 65.9 + - - +
346A THR* 3.1 8.4 + - - -
347A LYS* 3.1 21.7 + - - +
486A ARG* 2.9 38.7 + - - -
498A LEU* 5.2 2.1 - - - +
500A ASP* 4.8 2.1 - - - +
806A GOL 3.5 14.6 + - - +
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Residues in contact with LEU 344 (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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340A VAL 2.8 20.1 + - - +
341A VAL* 3.7 4.7 - - - +
343A GLU* 1.3 72.5 - - - +
345A TRP* 1.3 63.7 + - - +
347A LYS* 3.2 3.3 + - - +
348A LEU* 3.1 34.2 + - + +
475A LEU* 4.3 13.2 - - + -
479A THR* 3.1 33.2 - - + +
482A LEU* 4.4 8.1 - - + -
527A TRP* 4.6 13.5 - - + -
530A PHE* 4.8 7.0 - - + +
531A LEU* 5.8 0.7 - - + -
534A ALA* 3.8 26.9 - - + -
536A LEU* 4.5 12.6 - - + -
806A GOL 3.5 14.5 - - - -
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Residues in contact with TRP 345 (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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341A VAL* 2.8 22.3 + - + +
342A LYS* 3.7 8.5 - - - +
344A LEU* 1.3 74.2 - - - +
346A THR* 1.3 66.7 + - - +
348A LEU* 3.2 11.0 + - - +
349A GLU* 3.0 22.3 + - + +
354A ILE* 4.0 16.3 - - + +
405A TYR* 3.8 23.3 - + + -
449A VAL* 3.4 48.2 - - + -
463A VAL* 3.6 31.9 - - + +
464A PRO* 3.8 22.0 - - + -
471A VAL* 3.8 22.2 - - + -
475A LEU* 3.9 18.4 - - + +
807A GOL 3.6 27.1 + - - -
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Residues in contact with THR 346 (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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342A LYS 2.9 20.4 + - - -
343A GLU* 3.1 7.8 + - - -
345A TRP* 1.3 82.1 - - - +
347A LYS* 1.3 58.5 + - - +
349A GLU* 3.2 5.1 + - + +
350A GLN* 2.8 55.9 + - + +
464A PRO* 4.4 14.0 - - - +
807A GOL 5.8 1.6 - - - -
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Residues in contact with LYS 347 (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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343A GLU 3.1 11.7 + - - +
344A LEU 3.2 8.0 + - - +
346A THR* 1.3 74.9 - - - +
348A LEU* 1.3 66.5 + - - +
350A GLN* 3.2 13.4 + - + +
351A LYS* 2.9 27.4 + - + +
533A SER 5.6 0.4 - - - +
534A ALA* 3.3 38.0 + - + +
535A GLY* 5.3 3.2 + - - -
536A LEU* 5.5 4.4 - - - +
806A GOL 2.9 28.5 + - - +
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Residues in contact with LEU 348 (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 LEU* 3.1 28.6 + - + +
345A TRP* 3.2 8.9 + - - +
347A LYS* 1.3 77.2 - - - +
349A GLU* 1.3 61.3 + - - +
351A LYS* 3.5 3.3 + - - +
353A ASP* 3.2 27.0 + - - +
354A ILE* 3.8 22.2 - - + -
407A PHE* 4.0 9.9 - - + -
475A LEU* 4.2 20.4 - - + -
530A PHE* 3.5 37.5 - - + +
533A SER* 3.2 34.3 - - - +
534A ALA* 4.0 8.5 - - + +
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Residues in contact with GLU 349 (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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345A TRP* 3.0 17.7 + - - +
346A THR* 3.6 8.3 - - + +
347A LYS 3.1 0.2 - - - -
348A LEU* 1.3 75.2 - - - +
350A GLN* 1.3 76.0 + - - +
352A GLY* 2.9 16.1 + - - -
353A ASP 4.2 0.2 + - - -
354A ILE* 4.4 30.6 + - + +
807A GOL 3.3 41.6 - - - +
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Residues in contact with GLN 350 (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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346A THR* 2.8 41.4 + - + +
347A LYS* 3.8 12.2 - - + +
349A GLU* 1.3 85.7 - - - +
351A LYS* 1.3 59.4 + - - +
352A GLY* 3.1 1.8 + - - -
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Residues in contact with LYS 351 (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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347A LYS* 2.9 19.3 + - + +
348A LEU 3.7 7.0 - - - +
349A GLU 3.1 0.4 - - - -
350A GLN* 1.3 74.7 - - - +
352A GLY* 1.3 60.3 + - - +
353A ASP* 3.6 17.6 - - - +
415A ARG* 6.4 0.2 - - - +
532A LEU 5.5 1.6 - - - -
533A SER* 3.3 29.4 - - - +
534A ALA 5.9 0.2 - - - -
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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
------------------------------------------------------------
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