Contacts of the helix formed by residues 449 - 470 (chain P) in PDB entry 1E3C
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 THR 449 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448P ALA* 1.3 77.2 + - - +
450P PRO* 1.3 67.1 - - + +
451P GLU* 2.8 30.7 - - + +
452P VAL* 2.9 24.2 + - + +
453P LEU* 2.7 33.8 + - - +
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Residues in contact with PRO 450 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448P ALA 4.4 1.3 - - - +
449P THR* 1.3 93.3 - - + +
451P GLU* 1.3 59.6 + - - +
453P LEU* 4.2 8.9 - - + +
454P GLN* 3.1 24.1 + - - +
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Residues in contact with GLU 451 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393P LYS* 3.6 21.9 + - - -
394P TYR* 2.5 40.0 + - - +
449P THR* 2.8 14.6 - - + +
450P PRO* 1.3 78.5 - - - +
452P VAL* 1.3 60.2 + - - +
454P GLN* 3.2 4.6 + - - +
455P ALA* 2.9 29.3 + - - +
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Residues in contact with VAL 452 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394P TYR* 4.4 11.7 - - + +
428P LEU* 3.4 26.7 - - + -
441P LEU* 4.3 27.1 - - + +
442P LEU* 3.7 19.7 - - + -
448P ALA* 5.0 3.8 - - + -
449P THR* 2.9 27.7 + - + +
451P GLU* 1.3 78.4 - - + +
453P LEU* 1.3 60.5 - - + +
455P ALA* 2.9 9.9 + - - +
456P LEU* 2.7 25.9 + - + +
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Residues in contact with LEU 453 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442P LEU* 6.4 1.6 - - + -
448P ALA* 4.6 17.0 - - + +
449P THR 2.7 20.5 + - - +
450P PRO* 4.2 7.2 - - + +
452P VAL* 1.3 75.8 - - + +
454P GLN* 1.4 64.0 + - - +
456P LEU* 3.1 20.6 + - + +
457P LYS* 3.0 44.9 + - + +
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Residues in contact with GLN 454 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450P PRO 3.1 19.1 + - - +
451P GLU* 3.6 4.0 - - - +
452P VAL 3.1 0.4 - - - -
453P LEU* 1.4 76.5 - - - +
455P ALA* 1.3 64.7 + - - +
457P LYS* 3.2 8.1 + - - +
458P GLN* 3.1 27.8 + - + +
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Residues in contact with ALA 455 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394P TYR* 3.5 41.7 - - + -
428P LEU* 5.2 2.5 - - + -
451P GLU 2.9 12.9 + - - +
452P VAL* 3.2 9.9 - - - +
454P GLN* 1.3 77.0 - - - +
456P LEU* 1.3 62.1 + - - +
458P GLN* 3.4 5.8 + - - +
459P LEU* 2.9 32.1 + - + +
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Residues in contact with LEU 456 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425P PRO* 4.9 7.2 - - + -
426P PRO* 3.9 22.9 - - + -
428P LEU* 4.4 14.3 - - + +
442P LEU* 4.1 26.0 - - + -
452P VAL* 2.7 18.9 + - + +
453P LEU* 3.1 22.0 + - + +
455P ALA* 1.3 73.4 - - - +
457P LYS* 1.3 59.3 + - + +
459P LEU* 3.3 6.4 + - + -
460P GLN* 3.0 62.7 + - + +
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Residues in contact with LYS 457 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453P LEU* 3.0 35.6 + - + +
454P GLN* 3.2 7.2 + - - +
456P LEU* 1.3 79.1 - - + +
458P GLN* 1.3 65.9 + - - +
460P GLN* 3.4 8.4 + - - +
461P LEU* 2.8 31.0 + - - +
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Residues in contact with GLN 458 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391P THR* 5.9 6.7 - - + -
454P GLN* 3.1 17.1 + - + +
455P ALA* 3.8 6.1 - - - +
457P LYS* 1.3 83.6 - - - +
459P LEU* 1.3 58.1 + - + +
461P LEU* 2.9 26.1 + - - +
462P LEU* 2.9 40.5 + - + +
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Residues in contact with LEU 459 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389P VAL* 3.6 34.2 - - + +
391P THR* 3.8 30.7 - - - +
394P TYR* 3.9 17.7 - - + +
396P ALA* 3.8 24.0 - - + +
398P PHE* 3.9 11.1 - - + -
428P LEU* 3.6 31.0 - - + -
455P ALA* 2.9 24.5 + - - +
456P LEU* 3.9 4.7 - - + +
458P GLN* 1.3 70.6 - - + +
460P GLN* 1.3 63.4 + - + +
462P LEU* 3.4 5.0 + - - +
463P LYS* 3.1 18.0 + - - +
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Residues in contact with GLN 460 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398P PHE* 4.1 17.4 - - + -
424P GLU* 2.7 30.7 + - - -
425P PRO* 4.9 1.7 - - - +
426P PRO* 3.4 12.5 - - - +
456P LEU* 3.0 42.1 + - + +
457P LYS* 3.7 8.6 - - - +
459P LEU* 1.3 76.2 - - + +
461P LEU* 1.3 62.5 - - - +
463P LYS* 3.4 3.1 + - - +
464P ALA* 3.1 24.1 + - - +
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Residues in contact with LEU 461 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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457P LYS 2.8 17.3 + - - +
458P GLN* 3.6 26.2 - - - +
460P GLN* 1.3 78.8 - - - +
462P LEU* 1.3 56.7 + - - +
464P ALA* 3.3 6.2 + - + -
465P GLN* 3.0 60.7 + - + +
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Residues in contact with LEU 462 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372P SER* 3.4 19.5 - - - +
374P PHE* 4.0 21.1 - - + -
389P VAL* 4.2 10.5 - - + -
391P THR* 3.1 30.3 - - + +
458P GLN* 2.9 23.8 + - + +
459P LEU* 3.8 6.3 - - + +
461P LEU* 1.3 74.9 - - - +
463P LYS* 1.3 62.7 + - - +
465P GLN* 3.3 18.7 + - + +
466P LEU* 3.0 25.3 + - - +
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Residues in contact with LYS 463 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384P ARG 2.7 29.8 + - - -
386P VAL* 2.7 35.9 + - + +
389P VAL* 4.0 5.5 - - + +
398P PHE* 3.2 51.4 - - + -
399P PHE* 4.4 4.6 - - - -
459P LEU 3.1 16.3 + - - +
460P GLN 4.1 3.4 - - - +
462P LEU* 1.3 76.4 - - - +
464P ALA* 1.3 68.3 + - + +
466P LEU* 4.9 1.1 - - - -
467P ASP* 2.7 49.1 + - - +
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Residues in contact with ALA 464 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460P GLN 3.1 17.5 + - - +
461P LEU* 4.1 8.1 - - + +
463P LYS* 1.3 81.2 - - + +
465P GLN* 1.3 56.4 + - - +
467P ASP* 3.8 4.2 - - - +
468P ALA* 3.0 30.7 + - - +
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Residues in contact with GLN 465 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461P LEU* 3.0 46.3 + - + +
462P LEU* 3.6 25.9 - - + +
464P ALA* 1.3 73.6 - - - +
466P LEU* 1.3 69.0 + - - +
468P ALA* 3.3 5.7 + - - +
469P ALA* 3.1 22.6 + - - +
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Residues in contact with LEU 466 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81P LEU* 4.1 13.2 - - + -
84P ARG* 5.2 3.1 - - - +
354P ASP* 5.7 0.2 - - - +
374P PHE* 3.9 33.9 - - + -
376P TYR* 3.2 17.0 - - + +
386P VAL* 3.1 35.9 - - + -
462P LEU 3.0 15.5 + - - +
463P LYS 4.2 1.1 - - - +
465P GLN* 1.3 73.5 - - - +
467P ASP* 1.3 64.6 + - - +
469P ALA* 3.0 17.5 + - + -
470P VAL* 3.0 35.4 + - + +
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Residues in contact with ASP 467 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376P TYR* 4.3 4.8 + - - -
382P GLU 6.0 1.6 - - - +
384P ARG 3.9 1.0 - - - +
385P GLY* 3.1 14.7 - - - -
386P VAL* 2.9 28.6 + - - +
463P LYS* 2.7 58.0 + - - +
464P ALA* 4.0 4.7 - - - +
466P LEU* 1.3 73.4 - - - +
468P ALA* 1.3 59.8 + - - +
470P VAL* 4.1 11.7 - - - +
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Residues in contact with ALA 468 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464P ALA 3.0 22.0 + - - +
465P GLN* 4.0 4.3 - - - +
466P LEU 3.2 0.4 - - - -
467P ASP* 1.3 71.8 - - - +
469P ALA* 1.3 57.7 + - - +
470P VAL 5.0 1.2 - - - +
471P THR* 5.9 2.3 - - - +
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Residues in contact with ALA 469 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84P ARG* 5.1 2.6 + - - -
465P GLN 3.1 15.2 + - - +
466P LEU* 3.0 7.1 + - + +
468P ALA* 1.3 75.6 - - - +
470P VAL* 1.3 61.9 + - + +
471P THR* 3.7 3.2 + - - +
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Residues in contact with VAL 470 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81P LEU* 4.5 5.2 - - + -
83P VAL* 3.7 27.4 - - + -
84P ARG* 3.9 33.4 - - + +
376P TYR* 4.3 9.9 - - - +
382P GLU* 4.3 5.0 - - - +
466P LEU* 3.0 44.8 + - + +
467P ASP* 4.1 9.9 - - - +
468P ALA 5.0 0.9 - - - +
469P ALA* 1.3 71.9 - - + +
471P THR* 1.3 74.7 + - - +
472P PHE* 3.9 9.3 + - + -
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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
------------------------------------------------------------
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