Contacts of the helix formed by residues 435 - 457 (chain C) in PDB entry 5NTI
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 GLU 435 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343C GLU 5.0 0.9 - - - +
344C LEU* 4.5 1.7 - - + +
345C CYS* 3.7 38.8 + - - +
348C ASP* 2.9 12.9 + - - +
434C GLN* 1.3 82.7 - - + +
436C LYS* 1.3 63.9 + - - +
437C ARG* 3.3 3.1 - - - -
438C LYS* 3.2 60.2 + - + +
439C VAL* 3.4 10.1 + - - +
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Residues in contact with LYS 436 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428C ALA* 3.4 28.3 - - - +
429C HIS* 5.1 12.9 - - - +
433C LEU* 4.6 20.9 - - + +
434C GLN 3.7 3.0 - - - +
435C GLU* 1.3 73.5 - - - +
437C ARG* 1.3 57.9 + - + +
439C VAL* 3.2 5.9 + - - +
440C GLU* 2.9 51.0 + - + +
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Residues in contact with ARG 437 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435C GLU 3.3 1.0 - - - -
436C LYS* 1.3 78.4 - - + +
438C LYS* 1.3 56.4 + - - +
440C GLU* 3.4 13.9 + - - +
441C GLN* 3.0 27.9 + - - +
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Residues in contact with LYS 438 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343C GLU* 4.8 9.9 - - + +
344C LEU* 4.0 20.5 - - + +
435C GLU* 3.2 53.6 + - + +
437C ARG* 1.3 76.9 - - - +
439C VAL* 1.3 62.9 + - - +
441C GLN* 3.5 8.0 + - + +
442C LEU* 3.2 22.3 + - - +
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Residues in contact with VAL 439 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344C LEU* 4.4 19.5 - - + -
348C ASP* 4.0 13.9 - - - +
352C LEU* 4.3 11.0 - - + -
426C ILE* 3.8 19.5 - - + -
427C ASN 4.0 5.6 - - - +
428C ALA* 3.7 27.8 - - + +
433C LEU* 4.1 18.2 - - + -
435C GLU 3.6 14.1 - - - +
436C LYS 3.2 5.3 + - - +
438C LYS* 1.3 72.7 - - - +
440C GLU* 1.3 57.2 + - - +
442C LEU* 3.3 4.6 + - - +
443C GLN* 2.8 36.6 + - - +
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Residues in contact with GLU 440 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428C ALA* 3.7 19.9 - - + +
436C LYS* 2.9 41.2 + - + +
437C ARG* 3.5 16.5 - - - +
439C VAL* 1.3 76.7 - - - +
441C GLN* 1.3 55.2 + - - +
443C GLN* 3.5 9.8 + - - +
444C TYR* 3.1 29.8 + - - +
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Residues in contact with GLN 441 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264C TYR* 5.2 13.1 + - - +
437C ARG 3.0 17.0 + - - +
438C LYS* 3.6 9.0 - - + +
439C VAL 3.2 0.2 - - - -
440C GLU* 1.3 73.7 - - - +
442C LEU* 1.3 64.4 + - - +
444C TYR* 3.5 11.0 + - - +
445C ASN* 3.2 42.3 + - - +
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Residues in contact with LEU 442 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273C LEU* 5.3 7.0 - - + -
338C LEU* 5.8 0.7 - - + -
339C SER 3.5 20.9 - - - +
340C GLY* 3.8 31.9 - - - +
341C PHE* 4.0 2.5 - - + +
344C LEU* 4.6 9.6 - - + -
426C ILE* 3.9 34.3 - - + -
438C LYS 3.2 13.7 + - - +
439C VAL* 3.3 5.4 + - - +
441C GLN* 1.3 75.9 - - - +
443C GLN* 1.3 65.8 + - - +
445C ASN* 3.5 12.8 + - + +
446C LEU* 3.1 36.9 + - + +
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Residues in contact with GLN 443 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423C LEU* 3.7 6.4 - - + +
426C ILE* 3.6 25.5 - - + +
427C ASN* 4.0 7.3 - - - +
428C ALA* 3.5 36.2 + - + +
429C HIS* 4.5 14.0 + - - -
439C VAL 2.8 17.5 + - - +
440C GLU* 3.6 11.3 + - - +
442C LEU* 1.3 76.1 - - - +
444C TYR* 1.3 56.4 + - - +
446C LEU* 3.2 8.2 + - - +
447C GLU* 2.9 47.9 + - - +
469C LYS* 4.5 7.6 + - - -
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Residues in contact with TYR 444 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440C GLU 3.1 18.1 + - - +
441C GLN* 3.9 11.0 - - - +
442C LEU 3.3 0.2 - - - -
443C GLN* 1.3 73.7 - - - +
445C ASN* 1.3 70.2 + - - +
447C GLU* 3.2 24.0 + - + +
448C LEU* 3.0 59.9 + - + +
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Residues in contact with ASN 445 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265C ALA* 3.8 27.9 + - - +
270C ILE* 3.4 16.6 - - + +
273C LEU* 3.7 18.2 - - + -
441C GLN* 3.2 37.9 + - - +
442C LEU* 3.8 11.0 - - + +
444C TYR* 1.3 78.8 - - - +
446C LEU* 1.3 57.9 + - - +
448C LEU* 3.3 8.4 + - - +
449C ALA* 2.8 26.2 + - - +
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Residues in contact with LEU 446 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273C LEU* 4.0 17.5 - - + -
277C VAL* 3.7 30.5 - - + -
338C LEU* 5.3 2.9 - - + -
339C SER 5.9 1.3 - - - +
419C LEU* 5.3 6.0 - - + +
422C ALA* 3.8 21.3 - - + +
423C LEU* 3.5 15.0 - - + +
426C ILE* 3.7 36.6 - - + -
442C LEU* 3.1 26.2 + - + +
443C GLN* 3.4 8.1 - - - +
445C ASN* 1.3 75.0 - - - +
447C GLU* 1.3 60.3 + - - +
449C ALA* 3.3 7.4 + - + +
450C PHE* 2.9 28.9 + - - +
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Residues in contact with GLU 447 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423C LEU* 3.7 19.6 - - + +
443C GLN* 2.9 35.6 + - - +
444C TYR* 3.2 35.4 + - + +
446C LEU* 1.3 73.6 - - - +
448C LEU* 1.3 57.4 + - + +
450C PHE* 3.4 5.6 + - - +
451C HIS* 2.8 48.9 + - + +
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Residues in contact with LEU 448 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265C ALA* 5.2 7.2 - - + +
270C ILE* 3.8 27.6 - - + -
444C TYR* 3.0 56.0 + - + +
445C ASN* 3.4 12.3 - - - +
447C GLU* 1.3 76.3 - - + +
449C ALA* 1.3 59.2 + - - +
451C HIS* 3.8 8.3 - - + +
452C HIS* 2.8 34.0 + - - +
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Residues in contact with ALA 449 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270C ILE* 3.7 16.3 - - + +
273C LEU* 4.2 13.7 - - + -
274C VAL* 3.5 23.9 - - + +
419C LEU* 4.2 12.9 - - + +
445C ASN 2.8 14.4 + - - +
446C LEU* 3.4 14.1 - - + +
448C LEU* 1.3 75.3 - - - +
450C PHE* 1.3 61.8 + - - +
452C HIS* 4.0 0.3 - - - +
453C HIS* 3.2 25.8 + - - +
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Residues in contact with PHE 450 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412C PHE* 4.7 2.9 - + - -
416C GLU* 4.0 24.9 - - + -
419C LEU* 3.7 26.0 - - + +
420C TYR* 4.2 23.8 - + + -
423C LEU* 3.7 23.8 - - + -
446C LEU 2.9 16.3 + - - +
447C GLU* 3.5 5.8 - - - +
449C ALA* 1.3 74.9 - - - +
451C HIS* 1.3 68.1 + + - +
453C HIS* 3.4 2.6 + - + +
454C LEU* 3.1 59.6 + - + +
462C ILE* 4.7 7.6 - - + -
463C LEU* 4.4 7.4 - - + -
466C LEU* 4.1 24.7 - - + -
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Residues in contact with HIS 451 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447C GLU* 2.8 38.7 + - + +
448C LEU* 3.8 9.9 - - + +
450C PHE* 1.3 79.3 - + - +
452C HIS* 1.3 62.7 + - - +
454C LEU* 3.2 17.2 + - + +
455C SER* 3.2 14.6 + - - -
460C GLN* 4.0 22.7 + - - +
463C LEU* 4.1 29.2 - - + +
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Residues in contact with HIS 452 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267C LEU* 3.9 21.5 - - + +
270C ILE* 4.3 17.7 - - + -
271C GLU* 3.3 37.7 + - + +
274C VAL* 4.8 8.1 - - + -
448C LEU 2.8 21.3 + - - +
449C ALA 4.0 2.5 - - - +
451C HIS* 1.3 73.2 - - - +
453C HIS* 1.3 62.5 + - - +
455C SER* 3.2 24.9 + - - -
456C LYS* 3.3 36.3 + - + +
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Residues in contact with HIS 453 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274C VAL* 3.8 22.3 - - + +
413C SER* 5.1 1.2 + - - -
415C ASP* 3.5 37.3 - - + +
416C GLU* 4.3 20.6 + - + +
419C LEU* 3.9 19.7 - - + -
449C ALA 3.2 19.2 + - - +
450C PHE 3.8 3.6 - - - +
451C HIS 3.3 0.2 - - - -
452C HIS* 1.3 77.8 - - - +
454C LEU* 1.3 61.3 + - + +
456C LYS* 3.5 16.3 + - + +
457C THR* 3.1 44.5 + - + +
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Residues in contact with LEU 454 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416C GLU* 4.4 14.1 - - + +
450C PHE* 3.1 50.5 + - + +
451C HIS* 3.2 8.3 + - - +
453C HIS* 1.3 78.4 - - + +
455C SER* 1.3 55.5 + - - +
457C THR* 3.6 2.1 + - - -
458C HIS 3.1 3.8 + - - -
459C ARG* 2.6 58.3 + - + +
460C GLN* 3.3 13.7 + - + -
462C ILE* 3.7 19.7 - - + -
463C LEU* 3.8 34.8 - - + -
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Residues in contact with SER 455 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451C HIS 3.2 7.7 + - - -
452C HIS* 3.2 18.0 + - - -
453C HIS 3.3 0.2 - - - -
454C LEU* 1.3 73.9 - - - +
456C LYS* 1.3 70.1 + - - +
457C THR 3.2 0.2 - - - -
458C HIS* 3.0 21.6 + - - +
460C GLN* 3.4 27.5 - - - +
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Residues in contact with LYS 456 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271C GLU* 3.4 26.2 + - - +
274C VAL* 6.3 1.2 - - - +
452C HIS* 3.3 40.7 + - + +
453C HIS* 3.6 20.6 - - + +
455C SER* 1.3 84.0 + - - +
457C THR* 1.3 61.9 + - + +
458C HIS* 3.7 11.6 + - - -
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Residues in contact with THR 457 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416C GLU* 4.0 8.2 + - - +
453C HIS* 3.1 36.0 + - + +
454C LEU* 3.6 2.4 + - - -
456C LYS* 1.3 77.3 - - + +
458C HIS* 1.3 72.1 + - - +
459C ARG* 3.0 37.2 + - - +
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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