Contacts of the helix formed by residues 468 - 490 (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 PRO 468 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403C PHE* 5.7 0.3 - - - -
466C LEU 3.8 4.4 - - - +
467C PRO* 1.3 91.6 - - + +
469C LYS* 1.3 65.4 + - - +
470C GLY* 3.1 5.9 + - - +
471C LYS* 3.2 40.4 + - + +
472C LEU* 4.4 1.4 + - - +
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Residues in contact with LYS 469 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427C ASN* 3.7 32.8 + - - +
429C HIS* 3.9 17.0 + - - -
443C GLN* 4.5 6.5 + - - -
467C PRO 3.9 0.8 + - - -
468C PRO* 1.3 72.2 - - - +
470C GLY* 1.3 62.8 + - - +
471C LYS 3.3 0.9 + - - -
472C LEU* 3.5 17.0 + - - +
473C ARG* 3.5 29.9 + - - +
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Residues in contact with GLY 470 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468C PRO* 3.1 5.8 + - - +
469C LYS* 1.3 76.5 - - - +
471C LYS* 1.3 61.2 + - - +
473C ARG* 3.6 23.5 + - - +
474C SER* 2.9 32.8 + - - -
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Residues in contact with LYS 471 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402C ASP* 5.3 7.9 - - - +
403C PHE* 4.2 22.7 - - + -
467C PRO* 4.6 5.2 - - + -
468C PRO* 3.2 36.8 + - + +
470C GLY* 1.3 78.1 - - - +
472C LEU* 1.3 62.4 + - - +
474C SER* 3.2 12.0 + - - -
475C LEU* 3.0 29.9 + - + +
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Residues in contact with LEU 472 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359C GLU* 3.4 44.0 - - + +
362C LEU* 4.1 12.1 - - + -
363C VAL* 4.0 8.1 - - + -
403C PHE* 3.6 31.8 - - + -
420C TYR* 4.7 7.6 - - - +
424C VAL* 3.8 35.4 - - + -
468C PRO 4.4 0.6 + - - +
469C LYS* 3.5 12.0 + - - +
471C LYS* 1.3 77.6 - - - +
473C ARG* 1.3 63.8 + - - +
475C LEU* 3.2 8.9 + - + +
476C CYS* 3.1 26.3 + - - -
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Residues in contact with ARG 473 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359C GLU* 4.0 16.1 + - - +
430C ARG* 5.1 7.2 - - - +
469C LYS* 3.5 30.6 + - - +
470C GLY* 3.8 23.4 - - - +
471C LYS 3.4 0.2 - - - -
472C LEU* 1.3 77.2 - - - +
474C SER* 1.3 57.3 + - - +
476C CYS* 3.3 6.2 + - - +
477C SER* 2.9 35.8 + - - +
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Residues in contact with SER 474 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470C GLY 2.9 20.4 + - - -
471C LYS* 3.2 14.4 + - - -
473C ARG* 1.3 75.8 - - - +
475C LEU* 1.3 58.6 + - - +
477C SER* 3.8 6.9 - - - -
478C GLN* 3.0 51.1 + - - +
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Residues in contact with LEU 475 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358C MET* 5.6 0.7 - - - +
362C LEU* 3.8 27.1 - - + -
396C LEU* 3.5 13.0 - - + +
399C SER* 3.6 33.9 - - - +
400C ILE* 3.7 25.1 - - + +
403C PHE* 3.7 38.4 - - + -
471C LYS* 3.0 19.9 + - + +
472C LEU* 3.2 10.7 + - + +
474C SER* 1.3 77.6 - - - +
476C CYS* 1.3 57.0 + - - +
478C GLN* 4.5 6.7 - - - +
479C HIS* 3.1 24.1 + - - +
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Residues in contact with CYS 476 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355C ALA 5.2 3.1 - - - +
358C MET* 3.7 31.2 - - + -
359C GLU* 3.5 28.3 - - - +
362C LEU* 4.2 5.8 - - - -
472C LEU 3.1 16.8 + - - -
473C ARG* 3.7 8.7 - - - +
475C LEU* 1.3 74.4 - - - +
477C SER* 1.3 60.7 + - - +
479C HIS* 3.3 8.4 + - - +
480C VAL* 3.0 35.4 + - + +
506C PHE* 6.3 1.1 - - + -
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Residues in contact with SER 477 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473C ARG* 2.9 22.9 + - - +
474C SER* 3.8 7.8 - - - -
476C CYS* 1.3 74.6 - - - +
478C GLN* 1.3 61.5 + - - +
480C VAL* 3.3 7.4 + - - +
481C GLU* 2.9 37.3 + - - +
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Residues in contact with GLN 478 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395C GLU* 3.9 16.6 + - - +
396C LEU* 3.7 41.0 + - + +
399C SER* 4.1 16.4 + - - -
474C SER* 3.0 38.4 + - - +
475C LEU* 3.8 3.4 - - - +
477C SER* 1.3 76.5 - - - +
479C HIS* 1.3 54.0 + - - +
481C GLU* 3.6 10.5 - - - +
482C ARG* 2.8 44.1 + - + +
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Residues in contact with HIS 479 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317C TRP* 4.7 1.8 - + - -
324C LEU* 4.2 5.7 - - + +
358C MET* 4.2 16.0 - - + +
396C LEU* 3.9 14.7 - - + +
475C LEU 3.1 15.3 + - - +
476C CYS* 3.5 11.1 + - - +
477C SER 3.2 0.2 - - - -
478C GLN* 1.3 74.1 - - - +
480C VAL* 1.3 65.0 + - - +
482C ARG* 3.5 0.9 + - - +
483C LEU* 3.0 21.4 + - + +
502C TYR* 2.7 31.5 + + - -
506C PHE* 3.4 52.6 - + + -
601C C3S 3.7 31.9 - - + +
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Residues in contact with VAL 480 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476C CYS* 3.0 21.9 + - + +
477C SER* 3.7 7.6 - - - +
479C HIS* 1.3 74.9 - - - +
481C GLU* 1.3 64.9 + - + +
483C LEU* 3.3 6.2 + - - +
484C GLN* 3.1 24.5 + - - +
505C LEU 5.5 1.1 - - - +
506C PHE* 4.1 35.7 - - + +
508C THR* 3.5 21.9 + - + +
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Residues in contact with GLU 481 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477C SER* 2.9 24.2 + - - +
478C GLN* 3.6 11.3 + - - +
480C VAL* 1.3 77.7 - - + +
482C ARG* 1.3 67.2 + - - +
484C GLN* 3.2 28.3 + - - +
485C ILE* 3.3 18.0 + - + +
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Residues in contact with ARG 482 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317C TRP* 3.6 16.3 - - + -
392C GLY 3.1 24.3 + - - -
393C CYS* 3.7 27.0 - - + +
396C LEU* 4.1 18.4 - - + -
478C GLN* 2.8 29.7 + - + +
479C HIS 4.1 2.9 - - - +
481C GLU* 1.3 75.8 - - - +
483C LEU* 1.3 57.4 + - - +
485C ILE* 3.5 40.4 + - - +
486C PHE 3.1 19.9 + - - -
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Residues in contact with LEU 483 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317C TRP* 3.6 30.0 - - + -
479C HIS 3.0 18.1 + - - +
480C VAL 3.5 4.0 - - - +
481C GLU 3.2 0.2 - - - -
482C ARG* 1.3 75.0 - - - +
484C GLN* 1.3 55.2 + - + +
486C PHE* 3.2 8.4 + - + -
487C GLN* 2.7 44.7 + - - +
494C VAL* 4.9 3.8 - - + -
498C PHE* 4.2 9.2 - - + -
502C TYR* 3.7 22.4 - - + +
506C PHE* 3.4 46.2 - - + +
507C SER* 3.8 11.9 - - - +
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Residues in contact with GLN 484 (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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480C VAL* 3.1 14.2 + - - +
481C GLU* 3.2 24.5 + - - +
483C LEU* 1.3 77.4 - - + +
485C ILE* 1.3 58.0 - - + +
487C GLN* 3.3 7.5 + - - +
488C HIS* 3.0 28.3 + - - +
508C THR* 3.4 45.8 + - - +
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Residues in contact with ILE 485 (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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481C GLU* 3.3 13.8 + - + +
482C ARG* 3.6 50.7 - - - +
483C LEU 3.2 0.4 - - - -
484C GLN* 1.3 77.2 - - + +
486C PHE* 1.3 62.9 + - - +
488C HIS* 3.2 9.4 + - + +
489C LEU* 3.2 34.5 + - + +
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Residues in contact with PHE 486 (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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313C MET* 3.9 10.3 - - + -
314C TRP* 3.6 33.9 - - - -
317C TRP* 3.4 46.9 - + + +
482C ARG 3.1 14.5 + - - +
483C LEU* 3.2 12.1 + - + +
485C ILE* 1.3 77.7 - - - +
487C GLN* 1.3 52.2 + - - +
489C LEU* 3.0 10.6 + - - +
490C HIS* 2.8 58.1 + - + -
493C VAL* 4.0 7.0 - - + -
494C VAL* 3.7 21.5 - - + -
498C PHE* 3.5 26.7 - + - -
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Residues in contact with GLN 487 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483C LEU* 2.7 27.7 + - - +
484C GLN* 3.7 7.0 - - - +
486C PHE* 1.3 79.3 - - - +
488C HIS* 1.3 61.2 + - - +
490C HIS 4.3 0.7 - - - -
491C PRO* 3.2 34.0 + - + +
494C VAL* 3.8 34.1 - - + +
503C LYS* 5.1 6.1 - - - +
507C SER* 3.3 29.8 + - - -
508C THR 5.0 6.3 + - - -
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Residues in contact with HIS 488 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484C GLN 3.0 13.3 + - - +
485C ILE* 3.5 11.9 - - - +
486C PHE 3.2 0.2 - - - -
487C GLN* 1.3 78.2 - - - +
489C LEU* 1.3 70.6 + - + +
491C PRO* 3.7 8.5 - - - +
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Residues in contact with LEU 489 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313C MET* 3.6 32.3 - - + -
485C ILE* 3.2 27.8 + - + +
486C PHE* 3.0 7.2 + - - +
488C HIS* 1.3 88.7 - - - +
490C HIS* 1.3 81.8 + - + +
491C PRO* 3.6 5.1 - - - +
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Residues in contact with HIS 490 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313C MET* 4.2 26.5 - - + -
314C TRP* 4.3 23.4 - + + -
486C PHE* 2.8 36.4 + + + +
487C GLN 3.6 3.1 - - - -
489C LEU* 1.3 99.2 + - + +
491C PRO* 1.3 65.5 - - - +
492C ILE 3.3 3.9 + - - -
493C VAL* 3.5 24.9 + - + -
494C VAL* 3.7 17.2 + - - +
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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