Contacts of the helix formed by residues 471 - 491 (chain B) in PDB entry 4P3N
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 GLN 471 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427B TRP 4.6 3.8 + - - -
430B LEU* 3.5 32.8 + - - +
431B PRO* 3.7 16.4 - - + +
467B CYS* 3.2 18.8 - - + +
468B ALA* 2.7 45.5 + - + +
470B GLU* 1.3 81.8 - - + +
472B ILE* 1.3 63.2 + - - +
473B GLU 3.4 1.3 - - - -
474B ASP* 3.0 20.9 + - + +
475B GLU* 3.0 11.6 + - - +
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Residues in contact with ILE 472 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467B CYS* 4.1 15.7 - - - -
468B ALA 3.5 8.2 + - - +
469B MET* 2.9 49.1 + - + +
471B GLN* 1.3 76.2 - - - +
473B GLU* 1.3 65.0 + - - +
475B GLU* 2.9 14.5 + - - +
476B ILE* 2.9 34.4 + - + +
515B ALA* 4.2 6.7 - - + +
518B GLN* 3.4 15.9 - - + +
519B LEU* 4.7 1.6 - - + -
563B LEU* 3.6 34.8 - - + -
587B VAL* 3.9 11.2 - - + -
589B VAL* 5.6 1.6 - - + -
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Residues in contact with GLU 473 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470B GLU 5.2 1.6 - - - +
471B GLN 3.4 0.6 - - - -
472B ILE* 1.3 80.4 - - - +
474B ASP* 1.3 62.3 + - - +
476B ILE* 4.7 0.2 - - - -
477B LYS* 3.4 11.8 + - - +
518B GLN* 3.4 32.0 + - + +
521B ASN* 3.3 40.3 + - + +
522B SER* 2.7 34.3 + - - +
525B GLU* 5.9 1.7 - - - +
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Residues in contact with ASP 474 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470B GLU 5.2 1.1 + - - +
471B GLN* 3.0 13.8 + - + +
473B GLU* 1.3 78.9 - - - +
475B GLU* 1.3 69.5 + - + +
477B LYS* 3.7 19.4 + - - +
478B GLY* 3.4 16.1 + - - -
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Residues in contact with GLU 475 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369B PHE* 5.5 0.2 - - - -
431B PRO* 3.6 22.9 - - + +
433B ARG* 2.8 45.6 + - - -
465B ILE* 3.2 36.7 - - + +
467B CYS* 4.5 8.1 - - - -
471B GLN 3.0 11.0 + - - +
472B ILE* 2.9 10.8 + - - +
474B ASP* 1.3 81.6 - - + +
476B ILE* 1.3 62.1 + - + +
478B GLY* 3.5 2.0 + - - +
479B CYS* 2.9 33.3 + - - -
589B VAL* 5.8 2.5 - - + -
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Residues in contact with ILE 476 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472B ILE* 2.9 26.9 + - + +
473B GLU* 4.7 0.4 - - - -
474B ASP 3.3 0.2 - - - -
475B GLU* 1.3 76.8 - - + +
477B LYS* 1.3 60.7 + - - +
479B CYS* 2.9 8.2 + - + +
480B LEU* 2.8 34.1 + - + +
519B LEU* 3.6 24.9 - - + -
522B SER* 3.7 24.5 - - - +
544B ILE* 3.8 24.5 - - + -
561B ILE* 3.7 28.7 - - + -
563B LEU* 4.3 13.5 - - + -
589B VAL* 4.7 7.0 - - + -
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Residues in contact with LYS 477 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473B GLU 3.4 13.4 + - - +
474B ASP* 3.8 20.9 - - - +
475B GLU 3.4 0.6 - - - -
476B ILE* 1.3 78.5 - - - +
478B GLY* 1.3 61.7 + - - +
480B LEU* 3.2 13.6 + - + +
481B ASP* 3.0 27.5 + - + +
522B SER* 3.9 12.8 + - - +
525B GLU* 4.3 29.0 + - + +
526B PHE* 5.0 4.7 - - + -
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Residues in contact with GLY 478 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367B ARG* 4.0 4.7 + - - -
474B ASP 3.4 9.1 + - - -
475B GLU* 3.8 4.0 - - - -
476B ILE 3.2 0.4 - - - -
477B LYS* 1.3 83.6 - - - +
479B CYS* 1.3 61.6 + - - +
481B ASP* 2.9 10.2 + - - +
482B PHE* 2.9 24.2 + - - +
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Residues in contact with CYS 479 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369B PHE* 5.2 4.0 - - - -
465B ILE* 3.5 28.0 - - - -
475B GLU 2.9 24.2 + - - +
476B ILE* 2.9 13.6 + - - +
478B GLY* 1.3 74.6 - - - +
480B LEU* 1.3 59.0 + - - +
482B PHE* 3.4 16.4 - - - +
483B LEU* 3.4 19.1 - - - +
561B ILE* 3.9 26.3 - - + +
589B VAL* 5.0 1.3 - - - -
591B ARG* 4.2 21.8 - - + -
593B ILE* 4.9 0.9 - - - +
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Residues in contact with LEU 480 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476B ILE* 2.8 29.9 + - + +
477B LYS* 3.6 11.2 - - - +
478B GLY 3.1 0.2 - - - -
479B CYS* 1.3 74.8 - - - +
481B ASP* 1.3 65.5 + - - +
482B PHE 3.0 1.6 - - - -
483B LEU* 2.9 34.3 + - + +
484B ARG* 3.0 14.4 + - - +
496B LEU* 4.1 20.6 - - + -
522B SER 4.2 11.7 - - - +
523B LEU* 4.6 9.6 - - + -
526B PHE* 3.6 45.1 - - + -
544B ILE* 4.9 6.7 - - + -
561B ILE* 4.0 13.2 - - + -
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Residues in contact with ASP 481 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367B ARG* 2.5 32.7 + - - +
477B LYS* 3.0 13.5 + - + +
478B GLY* 2.9 12.4 + - - +
480B LEU* 1.3 76.1 - - - +
482B PHE* 1.3 59.4 + - - +
484B ARG* 3.8 6.3 + - - +
485B THR* 3.0 32.3 + - - -
526B PHE* 4.2 8.2 - - + -
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Residues in contact with PHE 482 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360B ILE* 4.4 8.5 - - + -
363B GLU* 3.3 34.5 - - + -
364B TYR* 3.7 27.4 - + - -
367B ARG* 3.4 30.9 - - - +
369B PHE* 4.1 14.6 - + - -
478B GLY 2.9 12.1 + - - +
479B CYS* 3.4 15.7 - - - +
481B ASP* 1.3 73.7 - - - +
483B LEU* 1.3 67.0 + - - +
485B THR* 3.0 6.6 + - - -
486B VAL* 2.9 35.3 + - + +
591B ARG* 3.3 29.4 - - - -
593B ILE* 3.3 13.7 - - + -
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Residues in contact with LEU 483 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479B CYS 3.4 12.3 - - - +
480B LEU* 2.9 26.6 + - + +
482B PHE* 1.3 77.7 - - - +
484B ARG* 1.3 59.0 + - - +
486B VAL 3.0 2.6 + - - -
487B TYR* 2.8 50.9 + - + +
494B PHE* 5.2 6.3 - - + -
496B LEU* 4.7 2.2 - - + -
546B ILE* 3.6 36.8 - - + -
559B ALA* 3.4 26.2 - - + -
561B ILE* 4.6 4.5 - - + -
592B ALA 4.9 0.2 - - - +
593B ILE* 3.6 31.6 - - + -
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Residues in contact with ARG 484 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480B LEU 3.0 10.8 + - - +
481B ASP* 4.1 7.4 - - - +
483B LEU* 1.3 79.0 - - - +
485B THR* 1.3 58.7 + - - +
487B TYR* 4.5 0.3 - - - +
488B SER* 2.5 42.3 + - - +
494B PHE* 4.0 28.0 - - + -
526B PHE* 3.2 49.3 + - + -
527B GLY 5.3 0.8 - - - -
528B GLU* 4.6 11.3 - - - +
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Residues in contact with THR 485 (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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359B PHE* 5.4 0.4 - - + -
363B GLU* 3.9 22.4 - - + +
367B ARG* 3.0 20.4 + - - +
481B ASP* 3.0 20.0 + - - -
482B PHE 3.0 10.1 + - - -
484B ARG* 1.3 74.8 - - - +
486B VAL* 1.3 69.9 + - - +
488B SER* 3.0 16.2 + - - -
489B VAL* 3.1 20.0 + - + +
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Residues in contact with VAL 486 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359B PHE* 3.6 32.3 - - + -
360B ILE* 4.6 8.1 - - + -
363B GLU* 4.7 4.0 - - + -
482B PHE* 2.9 47.9 + - + +
483B LEU 3.7 4.5 - - - +
485B THR* 1.3 70.2 - - - +
487B TYR* 1.3 60.3 + - + +
489B VAL* 2.9 26.3 + - - +
490B PHE* 3.3 24.0 + - + -
593B ILE* 4.1 24.2 - - + -
594B LEU* 4.3 7.9 - - + -
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Residues in contact with TYR 487 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483B LEU* 2.8 41.6 + - + +
484B ARG 4.5 0.7 - - - +
486B VAL* 1.3 78.3 - - + +
488B SER* 1.3 51.4 + - - +
490B PHE* 2.9 17.4 + + - +
491B GLY 2.7 31.4 + - - -
492B PHE* 3.1 22.4 + + + +
494B PHE* 3.9 19.1 - + + -
546B ILE* 4.1 12.1 - - + -
548B ILE* 3.5 41.7 - - + -
558B CYS* 3.9 6.0 - - + +
559B ALA* 3.1 20.1 + - - +
593B ILE* 2.7 40.1 + - + -
594B LEU* 5.2 3.6 - - + -
600B MET* 5.8 3.4 - - + -
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Residues in contact with SER 488 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484B ARG* 2.5 33.0 + - - +
485B THR* 3.0 8.7 + - - -
487B TYR* 1.3 77.3 - - - +
489B VAL* 1.3 57.7 + - - +
491B GLY* 3.5 4.0 + - - +
492B PHE 4.8 3.5 + - - -
494B PHE* 5.5 1.9 - - - -
717B LYS* 3.0 28.9 + - - -
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Residues in contact with VAL 489 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359B PHE* 3.5 31.2 - - + -
485B THR* 3.1 19.4 + - + +
486B VAL 2.9 11.2 + - - +
488B SER* 1.3 78.7 - - - +
490B PHE* 1.3 58.2 + - + +
491B GLY 3.6 0.2 + - - -
608B TYR* 4.9 1.2 + - - -
615B TRP* 3.9 23.3 + - + +
714B PHE 5.5 2.5 - - - +
715B ARG* 3.9 35.5 - - + +
717B LYS* 3.7 21.9 - - - +
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Residues in contact with PHE 490 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356B LEU* 3.7 22.4 - - + -
359B PHE* 4.4 11.7 - + - -
486B VAL* 3.3 26.4 + - + -
487B TYR* 2.9 13.3 + + - +
489B VAL* 1.3 81.6 - - + +
491B GLY* 1.3 59.8 + - - +
492B PHE* 3.6 22.2 - + + -
594B LEU* 3.8 19.5 - - + -
600B MET* 3.6 26.2 - - + -
604B LEU* 3.7 18.4 - - + -
607B ASN* 5.1 3.1 + - - -
608B TYR* 3.6 34.4 + - - +
615B TRP* 3.7 25.4 - + - -
616B LEU* 4.2 0.9 - - + -
717B LYS* 4.6 5.3 - - - +
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Residues in contact with GLY 491 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487B TYR 2.7 11.6 + - - -
488B SER* 3.5 3.9 + - - -
489B VAL 3.3 3.6 + - - -
490B PHE* 1.3 76.2 - - - +
492B PHE* 1.3 62.8 + - - -
493B SER 4.1 0.7 + - - -
549B LYS 5.1 0.3 - - - +
717B LYS* 4.0 20.9 - - - -
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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