Contacts of the helix formed by residues 480 - 499 (chain B) in PDB entry 3SRF
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 ALA 480 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478B GLN* 3.4 3.3 - - - +
479B GLU* 1.3 77.9 - - + +
481B TRP* 1.3 65.4 + - - +
482B ALA* 4.7 1.6 - - + +
483B GLU* 3.1 38.3 + - + +
484B ASP* 3.3 11.1 + - - +
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Residues in contact with TRP 481 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432B GLU* 4.5 14.1 - - - -
478B GLN 5.2 0.7 - - - -
479B GLU 3.7 4.2 + - - -
480B ALA* 1.3 72.0 - - - +
482B ALA* 1.3 62.9 + - - +
484B ASP* 3.4 10.3 + - + +
485B VAL* 3.1 40.8 + - + +
488B ARG* 3.4 30.5 - - - -
513B GLY* 3.3 21.5 + - - -
514B TRP 3.1 27.0 + - - -
515B ARG* 3.4 45.6 - - - +
516B PRO* 3.6 42.8 - - + -
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Residues in contact with ALA 482 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480B ALA* 3.2 2.3 + - + +
481B TRP* 1.3 82.1 - - - +
483B GLU* 1.3 74.1 + - - +
485B VAL* 3.5 5.0 + - - +
486B ASP* 2.9 33.3 + - - +
515B ARG* 5.2 6.1 - - - +
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Residues in contact with GLU 483 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478B GLN* 4.2 16.8 - - + +
480B ALA* 3.6 29.2 - - + +
482B ALA* 1.3 87.4 - - - +
484B ASP* 1.3 57.6 + - - +
486B ASP* 3.4 6.9 + - - +
487B LEU* 2.8 32.1 + - - +
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Residues in contact with ASP 484 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454B ARG* 2.6 34.9 + - - -
476B PRO 3.8 1.6 - - - +
477B VAL* 3.5 9.4 - - - +
478B GLN* 2.8 45.0 + - + +
480B ALA 3.3 5.8 + - - +
481B TRP* 3.7 15.4 - - + +
482B ALA 3.3 0.4 - - - -
483B GLU* 1.3 78.2 - - - +
485B VAL* 1.3 58.8 + - - +
487B LEU* 3.4 4.5 + - - +
488B ARG* 3.0 51.7 + - - +
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Residues in contact with VAL 485 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430B LEU* 3.7 6.2 - - + +
481B TRP* 3.1 53.1 + - + +
482B ALA* 3.8 5.8 - - - +
484B ASP* 1.3 72.8 - - - +
486B ASP* 1.3 63.9 + - - +
488B ARG* 3.1 14.3 + - - +
489B VAL* 2.8 37.0 + - + +
512B THR* 3.6 33.2 - - + +
513B GLY 4.6 3.6 - - - +
525B ARG* 4.7 8.5 - - - +
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Residues in contact with ASP 486 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482B ALA* 2.9 20.9 + - - +
483B GLU* 3.6 10.5 - - - +
485B VAL* 1.3 77.8 - - - +
487B LEU* 1.3 56.0 + - - +
489B VAL* 3.1 6.9 + - - +
490B ASN* 2.9 48.0 + - - +
525B ARG* 5.5 3.8 + - - +
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Residues in contact with LEU 487 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454B ARG* 3.8 18.8 - - - +
473B CYS* 4.1 5.8 - - - -
475B ASP* 3.7 38.1 - - + +
476B PRO* 4.1 3.8 - - + +
478B GLN* 3.7 31.6 - - + +
483B GLU 2.8 20.7 + - - +
484B ASP* 3.5 9.6 - - - +
485B VAL 3.2 0.2 - - - -
486B ASP* 1.3 72.7 - - - +
488B ARG* 1.3 63.2 + - + +
490B ASN* 4.5 3.1 - - - +
491B PHE* 3.4 21.5 + - - +
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Residues in contact with ARG 488 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430B LEU* 3.5 49.9 - - + +
431B THR 5.0 2.0 - - - +
432B GLU* 4.8 11.1 + - - +
452B VAL* 3.6 27.8 + - + +
453B THR* 5.9 0.2 - - - +
454B ARG* 3.5 19.0 - - - +
473B CYS* 3.8 24.7 - - - -
481B TRP* 3.4 33.5 - - - -
484B ASP* 3.0 38.8 + - - +
485B VAL* 3.8 16.4 - - - +
487B LEU* 1.3 74.5 - - + +
489B VAL* 1.3 65.5 - - - +
491B PHE* 3.6 6.6 - - - +
492B ALA 3.2 14.9 + - - -
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Residues in contact with VAL 489 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428B ILE* 4.3 3.5 - - + +
430B LEU* 3.9 20.6 - - + -
485B VAL* 2.8 22.9 + - + +
486B ASP* 3.7 7.0 - - - +
488B ARG* 1.3 75.3 - - - +
490B ASN* 1.3 65.2 + - - +
492B ALA* 3.1 8.4 + - - +
493B MET* 2.9 40.8 + - + +
510B VAL* 4.0 35.4 - - + -
512B THR* 4.1 5.6 - - + -
525B ARG* 4.1 15.0 - - - +
527B VAL* 6.1 0.9 - - + -
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Residues in contact with ASN 490 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486B ASP* 2.9 38.2 + - - +
487B LEU* 4.5 4.0 - - - +
489B VAL* 1.3 72.7 - - - +
491B PHE* 1.3 56.3 + - - +
493B MET* 3.1 9.6 + - - +
494B ASN* 2.8 43.8 + - - +
530B PRO* 4.2 23.8 - - - +
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Residues in contact with PHE 491 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B PRO* 3.5 34.8 - - + -
102B ILE* 3.7 26.0 - - + -
452B VAL* 3.7 16.8 - - + -
471B VAL* 3.8 26.7 - - + -
472B LEU 3.6 14.6 - - - -
473B CYS* 3.8 27.6 - - - -
474B LYS 4.9 2.0 - - - -
475B ASP* 5.5 9.4 - - - -
487B LEU 3.4 19.5 + - - +
488B ARG* 3.6 6.3 - - - +
490B ASN* 1.3 75.8 - - - +
492B ALA* 1.3 63.1 + - - +
494B ASN* 3.2 13.4 + - - +
495B VAL* 3.1 30.6 + - + +
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Residues in contact with ALA 492 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428B ILE* 3.7 21.1 - - + -
450B ILE* 3.8 21.6 - - + +
452B VAL* 3.4 29.4 - - + -
488B ARG 3.2 1.9 + - - +
489B VAL 3.1 10.6 + - - +
491B PHE* 1.3 78.9 - - - +
493B MET* 1.3 64.9 + - - +
495B VAL* 3.2 10.1 + - - +
496B GLY 3.1 18.7 + - - -
502B PHE* 4.0 0.5 - - - -
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Residues in contact with MET 493 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428B ILE* 3.8 8.7 - - + -
489B VAL* 2.9 30.4 + - + +
490B ASN* 3.1 19.2 + - - +
492B ALA* 1.3 76.1 - - - +
494B ASN* 1.3 63.2 + - - +
495B VAL 3.3 0.2 + - - -
496B GLY 3.4 1.4 + - - -
497B LYS* 3.1 29.8 + - - +
502B PHE* 3.4 40.6 - - + -
508B VAL* 3.8 19.7 - - + -
527B VAL* 5.8 3.4 - - - -
528B PRO 5.1 0.7 - - - +
529B VAL* 3.6 19.7 - - + -
530B PRO* 3.2 34.5 - - + -
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Residues in contact with ASN 494 (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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102B ILE* 3.7 24.7 - - + +
490B ASN* 2.8 27.0 + - - +
491B PHE* 3.2 13.0 + - - +
493B MET* 1.3 78.1 - - - +
495B VAL* 1.3 56.1 + - - +
497B LYS* 3.5 16.3 + - - +
498B ALA* 2.9 30.7 + - - +
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Residues in contact with VAL 495 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B ILE* 3.6 32.5 - - + +
450B ILE* 5.0 8.1 - - + -
469B PHE* 6.4 0.9 - - + -
471B VAL* 3.6 34.1 - - + -
491B PHE* 3.1 29.1 + - + +
492B ALA* 3.4 9.9 - - - +
493B MET 3.2 0.4 - - - -
494B ASN* 1.3 74.2 - - - +
496B GLY* 1.3 58.1 + - - +
498B ALA* 3.0 1.7 + - - -
499B ARG* 2.8 47.6 + - + +
501B PHE* 5.3 4.3 - - + -
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Residues in contact with GLY 496 (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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450B ILE* 4.2 5.5 - - - +
492B ALA 3.1 8.3 + - - -
495B VAL* 1.3 77.8 - - - +
497B LYS* 1.3 56.6 + - - +
500B GLY 2.9 6.9 + - - -
501B PHE* 2.7 41.3 + - - -
502B PHE* 3.4 33.1 + - - -
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Residues in contact with LYS 497 (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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493B MET* 3.1 21.1 + - - +
494B ASN* 3.6 16.9 + - - +
496B GLY* 1.3 76.2 - - - +
498B ALA* 1.3 62.1 + - - +
500B GLY* 3.2 12.8 + - - -
502B PHE* 3.4 20.8 + - + +
503B LYS* 4.6 5.2 - - - -
504B LYS* 4.6 9.6 - - - +
529B VAL* 3.7 15.7 - - - -
530B PRO* 3.0 33.8 + - - +
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Residues in contact with ALA 498 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B ILE* 3.8 19.3 - - + +
103B LEU* 4.0 21.8 - - + +
494B ASN 2.9 17.9 + - - +
495B VAL 3.6 2.9 - - - +
497B LYS* 1.3 77.4 - - - +
499B ARG* 1.3 61.3 + - - +
500B GLY* 3.6 0.3 + - - -
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Residues in contact with ARG 499 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B THR* 4.1 10.7 + - - +
102B ILE 4.8 1.3 + - - +
103B LEU* 2.6 58.7 + - + +
105B ARG* 3.4 48.9 - - - +
469B PHE* 6.1 1.3 - - - -
495B VAL* 2.8 35.5 + - + +
498B ALA* 1.3 74.1 - - - +
500B GLY* 1.3 60.0 + - - +
501B PHE* 3.4 37.3 + - + -
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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