Contacts of the helix formed by residues 504 - 518 (chain D) in PDB entry 3F7F
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 SER 504 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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493D TRP* 3.8 20.0 + - - +
503D GLY* 1.3 75.7 - - - +
505D GLU* 1.3 67.3 + - - +
506D LEU* 3.8 5.2 + - - +
507D PHE* 3.2 16.9 + - - +
508D LYS* 3.0 23.2 + - - +
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Residues in contact with GLU 505 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504D SER* 1.3 74.4 - - - +
506D LEU* 1.3 52.1 + - - +
508D LYS* 3.1 24.0 + - - +
509D TYR* 2.7 37.2 + - - +
576D SER 4.0 8.8 - - - +
577D PHE* 3.5 28.5 - - + -
578D ASP 5.5 0.5 + - - -
582D VAL* 4.4 16.6 - - + +
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Residues in contact with LEU 506 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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493D TRP* 3.3 38.4 - - + -
504D SER* 3.3 5.0 + - - +
505D GLU* 1.3 75.2 - - - +
507D PHE* 1.3 60.8 + - - +
509D TYR* 3.6 8.5 - - + +
510D LEU* 2.8 39.0 + - + +
582D VAL* 3.3 34.0 - - + +
585D ASP* 3.4 24.9 - - + +
586D LEU* 3.7 41.5 - - + +
590D GLN* 4.4 2.9 - - + +
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Residues in contact with PHE 507 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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493D TRP* 3.4 56.5 - + + +
496D ASN 3.9 5.8 - - - -
497D MET* 3.8 27.1 - - - -
500D GLU* 3.2 37.7 - - + -
502D ASP 3.6 16.8 - - - -
503D GLY* 3.9 6.3 - - - -
504D SER* 3.2 17.9 + - - +
506D LEU* 1.3 81.6 - - - +
508D LYS* 1.3 62.0 + - + +
510D LEU* 3.2 2.5 + - - +
511D ARG* 2.9 58.1 + - + +
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Residues in contact with LYS 508 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501D THR 5.4 1.8 - - - -
502D ASP* 3.9 15.2 - - - +
503D GLY 3.2 22.5 + - - -
504D SER 3.0 10.0 + - - +
505D GLU* 3.5 26.2 + - - +
507D PHE* 1.3 88.2 - - + +
509D TYR* 1.3 62.3 + - - +
511D ARG* 3.8 24.4 - - - +
512D THR* 3.1 31.8 + - + +
577D PHE* 3.6 14.1 - - + -
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Residues in contact with TYR 509 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505D GLU 2.7 20.2 + - - +
506D LEU* 3.6 11.0 - - + +
507D PHE 3.2 0.2 - - - -
508D LYS* 1.3 71.1 - - - +
510D LEU* 1.3 73.5 + - + +
512D THR* 3.1 5.2 + - - -
513D LEU* 3.1 58.9 + - + +
574D LEU* 3.9 11.2 - - + -
577D PHE* 3.5 35.4 - + + -
579D ILE* 4.6 16.9 - - + +
582D VAL* 3.5 28.5 - - + -
583D LEU* 3.6 36.0 - - + +
586D LEU* 4.9 0.9 - - + -
633D VAL* 3.9 11.3 - - + +
636D THR* 4.2 6.8 + - - -
637D PHE* 5.4 0.3 - - - -
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Residues in contact with LEU 510 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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493D TRP* 3.4 43.7 - - + -
497D MET* 3.7 15.7 - - + +
506D LEU* 2.8 22.3 + - + +
507D PHE 3.7 3.1 - - - +
509D TYR* 1.3 87.1 - - + +
511D ARG* 1.3 57.3 + - - +
513D LEU* 3.0 9.6 + - + +
514D ASN* 2.8 30.0 + - - +
586D LEU* 4.2 17.3 - - + -
629D ILE* 3.9 44.6 - - + -
632D GLN* 4.1 4.5 + - - +
633D VAL* 4.9 3.6 - - + -
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Residues in contact with ARG 511 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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497D MET* 3.3 46.8 + - + +
498D HIS* 6.1 2.0 - - + +
499D SER 5.7 0.2 - - - -
500D GLU 3.4 23.8 + - - -
501D THR 4.7 4.0 + - - -
502D ASP 4.7 2.0 + - - -
507D PHE* 2.9 34.0 + - + +
508D LYS* 3.8 25.0 + - - +
509D TYR 3.3 0.2 - - - -
510D LEU* 1.3 76.9 - - - +
512D THR* 1.3 65.2 + - - +
514D ASN* 3.3 3.7 + - - +
515D GLY* 2.8 25.3 + - - -
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Residues in contact with THR 512 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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508D LYS* 3.1 17.5 + - + +
509D TYR 3.1 11.4 + - - -
511D ARG* 1.3 83.6 - - + +
513D LEU* 1.3 65.7 + - - +
515D GLY* 3.4 3.3 + - - +
516D PHE* 3.4 15.4 + - - +
570D LEU* 3.9 12.9 - - - +
573D GLU* 3.3 48.9 - - + +
574D LEU* 4.3 9.0 - - - +
577D PHE* 3.8 17.6 - - + -
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Residues in contact with LEU 513 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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509D TYR* 3.1 35.1 + - + +
510D LEU* 3.0 13.3 + - + +
512D THR* 1.3 78.8 + - - +
514D ASN* 1.3 61.9 + - - +
516D PHE* 3.4 4.7 + - - +
517D ALA* 3.1 23.0 + - - +
570D LEU* 4.4 4.4 - - + +
574D LEU* 3.7 26.0 - - + -
632D GLN* 3.9 14.9 - - + +
633D VAL* 3.5 46.9 - - + +
635D LEU* 5.8 0.5 - - - +
636D THR* 3.6 26.9 - - + -
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Residues in contact with ASN 514 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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497D MET* 3.5 39.8 - - + +
498D HIS* 4.6 13.5 + - - -
510D LEU 2.8 6.1 + - - +
511D ARG* 3.5 4.7 - - - +
513D LEU* 1.3 75.6 - - - +
515D GLY* 1.3 66.7 + - - +
518D SER* 2.8 44.2 + - - +
628D ARG* 3.4 30.9 + - - +
632D GLN* 2.9 29.5 + - - +
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Residues in contact with GLY 515 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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511D ARG 2.8 17.1 + - - -
512D THR* 3.4 6.0 + - - -
513D LEU 3.3 0.6 - - - -
514D ASN* 1.3 77.5 - - - +
516D PHE* 1.3 57.9 + - - +
518D SER* 3.0 16.7 + - - -
519D THR* 3.6 13.0 - - - +
573D GLU* 6.0 0.2 - - - -
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Residues in contact with PHE 516 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512D THR 3.4 7.5 + - - +
513D LEU 4.0 5.2 - - - +
514D ASN 3.1 0.6 - - - -
515D GLY* 1.3 75.1 - - - +
517D ALA* 1.3 64.1 + - - +
518D SER 3.2 1.8 - - - -
519D THR* 2.6 28.8 + - - -
520D LEU* 4.0 11.2 + - + +
558D LEU* 5.6 0.4 - - + -
562D PHE* 3.9 38.8 - + + -
566D ASN* 3.7 29.6 - - + +
567D LEU* 3.9 20.0 - - + -
570D LEU* 3.3 35.7 - - + -
635D LEU* 4.1 19.7 - - + -
636D THR* 6.2 0.2 - - + -
639D LEU* 3.5 29.6 - - + -
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Residues in contact with ALA 517 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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513D LEU 3.1 10.0 + - - +
514D ASN* 4.1 0.4 - - - +
516D PHE* 1.3 84.6 - - - +
518D SER* 1.3 62.2 + - - +
519D THR 3.2 0.9 + - - -
520D LEU* 3.2 20.6 + - - +
525D LEU* 4.0 20.4 - - + +
632D GLN* 3.5 36.8 - - + +
635D LEU* 4.1 19.3 - - + -
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Residues in contact with SER 518 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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498D HIS* 6.1 1.0 - - - -
514D ASN* 2.8 35.6 + - - +
515D GLY* 3.0 14.2 + - - -
517D ALA* 1.3 77.5 - - - +
519D THR* 1.3 62.3 + - - +
520D LEU 3.3 7.7 - - - +
628D ARG* 6.0 1.6 - - - -
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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
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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