Contacts of the helix formed by residues 505 - 518 (chain A) in PDB entry 3VF1
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 ASP 505 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121A LEU* 3.4 4.8 - - - +
122A PRO* 3.3 17.6 - - - +
123A ASN* 3.9 9.2 - - - +
396A HIS* 2.8 16.7 + - - -
496A TYR* 2.6 29.1 + - + -
501A SER 3.5 16.6 + - - +
502A VAL 3.4 7.6 + - - +
503A LYS 3.3 3.0 - - - -
504A LYS* 1.3 73.8 - - - +
506A ASN* 1.3 61.4 + - - +
507A GLU* 2.9 16.5 + - - +
508A ILE* 3.0 16.4 + - + +
509A GLN* 3.2 19.1 + - - +
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Residues in contact with ASN 506 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A PRO* 3.3 23.9 - - - +
123A ASN* 5.5 0.2 - - - +
503A LYS 5.4 0.4 - - - -
504A LYS 3.1 9.5 + - - +
505A ASP* 1.3 73.2 - - - +
507A GLU* 1.3 71.4 + - - +
509A GLN* 3.6 9.4 + - - +
510A ASP* 3.0 40.5 + - - +
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Residues in contact with GLU 507 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A PRO* 3.5 11.5 - - + +
135A ARG* 2.8 54.1 + - - +
136A THR* 6.0 0.2 - - - -
139A VAL* 5.3 1.8 - - + +
391A ASN 3.7 14.2 - - - +
392A LEU* 3.5 11.4 - - + +
393A PRO* 3.3 16.6 - - + +
396A HIS* 3.3 18.8 - - + -
505A ASP* 2.9 7.8 + - - +
506A ASN* 1.3 90.2 + - - +
508A ILE* 1.3 61.3 + - - +
509A GLN 3.2 1.3 - - - -
510A ASP* 3.4 10.3 + - - +
511A TRP 3.1 19.9 + - - -
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Residues in contact with ILE 508 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392A LEU* 4.2 7.1 - - + +
396A HIS* 4.4 1.3 - - + +
398A VAL* 3.9 35.0 - - + -
496A TYR* 4.3 5.2 - - - +
502A VAL* 3.9 7.9 - - + +
505A ASP* 3.0 37.8 + - + +
507A GLU* 1.3 75.7 - - - +
509A GLN* 1.3 78.1 + - - +
511A TRP* 3.3 28.9 + - + +
512A ILE* 3.0 28.8 + - - +
535A PHE* 3.9 21.1 - - + -
541A LEU* 4.1 10.1 - - + -
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Residues in contact with GLN 509 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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502A VAL 2.8 25.7 + - - -
503A LYS* 3.7 16.0 + - - +
505A ASP 3.2 14.4 - - - +
506A ASN* 3.7 11.0 - - - +
507A GLU 3.2 0.6 - - - -
508A ILE* 1.3 84.3 - - - +
510A ASP* 1.3 56.9 + - - +
512A ILE* 3.5 3.6 - - - +
513A ARG* 3.0 44.7 + - - +
533A LYS 4.9 0.3 - - - +
534A SER* 3.3 16.9 - - - -
535A PHE* 3.0 41.5 + - - +
536A GLU* 5.6 0.2 - - - -
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Residues in contact with ASP 510 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A LYS* 5.9 1.5 + - - +
391A ASN* 3.4 23.8 - - + +
506A ASN* 3.0 30.5 + - - +
507A GLU* 3.6 12.0 - - - +
508A ILE 3.3 0.2 - - - -
509A GLN* 1.3 74.0 - - - +
511A TRP* 1.3 66.6 + - - +
513A ARG* 2.3 40.4 + - - +
514A ASP* 3.0 26.5 + - - +
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Residues in contact with TRP 511 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384A THR* 3.6 14.4 + - - -
387A SER* 2.8 55.7 + - - -
388A SER* 3.5 25.4 + - - +
391A ASN* 3.6 4.9 - - + +
392A LEU* 4.0 16.1 - - + +
398A VAL* 5.4 0.2 - - + -
402A LEU* 3.7 19.5 - - + -
507A GLU 3.1 14.6 + - - +
508A ILE* 3.3 30.3 - - + +
509A GLN 3.3 0.2 - - - -
510A ASP* 1.3 78.8 - - - +
512A ILE* 1.3 72.2 + - - +
515A LEU* 3.2 26.3 + - + +
535A PHE* 3.9 22.4 - + - -
544A PHE* 3.7 24.5 - + - -
545A LEU* 3.7 29.8 - - + -
548A VAL* 5.1 1.6 - - + -
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Residues in contact with ILE 512 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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508A ILE 3.0 12.8 + - - +
509A GLN* 3.5 15.0 - - - +
511A TRP* 1.3 78.7 - - + +
513A ARG* 1.3 61.0 + - - +
515A LEU* 3.4 8.7 + - + +
516A HIS* 3.0 26.3 + - - +
531A VAL* 3.8 20.9 - - + -
532A PRO* 3.4 20.4 - - + +
533A LYS 4.0 1.3 - - - +
534A SER* 3.8 24.7 - - - -
535A PHE* 3.4 46.9 - - + -
544A PHE* 4.0 16.8 - - + -
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Residues in contact with ARG 513 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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509A GLN* 3.0 44.8 + - - +
510A ASP* 2.3 37.0 + - - +
512A ILE* 1.3 75.9 - - - +
514A ASP* 1.3 65.3 + - - +
516A HIS* 3.5 4.6 + - + +
517A GLU* 3.2 50.7 + - + +
533A LYS 4.2 17.3 + - - +
534A SER* 6.4 0.2 - - - -
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Residues in contact with ASP 514 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A TRP* 3.1 18.2 + - - -
387A SER* 3.7 2.3 + - - +
390A ARG* 2.9 33.3 + - - -
391A ASN* 3.1 24.8 + - - +
510A ASP 3.0 18.2 + - - +
511A TRP 3.3 2.9 + - - +
513A ARG* 1.3 76.4 - - - +
515A LEU* 1.3 58.6 + - - +
517A GLU* 4.9 1.6 - - - -
518A ASN* 2.9 50.3 + - - +
519A GLY 3.2 4.9 + - - -
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Residues in contact with LEU 515 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A TRP* 4.7 0.7 - - + -
383A PRO* 3.2 45.3 - - + +
384A THR* 3.8 5.6 - - + +
387A SER* 3.5 10.1 - - - -
511A TRP* 3.2 41.9 + - + +
512A ILE* 3.6 13.2 - - + +
513A ARG 3.2 0.2 - - - -
514A ASP* 1.3 76.4 - - - +
516A HIS* 1.3 60.1 + - - +
519A GLY* 2.9 21.5 + - - +
520A TYR* 2.9 30.5 + - + -
531A VAL* 4.4 5.4 - - + -
544A PHE* 3.9 24.7 - - + -
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Residues in contact with HIS 516 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512A ILE 3.0 16.1 + - - +
513A ARG* 3.8 7.0 - - + +
514A ASP 3.4 0.2 - - - -
515A LEU* 1.3 76.8 - - - +
517A GLU* 1.3 74.8 + - + +
520A TYR* 4.0 14.0 - - - +
521A PRO* 5.2 0.7 - - - +
528A ASP* 4.1 18.4 - - - -
531A VAL* 2.9 36.3 + - + +
532A PRO 3.6 12.2 + - - +
533A LYS* 3.7 32.2 - - + +
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Residues in contact with GLU 517 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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513A ARG* 3.2 42.4 + - + +
514A ASP* 5.0 0.9 - - - -
516A HIS* 1.3 93.9 - - + +
518A ASN* 1.3 77.0 + - - +
520A TYR 5.0 0.4 - - - -
521A PRO* 4.7 12.7 - - - +
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Residues in contact with ASN 518 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A TRP* 3.5 36.5 - - + +
160A GLY* 3.6 13.0 - - - -
390A ARG* 5.5 1.0 - - - +
514A ASP* 2.9 26.1 + - - +
517A GLU* 1.3 94.1 + - - +
519A GLY* 1.3 65.4 - - - +
520A TYR 3.4 1.8 - - - -
521A PRO* 3.6 12.2 - - - +
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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
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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