Contacts of the helix formed by residues 505 - 518 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121B LEU* 3.4 5.5 - - - +
122B PRO* 3.3 17.6 - - - +
123B ASN* 3.9 9.6 - - - +
396B HIS* 2.8 17.0 + - - -
496B TYR* 2.6 29.2 + - + -
501B SER 3.5 16.3 + - - +
502B VAL 3.3 7.4 + - - +
503B LYS 3.3 2.4 - - - -
504B LYS* 1.3 74.0 - - - +
506B ASN* 1.3 61.9 + - - +
507B GLU* 2.9 16.3 + - - +
508B ILE* 3.0 16.8 + - + +
509B GLN* 3.2 18.5 + - - +
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Residues in contact with ASN 506 (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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122B PRO* 3.3 23.9 - - - +
123B ASN* 5.5 0.5 - - - +
503B LYS 5.4 0.7 - - - -
504B LYS 3.1 10.8 + - - +
505B ASP* 1.3 70.4 - - - +
507B GLU* 1.3 71.1 + - - +
509B GLN* 3.6 9.4 + - - +
510B ASP* 3.0 40.4 + - - +
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Residues in contact with GLU 507 (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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122B PRO* 3.5 11.8 - - + +
135B ARG* 2.8 54.5 + - - +
136B THR* 6.0 0.2 - - - -
139B VAL* 5.3 1.6 - - + +
391B ASN 3.7 15.0 - - - +
392B LEU* 3.5 11.8 - - + +
393B PRO* 3.3 16.6 - - - +
396B HIS* 3.3 19.8 - - + -
505B ASP* 2.9 7.2 + - - +
506B ASN* 1.3 92.4 + - - +
508B ILE* 1.3 59.6 + - - +
510B ASP* 3.4 10.2 + - - +
511B TRP 3.1 19.8 + - - -
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Residues in contact with ILE 508 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B LEU* 4.2 7.5 - - + +
396B HIS* 4.3 1.3 + - + +
398B VAL* 3.9 35.2 - - + -
496B TYR* 4.3 5.2 - - - +
502B VAL* 3.9 8.7 - - + +
505B ASP* 3.0 37.1 + - + +
507B GLU* 1.3 75.7 - - - +
509B GLN* 1.3 78.0 + - - +
511B TRP* 3.3 28.0 + - + +
512B ILE* 3.0 28.6 + - - +
535B PHE* 3.9 20.9 - - + -
541B LEU* 4.1 9.9 - - + -
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Residues in contact with GLN 509 (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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502B VAL 2.8 25.7 + - - -
503B LYS* 3.7 16.5 + - - +
505B ASP 3.2 15.0 - - - +
506B ASN* 3.7 10.3 - - - +
507B GLU 3.2 0.2 - - - -
508B ILE* 1.3 83.8 - - - +
510B ASP* 1.3 59.6 + - - +
512B ILE* 3.5 3.6 - - - +
513B ARG* 3.0 45.7 + - - +
533B LYS 4.9 0.7 - - - +
534B SER* 3.3 17.1 - - - -
535B PHE* 3.0 41.8 + - - +
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Residues in contact with ASP 510 (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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143B LYS* 5.9 1.7 + - - +
391B ASN* 3.4 24.0 - - + +
506B ASN* 3.0 31.3 + - - +
507B GLU* 3.6 12.8 - - - +
508B ILE 3.3 0.2 - - - -
509B GLN* 1.3 74.3 - - - +
511B TRP* 1.3 66.1 + - - +
513B ARG* 2.3 41.4 + - - +
514B ASP* 3.0 26.0 + - - +
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Residues in contact with TRP 511 (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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384B THR* 3.6 14.6 + - - -
387B SER* 2.9 56.4 + - - -
388B SER* 3.5 24.0 + - - +
391B ASN* 3.6 4.9 - - + +
392B LEU* 4.0 16.8 - - + +
402B LEU* 3.7 19.5 - - + -
507B GLU 3.1 12.9 + - - +
508B ILE* 3.3 32.5 + - + +
510B ASP* 1.3 79.7 - - - +
512B ILE* 1.3 70.9 + - - +
514B ASP 3.3 0.2 + - - -
515B LEU* 3.2 26.0 + - + +
535B PHE* 3.9 22.2 - + - -
541B LEU* 5.0 0.2 - - + -
544B PHE* 3.7 25.1 - + - -
545B LEU* 3.7 28.9 - - + -
548B VAL* 5.1 1.6 - - + -
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Residues in contact with ILE 512 (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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508B ILE 3.0 13.1 + - - +
509B GLN* 3.5 14.6 - - - +
511B TRP* 1.3 77.5 - - + +
513B ARG* 1.3 60.3 + - - +
515B LEU* 3.4 8.2 + - + -
516B HIS* 3.0 26.5 + - - +
531B VAL* 3.8 21.3 - - + -
532B PRO* 3.4 19.9 - - + +
533B LYS 4.0 1.8 - - - +
534B SER* 3.8 25.1 - - - -
535B PHE* 3.4 46.7 - - + -
544B PHE* 4.0 16.2 - - + -
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Residues in contact with ARG 513 (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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509B GLN* 3.0 46.6 + - - +
510B ASP* 2.3 36.0 + - - +
512B ILE* 1.3 75.9 - - - +
514B ASP* 1.3 65.4 + - - +
516B HIS* 3.4 4.9 + - + +
517B GLU* 3.2 51.0 + - + +
533B LYS 4.2 15.5 + - - +
534B SER* 6.4 0.2 - - - -
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Residues in contact with ASP 514 (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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148B TRP* 3.1 17.7 + - - -
387B SER* 3.7 2.5 + - - +
390B ARG* 2.9 33.3 + - - -
391B ASN* 3.1 24.5 + - - +
510B ASP 3.0 17.7 + - - +
511B TRP 3.6 3.1 - - - +
513B ARG* 1.3 78.4 - - - +
515B LEU* 1.3 57.8 - - - +
517B GLU* 5.0 2.0 - - - +
518B ASN* 2.9 51.2 + - - +
519B GLY 3.2 4.5 + - - -
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Residues in contact with LEU 515 (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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148B TRP* 4.7 0.9 - - + -
383B PRO* 3.2 46.4 - - + +
384B THR* 3.8 4.7 - - + +
387B SER* 3.5 9.6 - - - -
511B TRP* 3.2 43.2 + - + +
512B ILE* 3.6 13.9 - - + +
513B ARG 3.2 0.4 - - - -
514B ASP* 1.3 75.8 - - - +
516B HIS* 1.3 60.0 + - - +
519B GLY* 2.9 21.8 + - - +
520B TYR* 2.9 30.1 + - + -
531B VAL* 4.4 5.4 - - + -
544B PHE* 3.9 24.0 - - + -
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Residues in contact with HIS 516 (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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512B ILE 3.0 16.8 + - - +
513B ARG* 3.8 7.4 - - + +
515B LEU* 1.3 77.1 - - - +
517B GLU* 1.3 73.8 + - + +
520B TYR* 4.0 13.8 - - - +
521B PRO* 5.2 0.7 - - - +
528B ASP* 4.1 19.0 + - - -
531B VAL* 2.9 35.3 + - + +
532B PRO 3.6 11.6 + - - +
533B LYS* 3.7 30.5 - - + +
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Residues in contact with GLU 517 (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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513B ARG* 3.2 42.4 + - + +
514B ASP* 5.0 1.0 - - - -
515B LEU 4.3 0.2 - - - -
516B HIS* 1.3 93.8 - - + +
518B ASN* 1.3 77.3 + - - +
520B TYR 5.0 0.4 - - - -
521B PRO* 4.7 12.2 - - - +
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Residues in contact with ASN 518 (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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148B TRP* 3.5 37.2 - - + +
160B GLY* 3.6 12.6 - - - -
390B ARG* 5.5 1.2 - - - +
514B ASP* 2.9 26.1 + - - +
517B GLU* 1.3 93.1 + - - +
519B GLY* 1.3 68.1 + - - +
520B TYR 3.4 2.2 + - - -
521B PRO* 3.6 11.6 - - - +
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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