Contacts of the helix formed by residues 524 - 543 (chain C) in PDB entry 2VGB
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 ILE 524 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522C GLU* 4.0 4.3 - - - +
523C ALA* 1.3 79.0 - - + +
525C TRP* 1.3 66.2 + - - +
526C ALA* 4.0 16.2 - - + +
527C ASP* 2.9 46.4 + - - +
528C ASP 3.2 8.0 + - - -
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Residues in contact with TRP 525 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522C GLU 5.1 1.8 - - - -
523C ALA 3.5 6.6 + - - +
524C ILE* 1.3 71.0 - - - +
526C ALA* 1.3 67.8 + - + +
528C ASP* 2.7 31.4 + - + +
529C VAL* 2.9 32.6 + - + +
532C ARG* 3.9 6.4 - - - +
557C GLY 3.4 23.6 - - - -
558C TRP 3.6 16.2 - - - -
559C ARG* 3.4 17.9 - - - -
560C PRO* 3.3 40.3 - - + +
580C FBP 2.9 33.7 + - - -
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Residues in contact with ALA 526 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524C ILE* 3.3 12.7 - - + +
525C TRP* 1.3 85.5 - - + +
527C ASP* 1.3 63.3 + - - +
529C VAL* 3.3 9.8 + - - +
530C ASP* 3.0 29.1 + - - +
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Residues in contact with ASP 527 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522C GLU* 4.2 15.4 - - + +
524C ILE* 2.9 45.2 + - - +
526C ALA* 1.3 75.1 - - - +
528C ASP* 1.3 63.1 + - - +
530C ASP* 3.2 9.6 + - - +
531C ARG* 3.0 41.6 + - - +
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Residues in contact with ASP 528 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498C ARG* 3.0 35.4 + - - -
517C TYR* 4.6 4.2 + - - -
520C PRO 4.3 1.0 - - - +
521C PRO* 3.2 6.2 - - - +
522C GLU* 3.0 39.9 + - - +
524C ILE 3.2 4.6 + - - +
525C TRP* 2.7 24.9 + - + +
527C ASP* 1.3 74.3 - - - +
529C VAL* 1.3 60.5 + - - +
531C ARG* 3.5 3.3 + - - +
532C ARG* 3.0 52.8 + - - +
580C FBP 4.9 0.2 + - - -
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Residues in contact with VAL 529 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474C LEU* 3.8 19.2 - - + +
525C TRP* 2.9 51.8 + - + +
526C ALA* 3.4 10.5 - - - +
528C ASP* 1.3 76.8 - - - +
530C ASP* 1.3 71.5 + - - +
532C ARG* 3.2 20.2 + - - +
533C VAL* 3.1 23.5 + - + +
556C THR* 4.2 18.8 - - + +
557C GLY 5.6 0.9 - - - +
569C ARG* 5.1 2.5 - - - +
580C FBP 5.0 1.1 - - - -
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Residues in contact with ASP 530 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526C ALA* 3.0 20.3 + - - +
527C ASP* 3.2 12.7 + - - +
529C VAL* 1.3 83.2 - - - +
531C ARG* 1.3 53.5 + - + +
533C VAL* 3.1 7.0 + - - +
534C GLN* 2.7 48.1 + - - +
569C ARG* 4.5 12.1 + - - -
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Residues in contact with ARG 531 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517C TYR* 3.6 19.8 - - + +
522C GLU* 3.2 42.6 + - + +
527C ASP* 3.0 35.5 + - - +
528C ASP 3.8 2.9 - - - +
529C VAL 3.3 0.2 - - - -
530C ASP* 1.3 75.0 - - - +
532C ARG* 1.3 52.2 + - - +
534C GLN* 3.4 7.8 + - - +
535C PHE* 2.7 34.1 + - - +
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Residues in contact with ARG 532 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474C LEU* 4.2 25.5 - - + +
475C THR 6.0 0.6 - - - +
496C VAL* 4.0 24.1 + - + +
497C THR* 6.0 2.1 - - - +
498C ARG* 3.6 15.8 - - - +
517C TYR* 3.7 36.6 - - + -
525C TRP* 3.9 9.3 - - - +
528C ASP* 3.0 34.4 + - - +
529C VAL* 3.2 21.2 + - - +
530C ASP 3.1 0.4 - - - -
531C ARG* 1.3 76.6 - - - +
533C VAL* 1.3 59.0 + - - +
535C PHE* 3.0 9.6 + - - +
536C GLY* 2.9 25.6 + - - -
580C FBP 2.5 50.3 + - - -
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Residues in contact with VAL 533 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472C ILE* 4.3 9.4 - - + +
474C LEU* 3.8 19.1 - - + -
529C VAL* 3.1 16.7 + - + +
530C ASP* 3.6 8.5 - - - +
532C ARG* 1.3 73.9 - - - +
534C GLN* 1.3 68.9 + - - +
536C GLY* 3.2 3.6 + - - -
537C ILE* 3.0 28.6 + - + +
554C VAL* 3.7 44.6 - - + -
556C THR* 4.1 9.0 - - + -
569C ARG* 4.2 9.9 - - - +
571C LEU* 4.6 10.1 - - + -
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Residues in contact with GLN 534 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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530C ASP* 2.7 35.9 + - - +
531C ARG* 3.5 8.7 - - - +
533C VAL* 1.3 77.4 - - - +
535C PHE* 1.3 61.6 + - - +
537C ILE* 3.0 39.4 + - - +
538C GLU* 3.0 29.1 + - - +
571C LEU* 5.6 3.1 - - - +
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Residues in contact with PHE 535 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145C PRO* 3.6 32.8 - - + -
146C LEU* 3.2 31.9 - - + -
496C VAL* 4.1 11.4 - - + -
515C LEU* 3.9 20.9 - - + -
516C LEU 3.5 23.1 - - - -
517C TYR* 3.5 32.1 - + + -
518C ARG 5.6 0.7 - - - -
519C GLU* 6.1 1.1 - - + -
531C ARG 2.7 18.8 + - - +
532C ARG 3.0 9.2 + - - +
534C GLN* 1.3 73.6 - - - +
536C GLY* 1.3 53.6 + - - +
538C GLU* 3.4 6.0 + - - +
539C SER* 2.4 43.8 + - - -
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Residues in contact with GLY 536 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472C ILE* 4.2 9.6 - - - -
494C ILE* 4.4 8.9 - - - +
496C VAL* 4.0 18.8 - - - -
515C LEU* 4.1 8.4 - - - +
532C ARG 2.9 11.9 + - - -
533C VAL 3.2 4.9 + - - -
535C PHE* 1.3 76.5 - - - +
537C ILE* 1.3 50.7 + - - +
539C SER* 3.6 5.5 - - - -
540C GLY* 2.8 32.7 + - - -
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Residues in contact with ILE 537 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472C ILE* 3.7 15.9 - - + +
533C VAL* 3.0 21.1 + - + +
534C GLN* 3.0 36.6 + - + +
536C GLY* 1.3 74.0 - - - +
538C GLU* 1.3 53.3 + - + +
540C GLY* 2.9 2.9 + - - -
541C LYS* 2.6 56.2 + - + +
546C LEU* 3.7 9.8 - - + +
552C VAL* 5.1 1.1 - - + -
571C LEU* 4.8 11.9 - - + -
573C ILE* 3.8 32.8 - - + -
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Residues in contact with GLU 538 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146C LEU* 3.5 33.2 - - + +
534C GLN* 3.0 19.4 + - - +
535C PHE* 3.7 5.0 - - - +
537C ILE* 1.3 74.5 - - - +
539C SER* 1.3 68.3 + - - +
541C LYS* 3.0 13.0 + - + +
542C LEU* 2.9 24.8 + - - +
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Residues in contact with SER 539 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146C LEU* 3.6 36.6 - - - +
515C LEU* 3.2 31.4 - - - +
535C PHE* 2.4 35.0 + - - -
538C GLU* 1.3 75.5 - - - +
540C GLY* 1.3 63.8 + - - +
542C LEU* 3.2 2.1 + - - +
543C ARG* 3.0 33.8 + - - +
545C PHE* 5.5 0.2 - - - -
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Residues in contact with GLY 540 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494C ILE* 4.5 3.4 - - - -
515C LEU* 4.9 0.6 - - - +
536C GLY 2.8 16.3 + - - -
537C ILE 3.1 5.2 - - - -
539C SER* 1.3 77.6 - - - +
541C LYS* 1.3 64.2 + - - +
543C ARG* 3.3 3.6 + - - -
545C PHE* 3.1 35.8 + - - +
546C LEU* 3.9 20.9 - - - -
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Residues in contact with LYS 541 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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537C ILE* 2.6 37.7 + - + +
538C GLU* 3.0 12.7 + - + +
540C GLY* 1.3 68.4 - - - +
542C LEU* 1.3 62.8 + - - +
544C GLY* 3.0 16.5 + - - -
546C LEU* 3.5 23.5 + - + +
547C ARG* 5.3 3.6 - - - -
548C VAL* 5.3 14.8 - - + +
573C ILE* 4.3 23.5 + - + +
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Residues in contact with LEU 542 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144C SER* 6.3 0.4 - - - -
146C LEU* 4.4 22.0 - - + +
147C SER* 4.0 27.4 - - - -
538C GLU 2.9 15.7 + - - +
539C SER* 3.6 10.3 - - - +
541C LYS* 1.3 74.6 - - - +
543C ARG* 1.3 58.9 + - + +
544C GLY 3.2 2.6 + - - -
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Residues in contact with ARG 543 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145C PRO 4.5 2.2 + - - -
146C LEU 3.2 22.2 + - - +
147C SER* 3.2 25.3 + - - +
148C TYR 3.0 26.7 + - - +
149C ARG* 4.3 12.9 - - - +
150C PRO* 5.9 0.2 - - - +
513C PHE* 5.9 1.8 - - - +
514C PRO 4.7 2.2 + - - -
515C LEU* 3.4 30.0 - - - +
539C SER* 3.0 17.4 + - - +
540C GLY 3.3 1.5 + - - +
541C LYS 3.2 0.2 + - - -
542C LEU* 1.3 79.3 - - + +
544C GLY* 1.3 62.1 + - - +
545C PHE* 3.3 43.5 + - + -
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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