Contacts of the helix formed by residues 523 - 536 (chain C) in PDB entry 1V40
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 ASN 523 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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498C PHE* 3.9 17.3 - - + -
518C GLU* 3.7 5.9 + - - +
519C LEU* 2.9 40.7 + - + +
522C TYR* 1.3 87.6 - - - +
524C ALA* 1.3 67.5 + - - +
525C PRO* 3.2 2.7 - - - -
526C HIS* 3.2 19.5 + - - +
527C LEU* 3.7 7.3 + - - +
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Residues in contact with ALA 524 (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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498C PHE* 3.7 25.9 - - + -
519C LEU 2.8 11.8 + - - +
520C LEU* 3.5 24.2 - - + +
523C ASN* 1.3 71.4 - - - +
525C PRO* 1.4 66.2 - - - +
527C LEU* 3.0 6.5 + - - +
528C MET* 2.8 28.6 + - + +
567C LEU* 3.8 23.1 - - + -
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Residues in contact with PRO 525 (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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520C LEU 3.6 7.4 - - - +
521C THR* 3.1 29.4 - - - +
522C TYR 4.0 1.1 - - - -
523C ASN 3.2 7.4 - - - +
524C ALA* 1.4 93.2 - - + +
526C HIS* 1.3 69.3 + - + +
528C MET* 3.4 7.9 + - + +
529C GLN* 3.0 24.8 + - - +
567C LEU* 6.1 0.7 - - + -
571C HIS* 4.7 5.5 - - + -
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Residues in contact with HIS 526 (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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522C TYR 3.3 25.8 + - - -
523C ASN* 3.2 9.1 + - - +
524C ALA 3.1 1.2 + - - -
525C PRO* 1.3 83.1 - - + +
527C LEU* 1.3 62.2 + - - +
529C GLN* 3.5 4.8 + - - +
530C ASP* 3.1 32.1 + - - +
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Residues in contact with LEU 527 (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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248B PHE* 4.2 9.9 - - + -
494C THR* 3.9 28.3 - - + +
495C LEU* 4.5 13.9 - - + -
498C PHE* 3.7 44.6 - - + -
523C ASN 3.7 5.1 + - - +
524C ALA* 3.0 10.6 + - - +
526C HIS* 1.3 75.9 - - - +
528C MET* 1.3 76.1 + - + +
530C ASP* 3.2 4.9 + - + +
531C LEU* 2.9 41.3 + - + +
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Residues in contact with MET 528 (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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495C LEU* 5.6 0.2 - - + -
498C PHE* 5.3 0.2 - - + -
524C ALA* 2.8 27.6 + - + +
525C PRO* 3.7 4.7 - - + +
527C LEU* 1.3 104.0 - - + +
529C GLN* 1.3 57.4 + - - +
531C LEU* 3.4 2.4 + - + +
532C ASP* 2.9 28.8 + - - +
553C TRP* 3.5 37.0 - - + -
560C LEU* 4.9 12.8 - - + -
567C LEU* 4.0 36.6 - - + +
568C LEU* 5.1 2.0 - - - -
571C HIS* 3.7 23.3 - - + +
574C LEU* 3.6 12.4 - - + +
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Residues in contact with GLN 529 (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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525C PRO 3.0 17.4 + - - +
526C HIS* 3.9 5.8 - - - +
528C MET* 1.3 76.5 - - - +
530C ASP* 1.3 61.1 + - - +
532C ASP* 4.0 13.1 + - - +
533C THR* 2.8 60.2 + - - +
571C HIS* 3.6 19.3 + - - +
573C ARG* 5.9 0.4 - - - +
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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
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247B PRO 3.5 17.5 - - - +
248B PHE* 3.5 44.2 - - + +
249B GLY 4.4 0.6 + - - -
250B LYS* 5.6 0.3 + - - -
526C HIS* 3.1 21.2 + - - +
527C LEU* 3.2 10.0 + - - +
529C GLN* 1.3 80.5 - - - +
531C LEU* 1.3 56.6 + - - +
533C THR* 3.4 6.3 + - - -
534C TYR* 2.8 30.0 + - - +
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Residues in contact with LEU 531 (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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248B PHE* 3.5 23.8 - - + -
491C ILE* 4.7 16.6 - - + -
494C THR* 5.2 1.6 - - + -
495C LEU* 3.7 22.7 - - + -
527C LEU* 2.9 33.8 + - + +
528C MET* 3.8 7.6 - - + +
530C ASP* 1.3 77.7 - - - +
532C ASP* 1.3 58.1 + - - +
534C TYR* 3.3 4.3 + - + +
535C LEU* 2.8 30.5 + - - +
541C LEU* 4.6 13.5 - - + +
553C TRP* 3.6 35.2 - - + -
574C LEU* 4.2 12.9 - - + +
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Residues in contact with ASP 532 (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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528C MET 2.9 18.6 + - - +
529C GLN* 3.2 10.1 + - - +
531C LEU* 1.3 73.8 - - - +
533C THR* 1.3 65.4 + - - +
535C LEU* 3.3 2.8 + - - +
536C GLY 2.9 19.2 + - - -
570C ASN 4.3 1.4 - - - +
571C HIS* 2.8 41.4 - - + +
572C PRO* 5.5 0.5 - - - +
573C ARG* 3.1 52.9 + - - +
574C LEU* 4.2 11.6 - - + +
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Residues in contact with THR 533 (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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529C GLN* 2.8 40.7 + - - +
530C ASP* 3.7 7.1 - - - -
532C ASP* 1.3 74.2 - - - +
534C TYR* 1.3 64.7 + - - +
536C GLY* 3.4 10.0 + - - -
573C ARG* 4.6 4.0 - - - +
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Residues in contact with TYR 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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247B PRO* 4.9 9.6 - - + +
248B PHE* 3.8 26.2 - + + -
262B HIS* 5.0 6.9 - + - -
487C HIS* 3.6 36.6 + + - +
491C ILE* 3.6 31.6 - - + +
530C ASP 2.8 18.6 + - - +
531C LEU* 3.5 4.9 - - + +
533C THR* 1.3 79.2 - - - +
535C LEU* 1.3 57.5 + - - +
538C ARG* 3.0 29.4 + - - -
541C LEU* 3.3 35.7 + - + -
542C ILE* 4.1 4.9 - - - +
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Residues in contact with LEU 535 (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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531C LEU 2.8 16.6 + - - +
532C ASP* 3.9 3.8 - - - +
534C TYR* 1.3 80.2 - - - +
536C GLY* 1.3 72.8 + - - +
538C ARG* 3.1 49.1 + - - +
539C GLU 4.5 1.3 - - - +
540C TRP* 3.4 35.4 - - - +
541C LEU* 3.8 13.7 - - + +
573C ARG* 3.7 29.6 - - + +
574C LEU* 4.2 15.3 - - + -
577C LEU* 4.3 14.1 - - + -
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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
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532C ASP 2.9 10.5 + - - -
533C THR 3.4 7.4 + - - -
534C TYR 3.4 2.8 - - - -
535C LEU* 1.3 86.7 - - - +
537C GLY* 1.3 58.7 + - - -
538C ARG* 3.4 3.5 + - - +
573C ARG* 3.1 38.6 + - - -
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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