Contacts of the strand formed by residues 467 - 472 (chain C) in PDB entry 3SV1
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 467 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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378C LEU* 5.7 2.5 - - + -
402C VAL* 3.9 16.4 - - + -
406C LYS* 5.7 9.2 - - + -
462C ALA 3.1 12.6 - - - +
463C ASP 4.2 1.0 - - - -
464C ILE* 3.3 28.7 + - + +
465C GLY* 2.9 4.7 - - - +
466C ASN* 1.3 111.8 - - - +
468C VAL* 1.3 64.2 + - - +
469C VAL* 3.8 21.8 - - + -
504C VAL* 4.3 6.1 - - + -
505C PHE 3.1 12.6 - - - +
506C GLU* 4.8 5.2 - - + -
510C ALA* 4.4 0.2 - - - -
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Residues in contact with VAL 468 (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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375C ALA* 5.7 0.2 - - + -
461C ILE* 5.9 0.9 - - + -
462C ALA 3.4 12.8 - - - +
467C ILE* 1.3 74.1 - - - +
469C VAL* 1.3 66.2 + - - +
470C LEU* 6.0 2.0 - - + -
505C PHE* 2.7 57.5 + - + +
507C SER* 4.3 8.1 - - - +
510C ALA* 3.4 35.9 - - + +
513C ILE* 4.2 26.0 - - + -
514C ALA* 4.6 15.9 - - + +
517C ILE* 5.0 7.4 - - + -
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Residues in contact with VAL 469 (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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398C ALA* 4.5 16.2 - - + -
401C ALA* 4.6 0.9 - - + -
402C VAL* 3.2 32.5 - - + -
460C TYR* 3.9 4.1 - - + +
461C ILE* 3.4 4.0 - - - -
462C ALA* 3.0 44.1 + - + +
464C ILE* 4.6 5.8 - - + -
467C ILE* 3.8 9.2 - - + -
468C VAL* 1.3 83.8 - - - +
470C LEU* 1.3 64.7 + - - +
471C MET* 5.8 0.2 - - + -
502C CYS* 3.9 25.8 - - + -
503C HIS 3.4 9.6 - - - +
504C VAL* 4.3 7.9 - - + -
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Residues in contact with LEU 470 (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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432C LEU* 5.9 3.1 - - + -
439C ILE* 4.2 28.9 - - + -
441C VAL* 6.0 2.2 - - + -
453C HIS* 5.1 5.2 - - + -
458C ILE* 4.4 21.1 - - + -
460C TYR* 3.1 15.5 - - - +
461C ILE* 4.4 9.9 - - + -
468C VAL* 6.0 2.2 - - + -
469C VAL* 1.3 76.8 - - - +
471C MET* 1.3 63.6 + - - +
502C CYS* 3.3 2.2 - - - -
503C HIS* 2.8 66.1 + - + +
505C PHE* 3.6 15.9 - - + -
517C ILE* 5.5 5.6 - - + -
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Residues in contact with MET 471 (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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383C LEU* 4.4 8.5 - - + -
385C SER* 4.7 1.8 - - - +
394C ARG* 4.1 24.2 - - - +
397C GLN* 4.5 16.2 - - - +
398C ALA* 5.8 2.5 - - - -
458C ILE* 3.8 4.5 - - - +
459C SER* 3.2 21.8 + - - -
460C TYR* 3.3 32.6 + - + -
469C VAL* 5.8 0.2 - - + -
470C LEU* 1.3 78.4 - - - +
472C ALA* 1.3 59.8 + - - +
500C MET* 3.2 48.5 - - + -
501C ILE 2.8 15.7 - - - +
502C CYS* 3.5 23.1 - - - -
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Residues in contact with ALA 472 (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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453C HIS* 3.5 39.0 - - + +
457C THR* 3.3 23.6 - - - +
458C ILE* 4.2 2.9 - - + +
471C MET* 1.3 72.0 - - - +
473C ARG* 1.3 60.2 + - - +
474C ARG 3.4 2.5 - - - +
500C MET* 3.0 19.3 - - - +
501C ILE* 3.0 28.5 + - + +
503C HIS* 5.6 0.6 - - - -
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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