Contacts of the strand formed by residues 404 - 409 (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 TYR 404 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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402C PRO* 3.7 38.1 + - + +
403C ASN* 1.3 73.4 - - - +
405C LYS* 1.3 60.9 + - - +
406C LEU 4.2 0.4 - - - -
422C PHE* 3.9 13.5 - + + -
427C ILE* 3.7 23.1 - - + +
428C GLN 3.8 15.8 + - - -
429C TYR* 3.7 18.1 - - + +
430C GLU* 2.9 25.2 + - - +
454C LEU* 4.1 11.2 - - + -
455C GLU 3.3 1.6 - - - -
456C VAL* 3.7 40.3 - - + +
470C TYR* 4.6 9.6 + + - -
471C LEU* 4.1 24.7 - - + +
3003C GOL 5.7 0.5 - - - +
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Residues in contact with LYS 405 (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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404C TYR* 1.3 75.1 - - - +
406C LEU* 1.3 60.0 + - - +
407C THR* 3.9 4.6 + - - +
430C GLU* 3.6 42.7 + - + +
432C HIS* 3.8 32.6 + - + -
453C ILE 3.8 0.9 - - - +
454C LEU* 3.5 4.6 - - - +
455C GLU* 2.9 67.1 + - + +
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Residues in contact with LEU 406 (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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404C TYR 4.2 0.6 - - - -
405C LYS* 1.3 72.0 - - - +
407C THR* 1.3 63.7 + - - +
408C TYR* 5.1 1.8 - - + -
415C ALA* 4.4 8.7 - - + -
418C ILE* 4.0 31.0 - - + -
419C ARG* 3.7 33.0 - - + +
422C PHE* 4.9 0.2 - - + -
429C TYR* 3.9 18.8 - - + -
430C GLU 2.9 10.9 + - - +
431C ASP* 3.9 7.6 - - - +
432C HIS* 2.8 34.1 + - - +
452C PRO* 4.0 21.1 - - + -
453C ILE 3.5 17.0 - - - +
454C LEU* 3.8 13.6 - - + +
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Residues in contact with THR 407 (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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405C LYS* 3.9 10.6 + - - +
406C LEU* 1.3 73.8 - - - +
408C TYR* 1.3 64.8 + - - +
432C HIS* 3.5 30.3 - - + +
434C ILE* 4.1 14.4 - - + -
442C ILE* 4.8 13.0 - - + -
451C ILE* 3.7 17.3 - - + +
452C PRO* 3.2 25.6 - - - +
453C ILE* 3.0 34.6 + - + +
455C GLU* 4.3 4.3 + - - -
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Residues in contact with TYR 408 (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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406C LEU* 5.1 1.8 - - + -
407C THR* 1.3 76.7 - - - +
409C PHE* 1.3 87.4 + + - +
411C MET* 3.7 28.8 - - + -
412C ARG 3.6 16.2 - - - -
413C GLY* 3.4 5.4 - - - -
414C ARG* 2.8 22.5 + - + -
415C ALA* 3.5 25.4 - - + -
419C ARG* 4.0 6.3 - - - +
432C HIS 3.2 5.2 + - - -
433C ARG* 3.2 5.2 - - - -
434C ILE* 2.9 29.0 + - - +
451C ILE* 3.9 14.4 - - + -
452C PRO* 3.5 38.8 - - + -
3600C GSH 3.1 34.4 - - + -
3601C O16 4.7 2.1 + - - -
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Residues in contact with PHE 409 (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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408C TYR* 1.3 100.9 - + - +
410C ASN* 1.3 61.9 + - - +
411C MET* 2.9 37.9 + - + -
419C ARG* 3.6 9.0 + - - -
433C ARG* 4.0 2.7 - - - +
434C ILE* 3.6 25.4 - - + +
436C GLN* 3.7 39.3 - - + -
439C TRP* 3.7 37.7 - + + -
451C ILE* 3.4 24.9 - - + -
3600C GSH 4.3 4.3 - - + -
3601C O16 3.3 26.5 - + - -
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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
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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