Contacts of the strand formed by residues 3279 - 3284 (chain C) in PDB entry 1F38
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 VAL3279 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3117C THR* 5.3 4.5 - - + -
3118C ALA* 5.9 3.4 - - + +
3121C VAL* 3.9 40.4 - - + -
3233C THR* 4.4 11.4 - - + -
3234C ALA 3.6 8.1 - - - +
3235C ILE* 3.9 16.4 - - + -
3257C THR 3.9 1.2 - - - +
3258C GLU* 3.4 2.8 - - - -
3259C LEU* 2.9 36.0 + - - +
3261C ILE* 6.1 1.3 - - + -
3276C ARG* 6.2 0.7 - - + -
3277C ASN 3.5 11.4 - - - +
3278C PRO* 1.3 79.3 - - - +
3280C ALA* 1.3 71.4 + - - +
3281C LEU* 4.6 2.4 - - + +
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Residues in contact with ALA3280 (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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3233C THR* 3.6 0.2 - - - -
3234C ALA 2.8 33.4 + - - +
3240C LYS* 3.8 30.8 - - + +
3256C ILE* 4.1 11.9 - - + -
3257C THR 3.4 5.2 - - - +
3258C GLU* 3.7 21.8 - - + +
3279C VAL* 1.3 76.3 - - - +
3281C LEU* 1.3 67.2 + - - +
3282C ILE* 4.1 4.0 - - + -
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Residues in contact with LEU3281 (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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3121C VAL* 4.1 21.8 - - + +
3124C LEU* 3.7 37.5 - - + -
3125C ILE* 4.1 19.1 - - + -
3128C LEU* 3.9 20.0 - - + -
3231C ILE* 4.5 7.4 - - + -
3232C VAL 3.3 5.4 - - - +
3233C THR* 3.8 21.1 - - - +
3256C ILE* 3.3 4.3 - - - -
3257C THR* 3.0 35.5 + - - +
3259C LEU* 5.6 3.4 - - + -
3279C VAL* 4.6 4.7 - - + +
3280C ALA* 1.3 84.7 - - - +
3282C ILE* 1.3 61.2 + - - +
3283C TYR* 3.5 6.2 - - + -
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Residues in contact with ILE3282 (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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3230C ILE 4.0 0.3 - - - +
3231C ILE* 3.5 1.4 - - - -
3232C VAL* 2.8 45.3 + - + +
3234C ALA* 4.0 24.2 - - + -
3240C LYS* 4.1 9.6 - - - +
3243C ALA* 3.7 26.2 - - + -
3244C MSE 4.0 19.7 - - + +
3247C LEU* 3.6 17.7 - - + +
3254C VAL* 3.3 31.0 - - + -
3255C ASN 3.3 4.7 - - - +
3256C ILE* 4.1 14.6 - - + -
3280C ALA* 4.3 0.9 - - + -
3281C LEU* 1.3 79.7 - - - +
3283C TYR* 1.3 57.9 + - - +
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Residues in contact with TYR3283 (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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2120B GLU* 5.6 0.7 + - - -
2263B ARG* 6.1 0.7 - - - +
3128C LEU* 3.9 41.2 - - + +
3230C ILE 3.3 11.9 - - - +
3231C ILE* 4.1 14.4 - - + -
3247C LEU* 5.1 0.7 - - - -
3254C VAL* 3.6 3.3 - - - -
3255C ASN* 2.9 74.7 + - + +
3256C ILE 4.9 0.3 + - - -
3257C THR* 3.7 25.1 + - - -
3281C LEU 3.5 16.4 - - - -
3282C ILE* 1.3 76.0 - - - +
3284C THR* 1.3 71.9 + - - +
3285C GLY* 6.1 0.2 - - - -
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Residues in contact with THR3284 (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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3228C GLY 4.6 1.0 + - - -
3229C ARG* 3.9 6.6 - - - +
3230C ILE* 3.0 37.8 + - + +
3247C LEU* 4.1 22.0 - - + -
3252C PHE* 3.4 46.9 - - + -
3253C ASP 3.4 4.9 - - - +
3254C VAL* 5.5 0.4 - - - -
3255C ASN* 4.5 2.0 - - - -
3283C TYR* 1.3 87.7 - - - +
3285C GLY* 1.3 72.6 + - - +
3286C VAL* 3.6 5.4 + - - +
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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