Contacts of the helix formed by residues 3236 - 3250 (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 LEU3236 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3234C ALA* 4.2 0.2 - - - +
3235C ILE* 1.3 86.4 - - + +
3237C LEU* 1.3 66.3 + - - +
3238C GLU* 3.6 12.8 - - + +
3239C THR* 3.2 30.3 + - - +
3240C LYS* 3.3 14.7 + - - +
4267D LEU* 4.4 7.0 - - + -
4269D ARG* 3.7 53.4 - - + +
4270D GLY* 4.5 3.1 - - - +
4271D THR 3.6 4.0 - - - +
4272D MSE 3.5 29.8 - - + +
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Residues in contact with LEU3237 (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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1237A LEU* 4.6 12.5 - - + +
1240A LYS* 4.0 33.2 - - + +
1241A PHE* 4.8 10.8 - - + +
1244A MSE 4.0 41.7 - - + -
1256A ILE* 4.4 13.5 - - + -
1258A GLU* 5.5 2.7 - - - +
3235C ILE 3.9 1.2 + - - -
3236C LEU* 1.3 71.8 - - - +
3238C GLU* 1.3 68.4 + - + +
3240C LYS* 3.2 34.4 + - + +
3241C PHE* 3.4 7.4 + - - +
4271D THR* 2.9 22.2 + - + +
4273D MSE 5.1 12.0 - - + +
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Residues in contact with GLU3238 (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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1241A PHE* 4.0 30.8 - - + -
1244A MSE 4.3 6.4 - - - +
1248A ARG* 5.1 2.8 + - - -
3236C LEU* 3.6 7.1 - - + +
3237C LEU* 1.3 83.0 + - + +
3239C THR* 1.3 59.1 + - - +
3241C PHE* 3.3 4.2 + - - +
3242C GLU* 2.9 30.6 + - - +
4269D ARG 5.1 4.5 - - - +
4270D GLY* 3.3 13.8 - - - -
4271D THR* 2.8 48.5 + - - -
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Residues in contact with THR3239 (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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3207C GLY 5.7 0.2 - - - +
3209C SER* 4.2 15.7 + - - +
3213C LEU* 3.8 20.9 - - + -
3232C VAL* 4.4 8.7 - - + -
3233C THR 4.4 5.8 - - - +
3234C ALA* 3.7 22.9 - - + -
3235C ILE 5.0 0.2 - - - -
3236C LEU* 3.2 31.3 + - - +
3238C GLU* 1.3 74.3 - - - +
3240C LYS* 1.3 67.8 + - - +
3242C GLU* 4.4 5.2 - - - -
3243C ALA* 2.9 28.4 + - - +
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Residues in contact with LYS3240 (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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1237A LEU* 3.9 22.2 - - + -
1258A GLU* 5.5 2.4 + - - -
3234C ALA* 3.7 20.6 - - + +
3235C ILE 4.6 7.7 + - - -
3236C LEU 3.3 14.3 + - - +
3237C LEU* 3.2 18.6 + - + +
3239C THR* 1.3 79.4 - - - +
3241C PHE* 1.3 58.6 + - - +
3243C ALA* 4.0 1.0 - - - +
3244C MSE 3.0 31.4 + - - +
3256C ILE* 4.5 6.5 - - + -
3258C GLU* 3.0 35.7 + - - +
3278C PRO* 4.8 7.0 + - - +
3279C VAL 5.3 0.2 - - - -
3280C ALA* 3.8 21.8 - - + +
3282C ILE* 4.1 9.4 - - - +
4273D MSE 4.1 23.4 - - - +
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Residues in contact with PHE3241 (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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1237A LEU* 4.5 12.7 - - + +
1238A GLU* 4.0 37.2 - - + -
1241A PHE* 3.3 65.3 - + + -
3237C LEU* 3.4 5.0 + - + +
3238C GLU 3.3 7.0 + - - +
3239C THR 3.2 0.2 - - - -
3240C LYS* 1.3 77.9 - - - +
3242C GLU* 1.3 71.3 + - + +
3244C MSE 3.4 4.6 + - + +
3245C GLU* 3.0 55.7 + - + +
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Residues in contact with GLU3242 (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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3213C LEU* 3.8 22.4 - - + +
3214C GLN* 3.3 28.7 + - - +
3238C GLU 2.9 21.8 + - - +
3239C THR* 4.0 3.1 - - - +
3241C PHE* 1.3 79.6 - - + +
3243C ALA* 1.3 57.7 + - - +
3245C GLU* 3.2 20.2 + - - +
3246C CYS* 2.8 43.8 + - - +
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Residues in contact with ALA3243 (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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3213C LEU* 4.0 15.4 - - + +
3217C LEU* 4.4 7.0 - - - -
3232C VAL* 4.4 15.7 - - + -
3239C THR 2.9 22.1 + - - +
3242C GLU* 1.3 72.0 - - - +
3244C MSE 1.3 63.1 + - - +
3247C LEU* 3.0 30.7 + - - +
3282C ILE* 3.7 31.9 - - + -
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Residues in contact with MSE3244 (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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1237A LEU* 3.8 18.4 - - + -
1238A GLU* 4.2 4.0 - - - +
2271B THR* 3.3 36.6 - - + +
3240C LYS 3.0 22.9 - - - +
3241C PHE* 3.4 5.8 + - + +
3243C ALA* 1.3 78.5 - - - +
3245C GLU* 1.3 62.8 + - - +
3248C ARG* 3.1 48.7 + - - +
3254C VAL* 3.7 30.9 - - - +
3255C ASN* 4.3 2.5 - - - +
3256C ILE* 3.7 27.8 - - + -
3282C ILE* 4.0 9.0 - - + -
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Residues in contact with GLU3245 (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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3241C PHE* 3.0 44.8 + - + +
3242C GLU* 3.5 20.0 - - - +
3244C MSE 1.3 78.7 - - - +
3246C CYS* 1.3 52.8 + - - +
3248C ARG* 3.0 9.1 + - - +
3249C ASP* 2.7 57.0 + - - +
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Residues in contact with CYS3246 (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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3214C GLN* 3.6 44.0 - - - -
3217C LEU* 3.7 22.4 - - + -
3242C GLU* 2.8 34.9 + - - +
3245C GLU* 1.3 74.9 - - - +
3247C LEU* 1.3 52.7 + - - +
3249C ASP* 3.0 9.2 + - - +
3250C LEU* 2.7 44.5 + - + +
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Residues in contact with LEU3247 (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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3217C LEU* 4.0 30.1 - - + -
3230C ILE* 4.2 13.0 - - + -
3232C VAL* 4.3 15.7 - - + -
3243C ALA 3.0 18.7 + - - +
3246C CYS* 1.3 78.3 - - - +
3248C ARG* 1.3 60.5 + - - +
3250C LEU* 3.1 8.2 + - + -
3252C PHE* 2.9 44.5 + - + -
3254C VAL* 3.7 16.2 - - + -
3282C ILE* 3.6 28.0 - - + +
3283C TYR* 5.2 0.2 - - - -
3284C THR* 4.1 24.5 - - + -
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Residues in contact with ARG3248 (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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1238A GLU* 4.9 3.7 + - - -
2270B GLY* 6.3 1.6 - - - -
2271B THR* 4.0 8.1 + - - -
3244C MSE 3.1 53.1 + - - +
3245C GLU* 3.0 7.3 + - - +
3247C LEU* 1.3 76.4 - - - +
3249C ASP* 1.3 64.6 + - - +
3251C GLY* 2.9 21.8 + - - -
3252C PHE 3.8 8.4 - - - +
3254C VAL* 3.6 21.1 + - + +
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Residues in contact with ASP3249 (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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3245C GLU* 2.7 40.6 + - - +
3246C CYS* 3.0 8.4 + - - +
3248C ARG* 1.3 79.1 - - - +
3250C LEU* 1.3 62.0 + - + +
3251C GLY 3.1 7.8 + - - -
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Residues in contact with LEU3250 (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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3214C GLN 5.5 0.2 - - - +
3217C LEU* 4.0 39.7 - - + +
3218C ARG* 4.1 27.6 - - + +
3221C LYS* 3.1 46.0 + - + +
3246C CYS* 2.7 28.4 + - + +
3247C LEU* 3.6 9.6 - - + +
3248C ARG 3.1 0.8 - - - -
3249C ASP* 1.3 80.0 - - + +
3251C GLY* 1.3 61.6 + - - +
3252C PHE* 3.4 19.0 + - + -
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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