Contacts of the helix formed by residues 3212 - 3223 (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 GLU3212 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3163C ARG* 3.3 20.7 + - - +
3190C ASP* 3.1 35.5 - - - +
3191C ALA* 4.7 4.3 + - - +
3192C PRO* 3.7 18.2 - - + +
3209C SER 2.9 7.0 + - - +
3210C GLY 2.8 12.6 + - - +
3211C GLY* 1.3 74.2 - - - +
3213C LEU* 1.3 64.4 + - - +
3214C GLN 3.4 2.2 - - - -
3215C GLU* 3.1 22.9 + - - +
3216C ILE* 3.1 28.8 + - + +
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Residues in contact with LEU3213 (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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3206C VAL* 4.0 18.2 - - + -
3209C SER* 3.5 28.7 + - - +
3211C GLY* 3.2 5.7 + - - -
3212C GLU* 1.3 76.8 - - - +
3214C GLN* 1.3 65.2 + - - +
3216C ILE* 3.1 6.0 + - + +
3217C LEU* 2.9 48.8 + - + +
3232C VAL* 4.2 9.6 - - + -
3239C THR* 3.8 27.8 - - + -
3242C GLU* 3.8 25.8 - - + +
3243C ALA* 4.0 16.2 - - + +
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Residues in contact with GLN3214 (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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3212C GLU 3.4 0.8 - - - -
3213C LEU* 1.3 78.6 - - - +
3215C GLU* 1.3 64.4 + - - +
3217C LEU* 3.4 3.3 + - - +
3218C ARG* 3.1 57.1 + - + +
3242C GLU* 3.3 22.3 + - - +
3246C CYS* 3.6 26.8 - - - -
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Residues in contact with GLU3215 (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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3192C PRO* 3.6 30.6 - - + +
3212C GLU* 3.1 22.7 + - + +
3214C GLN* 1.3 80.4 + - - +
3216C ILE* 1.3 65.8 + - - +
3218C ARG* 3.1 20.6 + - - +
3219C ILE* 3.0 40.8 + - + +
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Residues in contact with ILE3216 (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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3140C VAL* 4.0 13.2 - - + -
3191C ALA* 3.7 29.6 - - + -
3192C PRO* 4.4 6.7 - - + -
3195C LEU* 3.9 15.9 - - + +
3206C VAL* 4.3 17.0 - - + -
3209C SER* 3.8 28.3 - - - +
3212C GLU* 3.1 20.7 + - + +
3213C LEU* 3.5 9.9 - - - +
3215C GLU* 1.3 77.1 - - - +
3217C LEU* 1.3 58.0 + - + +
3219C ILE* 3.4 5.0 + - - +
3220C ILE* 2.9 49.3 + - + +
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Residues in contact with LEU3217 (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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3206C VAL* 4.2 14.4 - - + -
3213C LEU* 2.9 40.0 + - + +
3214C GLN* 3.8 3.8 - - - +
3216C ILE* 1.3 74.7 - - - +
3218C ARG* 1.3 66.1 + - - +
3220C ILE* 3.0 7.5 + - + +
3221C LYS* 2.8 22.3 + - - +
3230C ILE* 4.1 21.3 - - + +
3232C VAL* 4.0 22.0 - - + -
3243C ALA* 4.4 7.9 - - - -
3246C CYS* 3.7 26.2 - - + -
3247C LEU* 4.0 19.5 - - + -
3250C LEU* 4.0 15.8 - - + +
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Residues in contact with ARG3218 (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* 3.1 51.1 + - + +
3215C GLU* 3.1 24.7 + - - +
3217C LEU* 1.3 73.1 - - - +
3219C ILE* 1.3 69.0 + - + +
3221C LYS* 2.8 16.9 + - - +
3222C ASP* 3.1 18.5 + - - +
3250C LEU* 4.1 28.6 - - + +
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Residues in contact with ILE3219 (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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3192C PRO* 3.6 40.4 - - + +
3195C LEU* 3.7 27.1 - - + -
3196C CYS* 4.4 12.8 - - - -
3215C GLU* 3.0 25.0 + - + +
3216C ILE 3.6 6.3 - - - +
3218C ARG* 1.3 80.0 - - + +
3220C ILE* 1.3 58.5 + - - +
3222C ASP* 2.9 33.9 + - + +
3223C LYS* 3.4 22.7 + - + +
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Residues in contact with ILE3220 (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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3138C VAL* 4.9 0.7 - - + -
3140C VAL* 4.2 10.1 - - + -
3195C LEU* 4.2 15.0 - - + -
3201C ILE* 4.0 15.2 - - + +
3204C ALA* 3.4 32.5 - - + -
3206C VAL* 3.7 30.3 - - + -
3216C ILE* 2.9 31.2 + - + +
3217C LEU* 3.0 9.2 + - + +
3219C ILE* 1.3 77.3 - - - +
3221C LYS* 1.3 64.7 + - - +
3223C LYS* 3.3 4.4 + - - +
3224C LEU* 3.2 20.4 + - + +
3230C ILE* 3.8 20.6 - - + -
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Residues in contact with LYS3221 (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 2.8 10.9 + - - +
3218C ARG* 2.8 17.8 + - - +
3220C ILE* 1.3 71.0 - - - +
3222C ASP* 1.3 67.2 + - - +
3223C LYS 3.0 6.9 + - - -
3224C LEU* 3.0 22.5 + - - +
3230C ILE* 4.9 1.1 - - - +
3250C LEU* 3.1 46.7 + - + +
3251C GLY* 5.3 0.2 - - - -
3252C PHE* 3.9 27.6 - - + -
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Residues in contact with ASP3222 (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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3200C ASP* 4.9 1.7 - - - +
3218C ARG* 3.5 18.7 - - - +
3219C ILE* 2.9 13.7 + - + +
3221C LYS* 1.3 86.1 - - - +
3223C LYS* 1.3 60.1 + - + +
3224C LEU 3.6 0.4 - - - -
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Residues in contact with LYS3223 (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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3195C LEU* 2.5 37.2 + - + +
3196C CYS* 3.1 22.5 + - - +
3198C ILE* 3.1 19.0 + - + +
3199C PRO 3.7 16.4 - - - +
3200C ASP* 3.2 30.8 - - - +
3201C ILE* 2.8 39.5 + - + +
3219C ILE* 3.9 20.6 - - + +
3220C ILE* 3.3 7.0 + - - +
3221C LYS 3.2 0.6 - - - -
3222C ASP* 1.3 81.5 - - + +
3224C LEU* 1.3 60.2 + - - +
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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