Contacts of the helix formed by residues 3995 - 4008 (chain C) in PDB entry 5Y3R
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 PRO3995 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3330C LEU* 6.6 0.2 - - + -
3334C TYR* 5.5 11.7 - - + +
3422C GLN* 3.1 33.9 - - + +
3991C PHE 5.4 2.0 - - - +
3992C ARG 5.1 1.9 - - - +
3993C SER 4.2 4.3 - - - +
3994C ASP* 1.3 95.6 - - - +
3996C GLY* 1.3 53.4 + - - +
3997C LEU 2.7 11.2 + - - -
3998C LEU* 3.7 3.8 + - - +
3999C THR* 2.4 28.0 + - - +
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Residues in contact with GLY3996 (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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3421C ASP* 4.9 3.8 - - - -
3422C GLN* 3.8 14.6 + - - -
3460C GLU* 5.7 6.3 - - - -
3994C ASP* 3.0 11.1 + - - -
3995C PRO* 1.3 81.1 - - - +
3997C LEU* 1.3 66.8 + - - +
3999C THR* 3.1 11.8 - - - -
4000C ASN* 2.9 28.1 + - - -
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Residues in contact with LEU3997 (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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3460C GLU* 5.4 13.7 - - + +
3463C LEU* 6.1 0.3 - - - +
3770C VAL* 4.7 16.2 - - + -
3774C ILE* 3.9 29.6 - - + -
3777C GLN* 4.2 15.0 - - - +
3991C PHE 5.9 0.4 - - - +
3993C SER* 5.6 0.4 - - - -
3994C ASP* 3.1 52.3 - - + +
3995C PRO 2.7 5.9 + - - -
3996C GLY* 1.3 77.0 - - - +
3998C LEU* 1.3 62.5 + - - +
4000C ASN* 3.2 3.8 + - - +
4001C THR* 2.8 21.3 + - - -
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Residues in contact with LEU3998 (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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3767C LEU* 3.4 28.0 - - + -
3770C VAL* 5.4 1.0 - - + +
3771C MET* 5.7 3.1 - - + -
3916C TRP* 5.4 5.8 - - + -
3917C ILE* 3.9 29.4 - - + -
3995C PRO 3.7 2.9 + - - +
3997C LEU* 1.3 81.3 - - + +
3999C THR* 1.3 57.3 + - - +
4001C THR* 2.7 40.3 + - - -
4002C MET* 2.8 38.9 + - + +
4052C ALA* 6.1 5.4 - - + -
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Residues in contact with THR3999 (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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3421C ASP* 4.5 3.1 - - - +
3422C GLN* 4.7 4.0 + - - +
3425C ARG* 3.2 39.3 - - + +
3995C PRO* 2.4 32.2 + - - +
3996C GLY* 3.1 16.1 - - - +
3998C LEU* 1.3 76.3 - - - +
4000C ASN* 1.3 52.5 + - - +
4002C MET* 4.8 0.2 - - - +
4003C ASP* 2.4 36.8 + - - +
4049C ARG* 5.3 10.8 - - + +
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Residues in contact with ASN4000 (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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3421C ASP* 3.7 10.3 + - - +
3425C ARG* 2.9 11.3 + - - -
3460C GLU* 3.4 46.6 + - - +
3463C LEU* 4.2 13.9 - - + -
3464C LYS* 4.0 3.0 - - - +
3467C ARG* 2.3 36.8 + - - +
3996C GLY 2.9 20.2 + - - +
3997C LEU 3.8 3.1 - - - +
3999C THR* 1.3 73.1 - - - +
4001C THR* 1.3 68.6 + - - +
4003C ASP* 3.4 5.2 - - - -
4004C VAL* 2.9 25.8 + - - +
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Residues in contact with THR4001 (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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3463C LEU* 5.6 8.5 - - - +
3763C ARG 5.6 0.2 - - - +
3766C GLN 5.1 2.7 - - - +
3767C LEU* 3.5 44.2 - - + +
3770C VAL* 4.5 10.1 - - + +
3997C LEU 2.8 19.8 + - - -
3998C LEU* 2.7 27.7 + - + -
4000C ASN* 1.3 78.0 - - - +
4002C MET* 1.3 59.4 + - - +
4004C VAL* 4.1 2.5 - - - +
4005C PHE* 2.4 35.7 + - + +
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Residues in contact with MET4002 (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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3767C LEU* 4.7 7.2 - - + -
3917C ILE* 5.0 9.0 - - + +
3918C LEU* 4.9 4.7 - - + -
3946C PHE* 3.3 26.0 - - + -
3998C LEU* 2.8 34.2 + - + +
3999C THR 4.8 0.2 - - - +
4001C THR* 1.3 85.6 - - - +
4003C ASP* 1.3 65.2 + - - +
4005C PHE* 3.2 45.8 - - + -
4006C VAL* 2.8 33.5 + - + +
4044C ILE* 6.4 0.2 - - + -
4048C LYS* 5.5 17.5 - - + -
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Residues in contact with ASP4003 (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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3425C ARG* 2.2 41.8 + - - +
3428C GLU* 5.4 1.2 - - - +
3467C ARG* 2.5 22.2 + - - -
3999C THR 2.4 24.7 + - - +
4000C ASN 2.9 8.3 + - - +
4002C MET* 1.3 83.0 - - - +
4004C VAL* 1.3 59.5 + - - +
4006C VAL* 3.8 4.1 - - - +
4007C LYS* 2.9 27.4 + - - +
4041C ARG* 5.6 3.3 + - - -
4045C CYS* 5.6 5.4 - - - -
4049C ARG* 5.3 5.5 + - - -
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Residues in contact with VAL4004 (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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3463C LEU* 4.3 10.8 - - + +
3466C PRO* 5.2 0.2 - - + -
3467C ARG* 3.4 29.2 - - + +
3470C GLN* 3.4 29.2 - - - +
3501C HIS* 3.3 37.7 - - + +
4000C ASN 2.9 15.0 + - - +
4001C THR* 4.1 2.5 - - - +
4003C ASP* 1.3 78.1 - - - +
4005C PHE* 1.3 70.3 + - - +
4007C LYS* 3.6 9.2 - - + -
4008C GLU* 2.9 25.9 + - + +
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Residues in contact with PHE4005 (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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3501C HIS* 5.2 4.7 - - - -
3760C GLN* 4.9 1.8 - - + -
3763C ARG* 2.3 91.2 + - + +
3764C VAL* 4.7 7.9 - - + -
3767C LEU* 6.1 0.9 - - + -
3918C LEU* 4.8 6.3 - - + -
3946C PHE* 3.3 36.3 - + - -
4001C THR* 2.4 29.8 + - + +
4002C MET* 3.1 27.6 - - + +
4003C ASP 3.0 0.2 - - - -
4004C VAL* 1.3 82.0 - - - +
4006C VAL* 1.3 84.6 + - + +
4009C PRO* 3.1 0.3 - - - +
4012C ASP* 4.6 4.7 - - - -
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Residues in contact with VAL4006 (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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3763C ARG* 3.8 1.6 - - - +
3946C PHE* 4.0 17.5 - - + -
4002C MET* 2.8 27.7 + - + +
4003C ASP* 3.8 4.5 - - - +
4005C PHE* 1.3 98.0 - - + +
4007C LYS* 1.3 68.6 + - - +
4008C GLU 3.2 0.2 - - - -
4009C PRO* 3.0 16.6 - - + +
4012C ASP* 5.8 1.1 - - + +
4013C TRP* 4.2 14.9 - - - +
4040C PRO 4.3 21.1 - - - +
4041C ARG* 4.1 21.1 - - - +
4044C ILE* 4.7 10.1 - - + -
4045C CYS* 5.3 6.5 - - + +
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Residues in contact with LYS4007 (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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3467C ARG* 3.8 27.8 - - + -
3470C GLN* 4.5 12.1 - - - +
3471C ILE* 3.6 46.8 - - - +
4003C ASP* 2.9 23.1 + - - +
4004C VAL* 3.5 6.7 - - + +
4005C PHE 3.1 0.6 - - - -
4006C VAL* 1.3 81.9 - - - +
4008C GLU* 1.3 63.8 + - - +
4009C PRO* 3.9 1.2 - - - +
4041C ARG* 3.2 43.7 + - - +
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Residues in contact with GLU4008 (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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3470C GLN* 5.8 3.4 - - - +
3500C SER* 4.8 0.5 + - - -
3501C HIS* 2.7 46.2 + - - +
3504C ALA* 3.0 12.2 - - + +
3505C LEU* 3.5 1.8 + - - -
3508C LYS* 2.8 25.5 + - - -
3509C ASP* 3.9 19.0 - - - +
3759C ARG* 2.3 32.8 + - - +
3763C ARG* 3.2 18.8 + - - +
4004C VAL* 2.9 17.1 + - + +
4007C LYS* 1.3 80.9 - - - +
4009C PRO* 1.3 64.6 - - + +
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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