Contacts of the helix formed by residues 4013 - 4023 (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 TRP4013 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3946C PHE* 6.4 0.2 - - - -
4006C VAL* 4.2 15.9 + - - +
4009C PRO* 4.1 25.7 - - + +
4010C SER* 4.0 3.7 + - - +
4011C PHE 2.6 6.5 + - - -
4012C ASP* 1.3 91.5 - - + +
4014C LYS* 1.3 61.7 + - + +
4015C ASN 3.3 0.4 - - - -
4017C GLU* 2.2 40.7 + - - +
4035C GLU* 2.9 27.5 - - + +
4038C TRP 4.4 5.2 - - - -
4039C TYR* 4.7 2.5 - + - -
4040C PRO* 3.0 40.3 + - + +
4041C ARG* 3.2 48.7 - - + -
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Residues in contact with LYS4014 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4010C SER 3.9 8.0 + - - +
4013C TRP* 1.3 85.6 - - + +
4015C ASN* 1.3 65.6 + - - +
4017C GLU* 3.0 42.6 - - - +
4018C GLN* 2.8 22.5 + - - +
4032C ASN* 4.4 8.5 - - - +
4035C GLU* 3.7 13.2 - - - +
4036C LYS* 4.9 12.0 - - - +
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Residues in contact with ASN4015 (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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3542C PHE* 5.7 12.7 - - + -
4010C SER* 2.8 22.9 + - - +
4011C PHE* 2.9 34.3 + - + +
4014C LYS* 1.3 81.2 - - - +
4016C PHE* 1.3 57.9 + - - +
4018C GLN* 2.9 26.2 + - - +
4019C LYS* 2.9 36.3 + - - +
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Residues in contact with PHE4016 (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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3760C GLN* 5.2 8.3 - - + -
3943C GLY* 3.0 33.2 - - - -
3944C HIS* 3.8 13.7 - - - -
3945C ALA 4.8 4.3 - - - -
3948C SER* 5.9 5.2 - - - -
3949C ALA* 5.8 2.0 - - + -
4011C PHE 2.5 8.9 + - - -
4012C ASP* 3.0 36.6 - - + +
4013C TRP 3.0 0.8 + - - -
4015C ASN* 1.3 70.9 - - - +
4017C GLU* 1.3 65.1 + - - +
4018C GLN 3.1 0.7 - - - -
4019C LYS* 3.0 28.7 - - + +
4020C MET* 2.8 61.9 + - + +
4035C GLU* 4.7 2.2 - - - -
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Residues in contact with GLU4017 (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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4013C TRP 2.2 33.4 + - - +
4014C LYS* 3.0 27.4 - - - +
4016C PHE* 1.3 68.0 - - - +
4018C GLN* 1.3 63.3 + - - +
4019C LYS 3.1 0.2 + - - -
4020C MET* 3.5 5.3 - - + +
4021C LEU 2.9 20.3 + - - -
4031C ILE* 2.6 61.3 - - + +
4032C ASN* 2.6 28.8 - - - +
4035C GLU* 2.7 36.6 + - - +
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Residues in contact with GLN4018 (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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3542C PHE* 5.0 13.8 - - - -
3591C ASP* 3.5 27.3 + - - +
3799C ARG* 5.2 0.8 - - - +
4014C LYS 2.8 11.7 + - - +
4015C ASN* 2.9 33.1 + - - +
4017C GLU* 1.3 75.2 - - - +
4019C LYS* 1.3 56.8 + - - +
4021C LEU* 3.0 16.3 - - + +
4022C LYS* 2.8 64.1 + - - +
4031C ILE* 4.5 0.9 - - - -
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Residues in contact with LYS4019 (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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3756C GLU* 3.1 28.5 - - - +
3757C ASP 4.3 3.4 - - - -
3760C GLN* 3.1 35.4 + - - +
4011C PHE* 3.3 18.8 + - - +
4012C ASP* 4.5 0.8 - - - +
4015C ASN* 3.0 21.1 + - - +
4016C PHE* 2.9 57.8 + - + +
4018C GLN* 1.3 75.4 - - + +
4020C MET* 1.3 57.7 + - - +
4021C LEU 3.1 1.1 - - - -
4022C LYS* 2.3 38.4 + - + +
4023C LYS* 2.9 6.9 + - - +
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Residues in contact with MET4020 (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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3944C HIS* 3.9 11.0 - - + -
3948C SER* 6.0 1.6 - - - -
3949C ALA* 5.3 0.2 - - - -
3952C PHE* 3.4 39.3 - - + -
4016C PHE* 2.8 63.8 + - + +
4017C GLU* 3.5 11.0 - - + +
4019C LYS* 1.3 69.5 - - - +
4021C LEU* 1.3 57.8 + - - +
4023C LYS* 5.7 0.4 - - - -
4024C GLY* 2.5 39.8 + - - +
4027C TRP* 3.4 20.6 - - + +
4031C ILE* 3.5 26.5 - - + -
4035C GLU* 4.4 6.1 - - + +
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Residues in contact with LEU4021 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3590C ASN* 4.2 23.8 - - + +
3591C ASP* 4.3 10.5 - - - +
3594C ALA* 4.6 20.2 - - + -
4017C GLU 2.9 13.8 + - - +
4018C GLN* 3.0 26.2 - - + +
4020C MET* 1.3 75.6 - - - +
4022C LYS* 1.3 72.0 + - + +
4023C LYS 2.7 20.1 + - - +
4024C GLY 3.8 6.3 - - - +
4027C TRP 4.8 4.7 - - - -
4028C ILE* 5.3 6.7 - - - +
4031C ILE* 3.7 24.1 - - + +
4032C ASN* 5.3 2.7 - - - +
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Residues in contact with LYS4022 (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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3542C PHE* 6.0 2.4 - - - -
3583C LEU* 5.9 2.3 - - - +
3587C ASP* 5.1 17.3 - - + +
3590C ASN* 5.6 5.8 + - + +
3591C ASP* 4.3 8.1 - - - +
3732C LEU* 5.4 1.2 - - - +
3755C GLY 3.5 16.0 + - - +
3756C GLU* 3.2 29.2 + - + +
3798C SER 4.8 3.0 + - - -
3799C ARG* 3.4 35.5 - - - +
4018C GLN* 2.8 52.3 + - - +
4019C LYS* 2.3 24.0 + - + +
4021C LEU* 1.3 77.9 - - + +
4023C LYS* 1.3 68.0 + - + +
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Residues in contact with LYS4023 (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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3583C LEU* 5.2 1.4 - - - +
3732C LEU* 3.1 55.1 + - + +
3733C ARG* 3.2 50.8 - - - +
3756C GLU* 5.7 0.2 - - - -
4019C LYS 2.9 8.6 + - - +
4020C MET* 3.3 1.1 - - - -
4021C LEU 2.7 6.8 + - - +
4022C LYS* 1.3 84.3 + - + +
4024C GLY* 1.3 65.6 + - - +
4025C GLY* 3.1 4.7 + - - -
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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