Contacts of the helix formed by residues 4100 - 4111 (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 GLU4100 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3289C ARG* 4.9 3.2 - - - +
3290C SER* 3.5 16.2 + - - -
3988C LEU* 3.5 14.9 - - + +
3992C ARG* 2.7 43.3 + - - +
4053C GLY 5.7 0.7 - - - +
4098C LEU* 6.0 2.2 - - + -
4099C SER* 1.3 74.2 - - - +
4101C GLU* 1.3 77.3 + - + +
4102C THR* 2.4 16.2 + - + +
4103C GLN* 2.5 31.4 + - - +
4104C VAL* 2.9 13.2 + - - +
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Residues in contact with GLU4101 (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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2954C GLN* 3.6 31.1 + - - +
2957C LEU* 5.3 5.4 - - - +
3981C TYR* 2.8 27.5 + - + +
3985C VAL* 4.3 18.4 - - + +
3988C LEU* 4.6 0.4 - - - +
4100C GLU* 1.3 84.8 - - + +
4102C THR* 1.3 63.8 + - + +
4104C VAL* 3.0 14.8 - - - +
4105C LYS* 2.9 33.5 + - - +
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Residues in contact with THR4102 (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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4093C GLU* 5.4 11.4 - - - +
4094C PRO* 6.0 2.9 - - - -
4095C GLU* 6.0 1.8 - - + -
4098C LEU 5.2 2.2 - - - +
4099C SER* 3.0 16.9 - - - -
4100C GLU* 2.4 25.6 + - + +
4101C GLU* 1.3 78.7 - - + +
4103C GLN* 1.3 67.9 + - - -
4104C VAL 2.8 0.3 - - - -
4105C LYS* 2.2 53.1 + - + +
4106C CYS* 3.0 15.4 + - - -
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Residues in contact with GLN4103 (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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3916C TRP* 5.6 2.8 - - - -
3988C LEU* 3.3 17.6 - - + +
4051C LEU 4.3 3.6 + - - -
4052C ALA 3.9 10.9 + - - +
4053C GLY 3.9 1.3 + - - +
4054C ALA* 3.1 16.4 - - - +
4055C ASN* 3.0 37.8 - - + +
4099C SER* 2.8 34.7 + - - +
4100C GLU* 2.5 17.6 + - - +
4102C THR* 1.3 79.8 + - - +
4104C VAL* 1.3 63.8 + - - +
4106C CYS* 3.0 11.0 - - - -
4107C LEU* 2.9 32.7 + - + +
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Residues in contact with VAL4104 (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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3981C TYR* 3.3 27.8 - - + +
3984C MET* 3.5 26.0 - - + -
3985C VAL* 4.2 12.1 - - + +
3988C LEU* 3.7 24.2 - - + +
4100C GLU 2.9 15.2 + - - +
4101C GLU* 3.0 16.4 - - - +
4103C GLN* 1.3 72.5 - - - +
4105C LYS* 1.3 67.5 + - - +
4107C LEU* 2.6 17.0 + - - -
4108C MET* 2.9 29.4 + - + +
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Residues in contact with LYS4105 (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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2954C GLN* 5.4 4.4 - - - +
3981C TYR* 3.0 33.9 - - + +
4093C GLU* 5.6 10.5 - - + +
4101C GLU* 2.9 29.5 + - - +
4102C THR* 2.2 42.3 + - + +
4104C VAL* 1.3 72.8 - - - +
4106C CYS* 1.3 68.5 + - - +
4108C MET* 3.1 15.8 - - - +
4109C ASP* 3.7 4.0 + - - +
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Residues in contact with CYS4106 (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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4055C ASN 4.9 7.9 - - - -
4057C ALA* 5.3 1.8 - - - -
4089C ILE* 6.2 0.7 - - - -
4090C ARG* 5.2 12.1 - - - +
4093C GLU* 4.5 18.8 + - + +
4094C PRO* 5.3 9.6 - - + -
4102C THR* 3.0 11.7 + - - -
4103C GLN* 3.0 24.0 - - - -
4104C VAL 3.0 0.2 + - - -
4105C LYS* 1.3 77.4 - - - +
4107C LEU* 1.3 75.8 + - - -
4108C MET 2.4 16.5 + - - -
4109C ASP* 2.7 16.9 + - - -
4110C GLN* 2.8 26.9 + - + +
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Residues in contact with LEU4107 (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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3916C TRP* 3.5 36.6 - - + +
3960C PRO* 3.1 26.3 - - + +
3961C PHE* 3.0 15.1 - - - -
4055C ASN* 3.1 28.7 - - - +
4058C VAL* 4.3 1.1 - - + -
4103C GLN* 2.9 29.6 + - + +
4104C VAL 2.6 8.1 + - - +
4106C CYS* 1.3 80.5 - - - +
4108C MET* 1.3 74.4 + - + +
4110C GLN* 3.1 34.0 - - - +
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Residues in contact with MET4108 (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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3912C CYS* 6.3 1.8 - - + -
3961C PHE* 3.1 33.5 - - + -
3977C THR* 5.5 9.2 - - + +
3981C TYR* 4.4 10.5 - - + -
3984C MET* 4.2 26.9 - - + -
4104C VAL* 2.9 56.7 + - + +
4105C LYS* 3.1 11.7 - - - +
4106C CYS 2.4 9.1 + - - -
4107C LEU* 1.3 87.9 - - + +
4109C ASP* 1.3 70.4 + - - +
4111C ALA* 3.2 8.7 + - - +
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Residues in contact with ASP4109 (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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3961C PHE* 5.8 0.3 - - - -
3963C LEU* 5.8 4.3 - - - +
3977C THR* 4.6 19.3 + - - +
4090C ARG* 4.2 10.4 - - + -
4105C LYS 3.7 3.1 + - - +
4106C CYS 2.7 5.8 + - - +
4108C MET* 1.3 83.5 - - + +
4110C GLN* 1.3 66.3 - - - +
4111C ALA 3.0 0.2 - - - -
4112C THR* 2.9 47.2 + - + +
4113C ASP* 3.6 3.3 + - - +
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Residues in contact with GLN4110 (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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3958C LEU* 5.9 1.1 - - + -
3960C PRO* 3.3 12.7 - - + +
4057C ALA* 3.6 20.0 - - - +
4058C VAL* 3.2 26.4 - - - +
4090C ARG* 3.7 32.8 + - + +
4106C CYS* 2.8 30.4 + - + +
4107C LEU* 3.1 47.2 - - - +
4109C ASP* 1.3 78.8 - - - +
4111C ALA* 1.3 62.2 + - - +
4113C ASP* 3.1 9.4 - - - +
4116C ILE* 3.0 24.0 - - + +
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Residues in contact with ALA4111 (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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3959C MET* 3.7 24.5 - - + -
3960C PRO* 4.7 1.5 - - + +
3961C PHE* 3.4 27.6 - - + +
3963C LEU* 5.0 3.1 - - + +
4107C LEU 4.0 0.4 + - - -
4108C MET 3.2 13.9 + - - +
4109C ASP 3.0 0.4 - - - -
4110C GLN* 1.3 75.6 - - - +
4112C THR* 1.3 53.8 + - - +
4113C ASP 2.7 17.1 + - - -
4116C ILE* 3.1 10.7 - - - +
4117C LEU* 3.0 26.0 - - + +
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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