Contacts of the helix formed by residues 3458 - 3472 (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 SER3458 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3410C ILE* 4.1 9.7 - - - +
3414C MET* 2.7 46.2 - - - +
3450C MET* 5.9 0.7 - - - -
3453C ALA* 5.6 3.5 - - - +
3454C LEU* 5.4 7.4 + - - -
3456C LEU* 4.1 10.8 + - - +
3457C ASN* 1.3 88.6 + - - +
3459C ASN* 1.3 49.6 + - - +
3460C GLU* 2.9 7.4 - - - -
3461C ALA* 2.6 41.5 + - - +
3462C ARG 3.7 0.5 + - - -
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Residues in contact with ASN3459 (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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3457C ASN* 2.8 41.7 + - - +
3458C SER* 1.3 72.0 - - - +
3460C GLU* 1.3 66.6 + - - +
3461C ALA 3.3 0.2 - - - -
3462C ARG* 2.9 59.8 + - - +
3463C LEU* 2.9 19.3 + - + +
3497C SER* 5.4 2.4 + - - -
3710C LYS* 5.1 10.3 - - - +
3770C VAL* 5.6 10.5 - - + +
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Residues in contact with GLU3460 (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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3414C MET* 4.0 21.0 - - + +
3417C ALA* 3.8 16.2 - - - +
3418C ASP* 3.4 28.9 + - - +
3421C ASP* 5.2 4.9 - - + +
3458C SER 3.9 4.6 - - - +
3459C ASN* 1.3 75.7 - - - +
3461C ALA* 1.3 91.4 + - - +
3463C LEU* 5.0 0.4 - - - -
3464C LYS* 2.9 48.9 + - - +
3465C PHE* 5.0 0.3 - - - -
3994C ASP* 6.1 1.1 - - - +
3996C GLY* 5.4 7.6 - - - +
3997C LEU* 5.4 14.4 - - + +
4000C ASN* 3.4 23.0 + - - +
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Residues in contact with ALA3461 (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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3414C MET* 5.7 1.8 - - + -
3450C MET* 3.6 20.0 - - + -
3457C ASN 5.6 0.2 - - - +
3458C SER* 2.6 22.8 + - - +
3460C GLU* 1.3 89.3 + - - +
3462C ARG* 1.3 62.3 + - - +
3465C PHE* 2.9 61.3 + - + -
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Residues in contact with ARG3462 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3450C MET* 5.8 1.3 - - - -
3454C LEU* 6.2 2.7 - - + -
3457C ASN 4.7 3.8 - - - +
3458C SER 3.7 0.8 + - - +
3459C ASN* 2.9 55.4 + - - +
3461C ALA* 1.3 80.7 - - - +
3463C LEU* 1.3 98.0 + - - +
3465C PHE* 4.3 6.8 - - - +
3466C PRO* 3.0 22.3 - - - +
3486C GLU* 5.5 0.9 - - - -
3494C GLN 5.2 0.4 - - - -
3497C SER* 3.2 35.4 + - - -
3498C TRP* 3.2 59.1 - - + +
3766C GLN 5.3 0.6 + - - -
3769C GLN* 4.2 15.0 - - - +
3770C VAL* 5.2 5.3 - - - +
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Residues in contact with LEU3463 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3459C ASN* 2.9 22.7 + - + +
3460C GLU* 3.9 1.3 - - - +
3462C ARG* 1.3 120.8 - - + +
3464C LYS* 1.3 66.4 + - - +
3466C PRO* 3.1 15.2 - - - +
3467C ARG* 2.8 17.8 + - - +
3498C TRP* 3.5 17.7 - - + -
3501C HIS* 3.7 19.3 - - + +
3770C VAL* 5.7 6.1 - - + -
3997C LEU 6.1 0.4 - - - +
4000C ASN* 4.2 19.1 - - + -
4001C THR* 5.6 8.7 - - - +
4004C VAL* 4.3 7.0 - - + +
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Residues in contact with LYS3464 (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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3417C ALA* 5.3 3.6 - - + -
3420C CYS* 6.0 1.3 - - - -
3421C ASP* 4.7 21.5 - - + +
3424C LEU* 6.4 0.9 - - - -
3443C PRO* 4.0 15.2 + - - +
3446C VAL* 4.3 10.1 - - + +
3447C VAL* 3.0 35.2 - - - +
3460C GLU* 2.9 35.7 + - - +
3461C ALA 3.5 1.8 - - - +
3463C LEU* 1.3 76.7 - - - +
3465C PHE* 1.3 72.4 + - + +
3467C ARG* 2.7 43.0 + - - +
3468C LEU* 3.1 37.3 + - + +
4000C ASN* 4.0 4.2 - - - +
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Residues in contact with PHE3465 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3417C ALA* 6.0 0.9 - - + -
3446C VAL* 4.1 3.8 - - + -
3447C VAL* 3.2 53.8 - - + -
3450C MET* 3.4 25.8 - - + -
3460C GLU* 5.0 0.7 - - - -
3461C ALA* 2.9 44.7 + - + +
3462C ARG* 4.3 3.8 - - - +
3464C LYS* 1.3 95.3 - - + +
3466C PRO* 1.3 71.7 - - + +
3468C LEU* 3.1 23.4 - - - +
3469C LEU* 4.0 2.1 + - - +
3479C THR* 5.3 0.2 + - - -
3483C MET* 3.3 26.8 - - - +
3486C GLU* 3.1 22.2 - - - +
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Residues in contact with PRO3466 (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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3462C ARG 3.0 27.1 - - - +
3463C LEU* 3.1 13.9 - - - +
3465C PHE* 1.3 86.5 - - + +
3467C ARG* 1.3 69.1 + - + +
3468C LEU 2.8 2.3 + - - -
3469C LEU* 3.1 5.4 + - + +
3470C GLN* 2.9 41.5 + - + +
3498C TRP* 4.3 19.7 - - + +
3501C HIS* 5.2 7.0 - - - +
3502C MET* 5.8 0.9 - - + -
3505C LEU* 4.0 14.6 - - + -
4004C VAL* 5.2 0.7 - - + -
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Residues in contact with ARG3467 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3421C ASP* 4.3 2.0 + - - -
3424C LEU* 6.0 1.0 - - - +
3425C ARG* 3.0 10.1 - - - +
3463C LEU 2.8 30.4 + - - +
3464C LYS* 2.7 32.8 + - - +
3466C PRO* 1.3 77.1 - - - +
3468C LEU* 1.3 65.0 + - - +
3470C GLN* 3.0 16.1 - - - +
3471C ILE* 3.0 25.3 + - + +
4000C ASN* 2.3 38.8 + - - +
4003C ASP* 2.5 35.4 + - - -
4004C VAL* 3.4 29.3 - - + +
4007C LYS* 3.8 20.6 - - + -
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Residues in contact with LEU3468 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3424C LEU* 5.6 10.8 - - + -
3443C PRO* 4.6 12.6 - - + -
3447C VAL* 3.4 17.5 - - + -
3464C LYS* 3.1 54.3 + - + +
3465C PHE* 3.1 22.2 - - - +
3466C PRO 2.8 0.6 + - - -
3467C ARG* 1.3 81.0 - - - +
3469C LEU* 1.3 56.2 + - - +
3471C ILE* 3.4 6.3 - - - +
3472C ILE* 2.5 31.8 + - - +
3473C GLU* 4.8 3.6 - - - +
3474C ARG* 5.5 7.2 - - - +
3483C MET* 4.1 10.8 - - + -
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Residues in contact with LEU3469 (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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3465C PHE 4.0 1.3 + - - +
3466C PRO 3.1 6.2 + - - +
3468C LEU* 1.3 79.6 - - - +
3470C GLN* 1.3 70.3 + - + +
3471C ILE 3.2 0.5 - - - -
3472C ILE 2.8 22.5 + - - +
3473C GLU* 3.1 27.2 + - + +
3476C PRO 5.2 0.2 - - - +
3479C THR* 3.5 37.5 - - + +
3480C LEU* 3.9 4.3 - - + -
3511C ALA 6.1 0.4 - - - +
3512C VAL* 3.5 50.3 - - + +
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Residues in contact with GLN3470 (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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3466C PRO* 2.9 42.8 + - + +
3467C ARG* 3.0 26.7 + - - +
3469C LEU* 1.3 81.6 - - + +
3471C ILE* 1.3 61.3 + - - +
3501C HIS* 4.9 4.4 + - - +
3505C LEU* 3.2 39.6 - - + +
3509C ASP* 5.0 3.1 + - + -
4004C VAL* 3.4 22.4 - - - +
4007C LYS* 4.5 12.3 - - - +
4008C GLU* 5.8 4.7 + - - +
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Residues in contact with ILE3471 (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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3424C LEU* 6.5 1.1 - - + -
3467C ARG* 3.0 13.3 + - + +
3468C LEU* 3.4 11.9 - - - +
3469C LEU 3.2 1.1 - - - -
3470C GLN* 1.3 79.3 - - - +
3472C ILE* 1.3 92.6 + - + +
4007C LYS* 3.6 30.0 - - - +
4041C ARG* 5.0 6.1 - - - +
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Residues in contact with ILE3472 (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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3424C LEU* 5.9 7.4 - - + -
3440C GLN* 3.3 30.7 - - + +
3468C LEU* 2.5 29.5 + - - +
3469C LEU* 2.8 17.1 + - - -
3471C ILE* 1.3 105.1 - - + +
3473C GLU* 1.3 62.1 + - - +
3474C ARG* 3.9 19.2 + - - +
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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