Contacts of the helix formed by residues 3491 - 3497 (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 PRO3491 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3454C LEU* 5.1 0.7 - - + -
3487C ILE* 3.1 5.0 - - - +
3489C SER 4.3 2.9 - - - +
3490C VAL* 1.3 90.6 - - + +
3492C CYS* 1.3 56.6 + - - +
3493C TRP 4.1 3.1 - - - +
3494C GLN* 2.6 58.6 + - + +
3711C PRO* 5.5 0.7 - - + -
3712C LEU* 3.7 32.3 - - + +
3713C PRO* 5.8 1.1 - - + -
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Residues in contact with CYS3492 (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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3487C ILE* 3.3 11.3 - - - +
3490C VAL 3.4 1.2 + - - -
3491C PRO* 1.3 69.9 - - - +
3493C TRP* 1.3 64.6 + - - +
3494C GLN 3.1 1.2 + - - -
3495C PHE* 3.6 2.4 + - - +
3496C ILE* 3.6 9.0 - - - +
3524C ASN* 3.0 47.6 - - - +
3527C GLN* 3.1 29.9 - - + +
3528C ALA 3.1 20.9 - - - +
3529C ILE* 3.3 19.1 - - - -
3713C PRO* 5.3 6.3 - - + -
3715C TYR* 6.0 0.4 - - - -
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Residues in contact with TRP3493 (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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3491C PRO* 2.9 1.2 - - - +
3492C CYS* 1.3 82.4 - - - +
3494C GLN* 1.3 66.4 + - - +
3495C PHE 2.9 2.3 + - - -
3496C ILE* 2.9 41.5 + - + +
3497C SER 4.8 0.2 + - - -
3529C ILE* 5.9 0.4 - - + -
3706C ASP 2.9 28.3 - - - -
3707C GLY* 3.3 6.7 - - - -
3709C GLY* 2.9 25.7 - - - -
3710C LYS 2.5 42.2 + - - +
3711C PRO* 3.3 5.8 - - + -
3712C LEU* 3.2 32.1 - - - +
3713C PRO* 3.7 6.5 - - + +
3714C GLU* 2.9 51.8 - - + -
3715C TYR* 4.0 15.7 - + - -
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Residues in contact with GLN3494 (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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3454C LEU* 3.5 31.8 + - + +
3462C ARG* 5.2 0.3 - - - -
3487C ILE* 3.4 2.5 - - + -
3490C VAL* 3.4 17.5 - - + -
3491C PRO* 2.6 64.0 + - + +
3493C TRP* 1.3 71.9 - - - +
3495C PHE* 1.3 56.3 + - - +
3497C SER* 5.0 0.5 + - - -
3498C TRP* 2.9 21.1 - - - -
3711C PRO* 3.3 43.6 - - - +
3712C LEU 3.3 1.9 + - - -
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Residues in contact with PHE3495 (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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3487C ILE* 3.2 28.5 - - + +
3492C CYS 4.2 2.7 - - - +
3493C TRP 2.9 1.0 + - - -
3494C GLN* 1.3 78.6 - - - +
3496C ILE* 1.3 70.5 + - + +
3497C SER 2.8 4.7 + - - -
3498C TRP* 2.8 73.9 + + - -
3499C ILE* 3.1 42.6 - - + -
3502C MET* 3.1 44.9 - - + -
3520C GLU* 5.0 4.0 - - - -
3524C ASN* 5.2 1.8 - - - +
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Residues in contact with ILE3496 (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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3492C CYS* 3.6 15.9 - - - +
3493C TRP* 2.9 64.4 + - + +
3494C GLN 3.4 0.2 - - - -
3495C PHE* 1.3 82.3 - - + +
3497C SER* 1.3 65.4 + - - +
3499C ILE* 2.9 57.9 + - + +
3529C ILE* 4.3 25.8 - - + -
3705C TYR* 5.1 4.0 - - + +
3706C ASP 5.4 0.4 - - - +
3707C GLY 4.6 7.9 - - - +
3709C GLY* 4.6 2.2 - - - +
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Residues in contact with SER3497 (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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3459C ASN* 5.4 2.4 + - - -
3462C ARG* 3.2 40.1 + - - -
3494C GLN 5.0 0.6 + - - -
3495C PHE 2.8 3.2 + - - -
3496C ILE* 1.3 80.1 - - - +
3498C TRP* 1.3 55.5 + - - -
3499C ILE* 4.4 0.3 - - - +
3501C HIS* 4.8 0.3 - - - -
3708C ARG 3.6 7.5 + - - -
3709C GLY* 3.1 32.4 + - - -
3710C LYS* 4.6 2.6 + - - -
3766C GLN* 3.6 24.8 + - - +
3769C GLN* 4.8 7.6 + - - +
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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