Contacts of the helix formed by residues 3516 - 3525 (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 HIS3516 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3479C THR* 2.8 23.6 + - - -
3480C LEU* 3.0 24.2 - - + -
3483C MET* 3.1 13.7 - - + +
3484C THR* 2.2 48.1 + - - -
3502C MET* 5.8 3.6 - - + -
3510C GLN* 5.7 2.7 - - - -
3512C VAL* 3.1 16.1 + - + +
3513C ALA 2.8 4.0 + - - -
3514C VAL 3.2 0.8 + - - -
3515C GLN* 1.3 80.7 - - - +
3517C SER* 1.3 67.6 + - - +
3518C VAL 3.4 0.4 - - - -
3519C GLU* 2.9 22.6 - - - +
3520C GLU* 3.0 25.3 + - - +
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Residues in contact with SER3517 (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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3502C MET* 2.6 38.3 - - - +
3506C LEU* 3.3 9.6 - - - +
3510C GLN* 2.9 37.2 - - - -
3513C ALA 2.9 4.2 + - - -
3516C HIS* 1.3 78.8 - - - +
3518C VAL* 1.3 67.2 + - - +
3520C GLU* 3.0 6.9 + - - +
3521C ILE* 2.8 27.2 + - - +
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Residues in contact with VAL3518 (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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3506C LEU* 3.6 10.8 - - + -
3513C ALA 2.8 15.1 + - - +
3514C VAL* 3.5 20.6 - - + +
3517C SER* 1.3 72.4 + - - +
3519C GLU* 1.3 58.5 + - - +
3521C ILE* 3.5 7.6 - - - -
3522C THR* 2.3 40.7 + - + +
3555C VAL* 3.6 31.9 - - + -
3557C ARG* 3.9 11.2 - - - +
3558C ILE* 3.5 37.0 - - + -
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Residues in contact with GLU3519 (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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3484C THR* 3.4 19.7 - - + +
3514C VAL 2.7 18.5 - - - +
3515C GLN* 3.0 31.9 - - - +
3516C HIS 2.9 7.4 - - - +
3517C SER 3.1 0.2 - - - -
3518C VAL* 1.3 78.8 - - - +
3520C GLU* 1.3 61.4 + - - +
3522C THR* 2.6 21.3 + - - -
3523C ASP* 2.7 25.2 - - - +
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Residues in contact with GLU3520 (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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3483C MET 2.4 33.7 - - - +
3484C THR* 3.2 7.5 - - - +
3486C GLU* 3.9 4.8 - - - +
3487C ILE* 3.2 31.7 + - + +
3488C SER* 3.0 29.6 - - - +
3495C PHE* 5.0 5.0 - - - -
3502C MET* 6.1 1.9 - - - +
3516C HIS* 3.0 26.4 + - - +
3517C SER* 3.0 4.9 + - - +
3519C GLU* 1.3 71.3 - - - +
3521C ILE* 1.3 55.8 + - - +
3523C ASP* 2.8 4.0 + - - +
3524C ASN* 2.6 39.0 + - - +
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Residues in contact with ILE3521 (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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3502C MET* 5.2 7.2 - - + -
3506C LEU* 3.7 26.5 - - + -
3517C SER* 2.8 23.6 + - - +
3518C VAL* 3.2 14.8 - - - +
3520C GLU* 1.3 76.3 - - - +
3522C THR* 1.3 71.8 + - + +
3524C ASN* 2.8 23.7 + - - +
3525C TYR* 2.9 52.4 + - + +
3529C ILE* 4.3 4.9 - - + +
3532C PRO* 4.7 9.9 - - + -
3536C SER* 5.4 4.7 - - - +
3558C ILE* 4.6 3.6 - - + -
3562C LEU* 5.1 2.2 - - + -
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Residues in contact with THR3522 (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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3518C VAL* 2.3 32.2 + - + +
3519C GLU* 2.6 11.8 + - - -
3521C ILE* 1.3 74.5 - - + +
3523C ASP* 1.3 60.8 + - - +
3525C TYR* 3.6 10.5 - - + -
3526C PRO* 2.9 23.0 - - - +
3558C ILE* 3.5 33.2 - - + -
3561C LYS* 3.4 29.8 - - - +
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Residues in contact with ASP3523 (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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3484C THR* 5.3 0.2 - - - +
3488C SER* 2.4 44.9 + - - +
3519C GLU* 2.7 34.2 + - - +
3520C GLU 2.8 10.2 + - - +
3522C THR* 1.3 84.7 + - - +
3524C ASN* 1.3 57.7 + - - +
3526C PRO* 3.0 19.2 - - - +
3527C GLN* 3.2 17.4 + - + +
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Residues in contact with ASN3524 (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* 2.3 47.8 + - - +
3488C SER 3.8 7.1 + - - +
3492C CYS* 3.0 36.2 - - - +
3495C PHE* 5.2 1.4 - - - +
3520C GLU* 2.6 21.6 + - - +
3521C ILE* 2.8 7.3 + - - +
3523C ASP* 1.3 80.0 + - - +
3525C TYR* 1.3 54.1 + - - +
3526C PRO 3.5 0.2 - - - -
3527C GLN* 3.5 7.0 - - - +
3528C ALA 3.0 7.6 + - - -
3529C ILE* 2.3 38.7 + - + -
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Residues in contact with TYR3525 (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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3521C ILE* 2.9 68.3 + - + +
3522C THR* 3.6 11.0 - - + -
3524C ASN* 1.3 76.7 - - - +
3526C PRO* 1.3 58.1 - - + +
3528C ALA* 2.6 25.6 + - - -
3529C ILE* 3.0 40.5 + - + +
3532C PRO* 3.7 15.8 - - + +
3533C PHE* 3.2 32.7 - + - -
3536C SER* 5.0 2.1 + - - -
3558C ILE* 4.6 2.9 - - + -
3562C LEU* 3.1 33.8 - - + +
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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