Contacts of the helix formed by residues 3432 - 3440 (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 SER3432 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3427C GLU* 2.9 13.5 + - - +
3430C ASN* 4.4 7.1 + - - -
3431C ALA* 1.3 75.9 + - - +
3433C VAL* 1.3 66.6 + - - +
3434C ILE 3.3 0.9 - - - -
3435C ASP* 3.0 36.5 + - - +
3436C SER* 2.9 20.7 + - - -
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Residues in contact with VAL3433 (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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3431C ALA 4.3 0.2 - - - -
3432C SER* 1.3 72.7 - - - +
3434C ILE* 1.3 72.1 + - + +
3436C SER* 2.2 30.5 + - - +
3437C ALA* 2.9 12.0 + - + +
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Residues in contact with ILE3434 (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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3383C GLN* 5.8 9.0 - - - +
3432C SER* 3.3 1.2 - - - -
3433C VAL* 1.3 86.3 - - + +
3435C ASP* 1.3 63.9 + - - +
3437C ALA* 2.6 32.7 + - + +
3438C GLU* 2.9 26.1 + - + +
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Residues in contact with ASP3435 (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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3382C PHE* 5.1 6.1 - - - +
3383C GLN* 6.1 1.4 - - - +
3426C LYS* 2.4 31.6 + - - +
3427C GLU* 2.9 26.4 - - + +
3432C SER* 3.0 21.7 + - - +
3434C ILE* 1.3 79.1 - - - +
3436C SER* 1.3 51.3 + - - +
3438C GLU* 5.8 0.4 - - - -
3439C LEU* 2.3 42.0 + - - +
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Residues in contact with SER3436 (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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3427C GLU* 4.6 4.2 - - - +
3432C SER 2.9 9.6 + - - -
3433C VAL* 2.2 36.6 + - - +
3435C ASP* 1.3 74.5 - - - +
3437C ALA* 1.3 58.9 + - - +
3439C LEU* 3.9 10.1 - - - -
3440C GLN* 2.9 56.8 + - - +
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Residues in contact with ALA3437 (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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3433C VAL* 2.9 7.6 + - + +
3434C ILE* 2.6 34.7 + - + +
3436C SER* 1.3 72.8 - - - +
3438C GLU* 1.3 59.8 + - + +
3440C GLN* 3.7 0.9 - - - +
3441C ALA* 2.9 26.3 + - - +
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Residues in contact with GLU3438 (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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3386C SER* 4.8 9.0 + - - -
3387C GLU* 3.6 20.2 - - - +
3434C ILE* 2.9 20.1 + - + +
3435C ASP* 5.8 0.7 - - - -
3437C ALA* 1.3 76.8 - - + +
3439C LEU* 1.3 61.8 + - - +
3440C GLN 3.0 1.8 - - - -
3441C ALA* 3.6 7.6 - - + -
3442C TYR* 2.8 78.0 + - + +
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Residues in contact with LEU3439 (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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3420C CYS* 4.1 18.7 - - + +
3423C GLN* 4.1 5.6 - - + -
3424C LEU* 3.4 57.4 - - + +
3427C GLU* 3.5 30.1 - - + -
3435C ASP 2.3 32.5 + - - +
3436C SER* 3.9 7.4 - - - -
3438C GLU* 1.3 78.1 - - - +
3440C GLN* 1.3 64.8 + - + +
3442C TYR* 4.8 3.7 - - - +
3443C PRO* 2.9 27.4 - - + +
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Residues in contact with GLN3440 (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* 6.0 1.8 - - + +
3436C SER* 2.9 40.2 + - - +
3437C ALA* 3.7 2.0 - - - +
3439C LEU* 1.3 87.5 - - + +
3441C ALA* 1.3 61.6 + - - +
3442C TYR 3.4 0.2 - - - -
3443C PRO* 3.5 1.3 - - - -
3472C ILE* 3.3 27.8 - - + +
3474C ARG* 2.2 63.2 + - - +
3475C TYR* 2.8 6.9 + - - -
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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