Contacts of the strand formed by residues 3736 - 3741 (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 LYS3736 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3578C LEU* 4.2 12.6 - - + -
3579C SER* 3.0 62.4 + - - +
3580C ASN* 4.4 4.3 - - - +
3632C PHE* 3.0 17.3 - - - -
3678C GLY* 4.8 0.4 - - - -
3680C LEU* 3.3 19.4 - - - +
3683C CYS* 2.9 36.0 - - - -
3726C VAL* 3.4 15.0 - - + -
3727C THR 3.6 0.9 - - - -
3728C VAL* 3.5 13.9 - - + +
3735C PRO* 1.3 71.8 - - - +
3737C ARG* 1.3 59.7 + - - +
3738C ILE* 3.9 8.7 - - + -
3751C LEU* 3.4 1.2 - - - -
3752C VAL* 3.2 35.8 + - + +
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Residues in contact with ARG3737 (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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3725C ARG 3.5 1.9 - - - +
3726C VAL* 2.9 26.4 - - - +
3727C THR* 2.7 34.9 + - - +
3735C PRO 3.4 0.2 + - - -
3736C LYS* 1.3 70.9 - - - +
3738C ILE* 1.3 58.6 + - - +
3739C ILE* 4.9 2.5 - - + +
3749C PRO* 5.3 5.4 - - + -
3750C PHE 3.0 25.6 - - - +
3751C LEU* 3.6 11.2 - - + -
3805C TRP* 3.2 35.1 - - + +
3807C GLU* 2.2 38.4 + - - -
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Residues in contact with ILE3738 (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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3576C ASP* 5.5 3.8 - - - +
3578C LEU* 5.7 9.2 - - + -
3687C MET* 5.4 14.4 - - + -
3722C PHE* 5.7 3.1 - - + -
3723C ASP 5.2 1.3 - - - +
3725C ARG 3.8 6.1 - - - -
3726C VAL* 3.5 17.9 - - + -
3736C LYS* 3.7 18.4 - - + +
3737C ARG* 1.3 76.6 - - - +
3739C ILE* 1.3 68.4 + - - +
3740C ILE* 5.0 9.0 - - + -
3749C PRO* 3.2 3.8 - - - +
3750C PHE* 2.8 39.6 + - + +
3751C LEU 5.0 0.4 - - - +
3752C VAL* 3.7 22.4 - - + -
3802C LEU* 4.1 20.0 - - + -
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Residues in contact with ILE3739 (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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3722C PHE* 3.0 29.6 - - - +
3723C ASP* 3.2 34.8 + - + +
3725C ARG* 3.1 36.0 + - + +
3737C ARG* 4.9 3.4 - - + +
3738C ILE* 1.3 76.5 - - - +
3740C ILE* 1.3 64.0 + - - +
3741C ARG* 3.4 32.8 - - - +
3749C PRO* 3.6 26.5 - - + -
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Residues in contact with ILE3740 (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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3703C GLY* 5.3 2.7 - - - +
3704C GLN* 3.7 13.9 - - + -
3719C ILE* 3.4 54.5 - - + +
3721C GLY 3.6 2.0 - - - +
3722C PHE* 3.5 11.0 - - + -
3738C ILE* 4.8 7.2 - - + +
3739C ILE* 1.3 72.9 - - - +
3741C ARG* 1.3 63.5 + - - +
3742C GLY* 4.0 0.6 + - - -
3748C HIS* 2.3 72.2 + - + +
3749C PRO* 3.7 0.6 - - + +
3750C PHE* 3.4 22.0 - - + +
3802C LEU* 4.6 12.3 - - + -
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Residues in contact with ARG3741 (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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1066C LEU* 4.3 13.0 + - - +
1069C HIS* 3.0 26.2 - - + +
1070C PRO* 3.0 45.4 - - - +
1074C LYS* 5.1 2.6 - - - +
1075C ARG* 4.5 0.4 - - - +
3719C ILE 2.6 14.0 - - - +
3721C GLY* 2.3 65.4 + - - +
3722C PHE 3.2 1.6 - - - +
3723C ASP* 3.0 52.3 + - - +
3739C ILE* 3.4 11.3 - - + +
3740C ILE* 1.3 69.6 - - - +
3742C GLY* 1.3 56.3 + - - +
3746C ARG 4.7 0.6 + - - -
3747C GLU* 4.1 22.6 - - - +
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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