Contacts of the helix formed by residues 65 - 70 (chain R) in PDB entry 3L73
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 SER 65 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167C GLY 4.7 0.6 + - - -
55P HIS* 6.1 0.7 - - - -
69P HIS* 3.9 6.5 + - - -
73P ASN* 3.2 24.0 - - - -
74P VAL* 4.0 14.4 - - - +
75P GLN* 4.1 3.8 - - - +
63R SER 3.4 3.8 + - - -
64R ALA* 1.3 74.4 - - - +
66R ALA* 1.3 56.3 + - - +
67R ASP* 2.4 24.6 + - - -
68R VAL* 2.7 38.0 + - - +
69R LEU* 2.9 12.2 + - - -
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Residues in contact with ALA 66 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72P ARG 4.7 2.9 - - - +
73P ASN* 3.1 25.3 + - - +
75P GLN* 4.0 7.9 - - - +
49Q ARG* 3.7 21.6 + - - +
65R SER* 1.3 73.0 - - - +
67R ASP* 1.3 56.6 + - - +
69R LEU* 3.5 10.1 + - - +
70R ALA* 3.0 27.9 + - - +
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Residues in contact with ASP 67 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69P HIS* 3.5 18.5 + - - -
73P ASN* 3.4 20.0 - - - +
49Q ARG* 3.6 17.0 - - - +
90Q TYR* 4.5 5.2 - - - +
65R SER* 2.4 31.6 + - - -
66R ALA* 1.3 77.1 - - - +
68R VAL* 1.3 73.0 + - - +
70R ALA* 3.1 17.4 - - - +
71R LEU* 3.8 12.0 - - - +
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Residues in contact with VAL 68 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167C GLY 4.4 6.7 - - - +
168C GLY* 4.1 25.1 - - - -
169C PHE* 4.1 14.9 - - + +
174C PRO* 5.2 11.9 - - + -
64R ALA* 4.2 6.7 - - + -
65R SER* 2.7 35.2 + - - +
67R ASP* 1.3 79.1 - - - +
69R LEU* 1.3 63.9 + - - +
70R ALA 3.0 2.0 - - - -
71R LEU* 3.0 19.4 + - - +
72R SER 3.5 5.4 + - - -
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Residues in contact with LEU 69 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169C PHE* 4.2 16.6 - - + -
75P GLN* 4.7 7.9 - - - +
64R ALA* 3.8 35.7 - - + +
65R SER 2.9 17.0 + - - +
66R ALA* 4.0 7.4 - - - +
68R VAL* 1.3 76.2 - - - +
70R ALA* 1.3 57.8 + - - +
71R LEU 3.0 0.4 - - - -
72R SER* 2.8 33.0 + - - +
73R LYS* 4.5 0.3 + - - +
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Residues in contact with ALA 70 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49Q ARG* 3.7 29.2 - - - +
87Q ILE* 6.1 0.7 - - - +
88Q SER* 4.6 10.0 - - - -
66R ALA 3.0 15.3 + - - +
67R ASP* 3.1 15.9 - - - +
69R LEU* 1.3 77.5 - - - +
71R LEU* 1.3 68.1 + - + +
72R SER 3.4 0.4 - - - -
73R LYS 4.6 6.3 - - - +
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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
------------------------------------------------------------
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