Contacts of the strand formed by residues 42 - 46 (chain C) in PDB entry 1SNF
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 ARG 42 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68B ALA 3.5 15.2 + - - -
69B THR* 3.1 29.9 + - - +
70B ARG 3.5 9.1 + - - -
71B VAL* 3.4 16.2 - - - +
72B GLY* 3.5 13.0 - - - -
97B LEU 4.7 1.7 + - - -
98B ASP* 2.7 42.0 + - - +
99B PRO* 4.5 4.2 - - - +
37C LEU* 3.6 6.3 - - - +
40C GLY 4.2 0.4 + - - +
41C ARG* 1.3 78.6 - - - +
43C ALA* 1.3 65.5 + - - +
76C VAL* 4.1 14.1 - - + -
93C ALA* 5.6 2.0 - - + -
94C LEU 3.2 14.8 - - - +
95C ILE* 4.1 14.1 - - + -
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Residues in contact with ALA 43 (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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35C VAL* 3.9 19.5 - - + -
37C LEU* 3.7 17.4 - - + +
42C ARG* 1.3 80.9 - - - +
44C LEU* 1.3 59.8 + - - +
45C VAL* 3.6 8.9 + - + +
92C VAL 3.3 1.9 - - - +
93C ALA* 3.5 3.1 - - - -
94C LEU* 2.9 30.6 + - - +
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Residues in contact with LEU 44 (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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69B THR* 3.4 42.2 - - + +
33C GLU* 3.9 7.4 - - - +
43C ALA* 1.3 71.4 - - - +
45C VAL* 1.3 60.6 + - - +
46C ARG* 4.1 1.4 + - - +
91C LYS* 3.7 47.6 - - + +
92C VAL 3.6 14.6 - - - -
93C ALA* 4.0 5.6 - - + +
3170C UMP 6.4 0.2 - - + -
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Residues in contact with VAL 45 (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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31C SER* 3.3 26.5 - - - +
33C GLU* 3.5 15.3 - - + -
35C VAL* 3.9 22.2 - - + -
43C ALA* 3.8 18.6 - - + +
44C LEU* 1.3 76.5 - - - +
46C ARG* 1.3 68.8 + - - +
47C THR* 3.7 0.7 + - - +
91C LYS* 3.2 5.1 - - - -
92C VAL* 2.8 41.4 + - - +
94C LEU* 3.9 19.5 - - + -
105C VAL* 5.4 1.1 - - + -
111C ILE* 4.1 15.9 - - + -
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Residues in contact with ARG 46 (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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11C ASP* 4.9 5.1 + - - +
31C SER* 3.8 1.2 - - - -
32C ALA* 3.0 42.6 + - + +
33C GLU* 2.9 39.3 + - - +
44C LEU 5.5 1.1 - - - +
45C VAL* 1.3 78.8 - - - +
47C THR* 1.3 57.3 + - - +
48C GLY* 4.3 0.9 - - - +
89C GLU* 3.3 35.6 + - - +
90C ILE 4.1 4.3 - - - -
91C LYS* 4.4 20.6 - - + +
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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