Contacts of the strand formed by residues 31 - 37 (chain C) in PDB entry 3ARG
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 HIS 31 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C ASP* 3.6 1.3 - - - +
30C ASN* 1.3 101.0 + - - +
32C LEU* 1.3 65.8 + - - +
33C ARG* 4.6 13.7 + - + -
48C VAL* 4.3 16.4 - - + -
49C LEU 3.3 13.9 - - - +
50C VAL* 4.1 15.0 - - + +
66C LEU* 5.6 0.9 - - - -
68C LYS* 4.8 2.7 - - - +
91C VAL 5.0 0.2 - - - -
92C VAL* 3.5 7.8 - - - +
93C GLY* 2.9 45.0 + - - +
95C ARG 4.4 12.8 - - - -
96C GLY* 5.3 0.9 - - - -
104C LEU* 3.9 13.4 - - + +
102D ALA* 4.3 25.2 + - + -
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Residues in contact with LEU 32 (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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24C TYR* 3.8 30.5 - - + -
31C HIS* 1.3 80.8 - - - +
33C ARG* 1.3 66.5 + - - +
34C TRP* 3.7 23.6 - - + +
48C VAL* 3.5 5.2 - - - -
49C LEU* 3.0 45.2 + - + +
66C LEU* 4.7 9.6 - - + -
73C SER* 3.9 16.6 - - - +
90C CYS* 3.5 33.0 - - - -
91C VAL 3.3 10.8 - - - +
92C VAL* 3.8 9.6 - - + -
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Residues in contact with ARG 33 (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 HIS* 4.6 13.1 + - + -
32C LEU* 1.3 80.5 - - - +
34C TRP* 1.3 59.3 + - - +
35C PHE* 3.8 27.9 - - + -
45C SER* 3.5 26.9 + - - +
47C THR 3.4 7.6 - - - +
48C VAL* 3.3 37.0 - - - +
91C VAL* 2.7 47.1 + - + +
104C LEU* 6.4 1.6 - - + -
102D ALA 3.5 22.4 + - - -
103D GLU* 2.9 46.8 + - - +
106D GLN 5.0 1.9 - - - +
107D PHE* 5.5 0.6 - - - -
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Residues in contact with TRP 34 (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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5C GLN* 3.5 18.4 - - - -
20C LEU* 4.2 18.4 - - + -
21C GLN 3.8 19.3 - - - -
22C CYS* 3.9 12.8 - - + -
32C LEU* 3.7 12.2 - - + +
33C ARG* 1.3 72.8 - - - +
35C PHE* 1.3 61.2 + - - +
45C SER* 3.7 4.5 + - - -
46C LEU* 2.9 41.6 + - + +
47C THR* 3.1 15.7 + - + +
49C LEU* 4.3 6.7 - - + -
64C ALA* 4.3 21.3 - - + +
73C SER* 3.0 28.7 + - - -
74C THR 4.4 0.6 + - - -
75C LEU* 3.8 40.5 - - + +
88C TYR* 4.1 17.7 - - + -
89C ILE 3.5 18.2 - - - -
90C CYS* 3.9 11.9 - - + -
110C THR* 5.6 0.7 - - - -
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Residues in contact with PHE 35 (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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33C ARG* 3.8 30.3 - - + -
34C TRP* 1.3 77.0 - - - +
36C LYS* 1.3 59.6 + - - +
37C GLN 4.2 0.7 - - - +
43C LEU* 3.6 37.2 - - + -
44C VAL 3.3 18.6 - - - -
45C SER* 3.5 20.6 - - - -
46C LEU* 4.3 2.5 - - - +
88C TYR* 3.3 12.3 - - - +
89C ILE* 2.7 38.0 + - + +
91C VAL* 3.9 30.1 - - + -
104C LEU* 5.8 2.9 - - + -
106D GLN* 4.1 10.8 - - + -
108D PHE* 3.8 32.5 - + - -
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Residues in contact with LYS 36 (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 PHE* 1.3 75.0 - - - +
37C GLN* 1.3 61.7 + - - +
38C ASP 3.8 2.2 + - - -
42C GLY 3.7 3.3 - - - +
43C LEU* 4.5 0.7 - - - -
44C VAL* 2.8 38.1 + - + +
46C LEU* 3.5 20.9 - - + -
62C TYR* 5.6 0.4 - - - +
86C ALA* 5.3 2.7 - - + -
87C THR 3.7 2.9 - - - -
88C TYR* 3.5 24.7 - - + -
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Residues in contact with GLN 37 (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 PHE 4.2 0.6 - - - -
36C LYS* 1.3 72.5 - - - +
38C ASP* 1.3 65.4 + - - +
39C THR* 3.5 3.9 + - - +
40C GLY* 5.6 2.2 - - - +
41C LYS 3.1 30.6 + - - +
42C GLY 3.4 9.0 - - - +
43C LEU* 4.5 13.4 - - + +
86C ALA* 3.3 5.8 - - - +
87C THR* 2.7 48.2 + - - +
89C ILE* 3.8 13.3 - - + +
37D GLN* 3.1 37.3 + - - +
91D PHE* 3.4 15.0 - - - -
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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