Contacts of the strand formed by residues 31 - 38 (chain I) in PDB entry 4R2G
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 31 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27I ALA* 3.8 31.8 - - + +
29I GLY 4.9 0.2 - - - +
30I SER* 1.3 75.4 - - - +
32I ALA* 1.3 56.0 + - - +
33I VAL* 3.7 13.2 - - - +
51I ASN* 2.7 38.8 + - - +
65I THR* 2.7 40.0 + - - -
66I ASP* 3.0 46.8 + - - +
67I PHE 5.8 1.0 + - - -
69I THR* 3.1 28.3 + - - -
70I THR 4.0 0.8 + - - -
71I ALA* 3.8 19.8 - - - +
90I MET* 3.9 5.6 - - + -
91I TRP 3.2 11.7 - - - +
92I ASP* 4.3 0.7 - - + -
100J ARG* 2.9 17.8 + - - +
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Residues in contact with ALA 32 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31I ARG* 1.3 73.4 - - - +
33I VAL* 1.3 62.8 + - - +
34I GLN* 4.2 1.6 - - - +
50I ASN* 4.9 3.4 - - - +
51I ASN* 4.1 4.3 - - - +
91I TRP* 2.9 38.6 + - + -
100J PHE* 3.7 63.4 - - - +
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Residues in contact with VAL 33 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23I CYS* 4.3 2.7 - - - -
31I ARG* 3.7 14.8 - - - +
32I ALA* 1.3 69.9 - - - +
34I GLN* 1.3 73.0 + - - +
35I TRP* 3.3 33.9 - - + +
48I ILE* 4.1 1.4 - - - +
49I TYR* 3.7 1.6 - - - -
50I ASN 3.3 2.1 + - - -
51I ASN* 3.0 48.1 + - - +
71I ALA* 4.1 10.8 - - + -
88I CYS* 3.8 12.8 - - - -
89I HIS 3.7 1.6 - - - -
90I MET* 3.3 33.2 - - - -
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Residues in contact with GLN 34 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32I ALA 3.7 2.7 + - - -
33I VAL* 1.3 78.6 + - - +
35I TRP* 1.3 64.3 + - - +
36I TYR* 3.7 20.6 - - + +
46I LEU* 4.5 1.6 - - + -
48I ILE 3.1 4.5 - - - +
49I TYR* 3.5 21.7 - - + +
50I ASN* 2.7 28.4 + - - -
87I TYR 3.8 0.5 - - - +
88I CYS* 3.5 1.0 - - - -
89I HIS* 2.8 40.7 + - + +
91I TRP* 3.5 31.5 - - - +
100J TYR* 3.5 43.7 + - + +
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Residues in contact with TRP 35 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21I ILE* 3.3 41.1 - - + -
22I SER 4.0 0.4 - - - -
23I CYS* 3.7 29.2 - - - -
33I VAL* 3.3 22.4 - - + +
34I GLN* 1.3 72.1 - - - +
36I TYR* 1.3 56.7 + - - +
46I LEU* 3.5 2.9 - - - +
47I LEU* 2.8 36.1 + - + -
48I ILE* 2.9 27.9 + - + +
64I GLY* 4.9 6.1 - - - -
65I THR 5.7 0.2 - - - +
71I ALA 3.8 4.3 - - - -
72I THR 4.0 3.0 - - - +
73I LEU* 3.3 63.9 - - + +
86I TYR* 4.8 6.5 - - + -
87I TYR 3.2 21.3 - - - -
88I CYS* 3.4 22.2 - - + -
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Residues in contact with TYR 36 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34I GLN* 3.7 25.1 - - + +
35I TRP* 1.3 76.6 - - - +
37I GLN* 1.3 66.1 + - - +
44I PRO* 4.7 5.4 - - + -
45I ILE 3.3 7.6 - - - +
46I LEU* 3.9 22.0 - - + -
47I LEU* 4.6 2.0 - - - -
85I ASP 4.0 0.2 - - - +
86I TYR* 3.7 2.1 - - - +
87I TYR* 2.8 51.1 + - + +
89I HIS* 4.1 19.0 + - + -
98I PHE* 4.6 10.5 - + - -
45J LEU* 5.2 3.8 - - + -
100J MET* 2.7 72.9 - + - +
103J TRP* 4.0 22.4 - + - -
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Residues in contact with GLN 37 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36I TYR* 1.3 75.3 - - - +
38I HIS* 1.3 67.3 + - - +
39I LYS* 4.3 12.3 + - + -
44I PRO* 3.3 2.8 - - - +
45I ILE* 2.8 57.3 + - + +
47I LEU* 3.7 27.3 - - + +
62I PHE* 4.3 6.2 - - - -
81I GLY 4.3 2.8 + - - -
82I ASP* 4.1 16.2 + - - +
84I ALA* 3.7 20.0 - - + +
85I ASP 3.9 2.7 - - - -
86I TYR* 2.8 36.6 + - + -
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Residues in contact with HIS 38 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36I TYR 5.3 0.2 - - - -
37I GLN* 1.3 81.2 - - - +
39I LYS* 1.3 68.2 + - - +
40I PRO* 3.2 18.8 - - + +
42I GLN 3.5 22.4 + - - -
43I ALA 5.0 0.7 - - - -
44I PRO* 3.5 35.6 - - + +
45I ILE* 5.0 0.7 - - - +
84I ALA* 4.2 0.2 - - - -
85I ASP* 2.9 45.1 + - - +
87I TYR* 4.0 29.8 - + + -
39J GLN* 3.2 40.1 + - - +
45J LEU* 4.5 6.7 - - + +
91J PHE* 4.7 1.1 - + - -
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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