Contacts of the strand formed by residues 30 - 35 (chain E) in PDB entry 2RHB
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 ALA 30 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25E SER 3.8 0.9 - - - +
26E ILE* 3.6 5.9 - - - -
27E ILE 3.0 32.5 + - - +
28E ASN* 4.0 5.6 - - + +
29E ASN* 1.3 79.2 - - - +
31E VAL* 1.3 65.7 + - - +
32E TYR* 3.8 13.9 - - + +
41E GLU* 3.5 17.9 - - - +
43E PHE 3.4 14.4 - - - +
44E GLU* 4.4 4.3 - - + +
51E VAL* 3.5 7.8 - - - +
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Residues in contact with VAL 31 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2E LEU* 5.3 2.2 - - + -
24E VAL* 3.8 28.0 - - + -
25E SER 3.7 2.2 - - - -
26E ILE* 4.6 8.7 - - + -
30E ALA* 1.3 77.4 - - - +
32E TYR* 1.3 66.3 + - - +
41E GLU* 3.6 5.5 - - - +
42E ILE* 3.0 29.2 + - + -
43E PHE* 3.0 25.5 + - + +
51E VAL* 4.1 16.4 - - + +
55E PHE* 3.9 45.8 - - + -
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Residues in contact with TYR 32 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D LYS* 3.3 26.7 + - - -
47D THR* 4.4 3.8 + - - -
48D THR* 3.7 21.8 - - + -
24E VAL* 3.2 11.3 - - - +
25E SER* 2.9 41.3 + - - +
27E ILE* 3.7 31.6 - - + -
28E ASN* 4.8 6.8 + - - +
30E ALA* 3.8 21.0 - - + +
31E VAL* 1.3 78.8 - - - +
33E THR* 1.3 62.1 + - - +
39E ASP* 4.0 19.3 - - + -
40E VAL 3.7 5.2 - - - -
41E GLU* 3.5 43.7 + - + +
42E ILE* 4.6 1.3 - - - +
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Residues in contact with THR 33 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A MET* 4.7 0.4 - - - -
269D ILE* 5.0 0.9 - - + -
10E VAL* 3.8 17.3 - - + +
22E ALA* 4.2 13.8 - - - +
23E PRO* 3.0 19.0 + - - +
24E VAL* 4.5 3.4 - - - +
32E TYR* 1.3 74.8 - - - +
34E LYS* 1.3 65.6 + - - +
35E VAL* 3.5 9.9 + - + +
39E ASP* 3.4 5.4 - - - -
40E VAL* 3.0 39.0 + - + +
42E ILE* 3.7 35.0 - - + -
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Residues in contact with LYS 34 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A THR 6.0 0.2 - - - -
104A MET* 3.8 43.7 + - + +
96D VAL* 5.9 3.0 - - - +
23E PRO* 3.4 24.6 + - + +
33E THR* 1.3 76.2 + - - +
35E VAL* 1.3 62.0 + - - +
36E ASP 4.1 1.5 + - - +
37E GLY* 3.4 43.9 + - - +
38E ILE* 3.4 2.7 - - - +
39E ASP* 3.3 29.5 + - - +
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Residues in contact with VAL 35 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269D ILE* 3.8 15.5 - - + -
271D MET* 3.8 30.4 - - + +
10E VAL* 6.0 1.3 - - + -
33E THR* 3.5 9.4 + - + +
34E LYS* 1.3 75.7 - - - +
36E ASP* 1.3 80.7 + - + +
38E ILE* 2.8 27.5 + - + +
40E VAL* 3.8 22.2 - - + -
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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