Contacts of the strand formed by residues 34 - 44 (chain A) in PDB entry 2RNZ
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 GLU 34 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A GLN* 5.1 0.7 - - - +
31A LYS* 3.1 46.1 + - + +
32A ASN 3.6 0.4 - - - -
33A ASP* 1.3 86.7 - - + +
35A GLU* 1.3 71.9 + - - +
36A ARG* 3.4 26.8 + - + +
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Residues in contact with GLU 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A TRP* 5.3 12.6 - - + -
29A VAL 4.0 5.4 - - - +
30A GLN* 5.5 7.6 - - + -
31A LYS 5.5 0.4 - - - +
34A GLU* 1.3 84.6 - - - +
36A ARG* 1.3 63.5 + - - +
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Residues in contact with ARG 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A TRP* 3.2 13.2 - - - -
29A VAL* 2.8 45.5 + - + +
31A LYS* 3.7 31.1 - - - +
34A GLU* 3.4 24.0 + - + +
35A GLU* 1.3 75.4 + - - +
37A LEU* 1.3 67.2 + - - +
56A TYR* 3.7 33.2 + - + -
63A LEU* 5.3 13.5 - - - +
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Residues in contact with LEU 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A GLN* 4.8 9.0 - - + -
27A CYS 3.1 31.0 - - - +
28A TRP* 3.8 41.7 - - + +
29A VAL* 4.0 2.9 - - - +
36A ARG* 1.3 81.4 - - - +
38A ALA* 1.3 69.3 + - - +
39A GLU* 5.4 3.1 - - - +
56A TYR* 3.1 24.3 - - - +
57A VAL* 6.2 4.3 - - + -
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Residues in contact with ALA 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A CYS* 2.6 45.8 + - - +
29A VAL* 3.7 19.2 - - + +
37A LEU* 1.3 81.0 - - - +
39A GLU* 1.3 63.7 + - - +
54A VAL* 4.3 14.6 - - + -
55A HIS 3.7 7.6 - - - +
56A TYR* 4.0 19.7 - - + +
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Residues in contact with GLU 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A LYS* 3.3 18.8 - - - +
25A CYS 2.8 32.6 - - - +
26A GLN* 2.9 24.8 + - - +
27A CYS* 3.9 1.6 - - - -
37A LEU* 5.1 3.6 - - - +
38A ALA* 1.3 76.9 - - - +
40A ILE* 1.3 66.6 + - - +
41A LEU* 3.8 6.2 + - + -
53A TYR 3.5 0.3 - - - +
54A VAL* 3.2 7.3 - - - -
55A HIS* 2.8 46.6 + - + +
57A VAL* 5.1 15.8 - - + +
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Residues in contact with ILE 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ILE* 4.2 15.9 - - + -
22A ILE 3.8 19.5 - - - +
23A ILE* 5.0 0.4 - - - -
24A LYS* 2.8 36.0 + - - -
25A CYS* 2.9 16.9 + - + +
27A CYS* 3.4 33.2 - - + -
39A GLU* 1.3 75.3 - - - +
41A LEU* 1.3 61.5 + - - +
42A SER 3.6 20.4 - - - +
43A ILE* 3.9 13.5 - - + -
52A PHE* 4.2 14.8 - - + -
53A TYR 3.6 3.8 - - - +
54A VAL* 4.4 2.0 - - + -
72A ILE* 4.1 22.4 - - + -
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Residues in contact with LEU 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ILE* 3.2 26.3 - - - +
24A LYS* 5.3 10.3 - - + -
39A GLU* 5.3 6.7 - - + -
40A ILE* 1.3 80.4 - - - +
42A SER* 1.3 63.2 + - - +
53A TYR* 3.0 26.4 + - + +
55A HIS* 3.2 50.0 - - + +
64A ASP* 4.0 12.8 - - - +
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Residues in contact with SER 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ILE* 4.4 5.2 - - - -
40A ILE* 3.6 5.4 - - - +
41A LEU* 1.3 78.3 - - - +
43A ILE* 1.3 78.9 + - - +
44A ASN* 4.6 6.9 + - - -
52A PHE* 3.7 1.0 - - - -
53A TYR* 3.0 40.8 + - - +
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Residues in contact with ILE 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A VAL* 4.3 10.1 - - + -
21A ILE* 3.9 37.2 - - + +
22A ILE* 4.3 4.3 - - - +
23A ILE* 4.2 20.9 - - + +
40A ILE* 3.9 9.2 - - + -
42A SER* 1.3 87.5 + - - +
44A ASN* 1.3 68.0 + - - +
45A THR* 4.2 13.4 + - + +
51A LYS 4.1 0.4 - - - -
52A PHE* 3.2 33.2 - - + -
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Residues in contact with ASN 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A SER* 4.6 9.7 + - - -
43A ILE* 1.3 84.7 - - - +
45A THR* 1.3 61.9 + - - +
46A ARG* 3.6 8.8 - - + +
47A LYS 5.3 0.9 - - - +
50A PRO* 3.1 17.7 - - - +
51A LYS* 2.8 42.4 + - + +
52A PHE* 4.3 1.3 - - - -
53A TYR* 4.8 7.3 - - - +
66A TRP* 5.6 10.7 - - + +
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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