Contacts of the strand formed by residues 22 - 29 (chain A) in PDB entry 4RA2
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 LEU 22 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A GLN* 3.2 5.2 - - - +
19A GLY 2.8 33.1 + - - +
20A ASN* 3.8 7.9 - - + +
21A GLY* 1.3 84.6 - - - +
23A ARG* 1.3 65.1 + - - +
44A ILE* 4.3 7.9 - - + -
54A SER* 3.6 32.8 - - - +
56A PHE* 4.2 7.9 - - + -
134A ILE* 3.9 23.1 - - + -
226A ARG* 4.2 9.6 - - - +
289A ILE* 4.3 10.5 - - + -
290A CYS 3.6 7.6 - - - +
291A PHE* 3.6 37.5 - - + -
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Residues in contact with ARG 23 (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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17A GLY 3.4 6.3 - - - +
18A GLN* 3.5 34.6 - - + +
21A GLY 5.5 0.9 - - - +
22A LEU* 1.3 76.7 - - - +
24A TYR* 1.3 61.3 + - - +
262A ASP* 2.9 46.2 + - - +
263A ASP* 5.0 1.6 - - - +
264A LEU* 3.5 32.4 - - + +
289A ILE* 3.5 1.6 - - - +
290A CYS* 2.7 43.1 + - + +
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Residues in contact with TYR 24 (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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15A ALA* 4.3 3.3 - - + +
16A GLN* 3.2 30.5 + - - +
17A GLY* 2.9 56.7 + - - +
18A GLN* 4.8 1.9 + - - -
23A ARG* 1.3 76.3 - - - +
25A GLY* 1.3 69.7 + - - +
26A LEU* 4.2 10.1 - - + -
42A ALA* 3.7 32.9 + - + +
43A VAL* 5.5 0.2 - - - -
44A ILE* 3.8 22.2 - - + -
56A PHE* 3.5 33.4 - + + -
264A LEU* 3.6 10.1 - - - +
287A ILE* 4.8 1.6 - - + -
288A LEU 3.2 11.9 - - - +
289A ILE* 4.1 7.4 - - + -
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Residues in contact with GLY 25 (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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15A ALA 3.4 10.1 - - - -
16A GLN* 4.3 1.1 - - - -
24A TYR* 1.3 76.3 - - - +
26A LEU* 1.3 62.2 + - - +
264A LEU* 3.6 25.6 - - - +
265A GLU 4.2 1.6 - - - -
268A CYS* 3.4 7.3 - - - -
287A ILE* 3.6 2.8 - - - +
288A LEU 2.8 31.0 + - - +
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Residues in contact with LEU 26 (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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13A HIS 4.0 9.2 - - - +
14A ASN* 2.9 28.7 - - - +
15A ALA* 3.0 37.9 + - + +
24A TYR* 4.2 6.1 - - + -
25A GLY* 1.3 75.0 - - - +
27A SER* 1.3 65.1 + - - +
40A HIS* 3.6 49.1 - - + +
42A ALA* 3.9 23.1 - - + -
265A GLU* 4.3 3.3 - - - +
268A CYS* 3.7 6.7 - - - +
286A VAL 3.2 15.0 - - - +
287A ILE* 4.0 13.9 - - + -
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Residues in contact with SER 27 (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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12A LYS* 3.8 14.9 - - - +
13A HIS 3.3 5.8 - - - -
14A ASN* 3.5 1.8 + - - -
26A LEU* 1.3 78.9 - - - +
28A SER* 1.3 61.9 + - - +
268A CYS* 3.6 22.2 - - - +
269A ASN* 2.8 28.9 + - - -
272A VAL* 3.9 10.2 - - - +
284A MET 4.0 0.5 - - - +
285A SER* 3.3 2.8 - - - -
286A VAL* 3.0 34.3 + - - +
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Residues in contact with SER 28 (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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12A LYS* 3.6 2.9 - - - -
13A HIS* 2.9 54.6 + - - +
26A LEU* 4.8 0.2 - - - +
27A SER* 1.3 74.6 + - - +
29A MET* 1.3 63.8 + - - +
36A MET* 3.7 13.7 - - - +
38A ASP* 5.5 0.4 - - - -
40A HIS* 4.4 18.8 - - - -
284A MET 3.2 4.3 - - - -
285A SER* 3.6 20.4 - - - -
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Residues in contact with MET 29 (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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9A LYS 3.3 17.3 - - - +
10A MET* 3.5 27.1 - - - +
11A GLU 3.7 13.9 - - - +
12A LYS* 3.6 22.2 - - + -
13A HIS* 5.1 1.1 - - - -
28A SER* 1.3 76.8 - - - +
30A GLN* 1.3 61.9 + - - +
31A GLY* 3.6 13.1 + - - +
36A MET* 3.5 7.3 - - - +
272A VAL* 3.4 27.6 - - + +
273A ASP* 4.1 3.4 - - - +
276A LEU* 4.1 17.9 - - + -
284A MET* 2.8 58.4 + - + +
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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