Contacts of the strand formed by residues 34 - 42 (chain A) in PDB entry 5AKF
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 SER 34 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A LEU 3.5 13.7 - - - -
28A LYS* 4.3 13.5 - - - -
29A TYR* 4.2 7.1 - - - +
32A ASN 4.8 0.9 - - - -
33A ARG* 1.3 77.6 - - - +
35A GLU* 1.3 61.5 + - - +
36A TYR* 3.8 5.0 - - - -
3D C 3.4 4.5 - - - +
4D G 2.8 51.5 + - - -
5D C 3.1 27.5 + - - -
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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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25A TYR 3.7 0.7 - - - +
26A LYS* 3.6 1.2 - - - -
27A LEU* 2.7 40.2 + - + +
29A TYR* 2.7 37.5 + - + +
34A SER* 1.3 80.3 - - - +
36A TYR* 1.3 72.1 + - - +
37A ARG* 3.0 32.7 + - + -
70A GLN* 5.0 0.3 + - - -
81A ARG* 4.7 1.4 - - - -
83A SER* 2.7 34.3 + - - +
4D G 5.0 0.9 - - - -
5D C 4.0 9.2 - - + -
6D C 3.0 31.6 + - - -
7D G 5.0 0.3 - - - +
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Residues in contact with TYR 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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25A TYR 3.3 4.7 - - - -
26A LYS* 3.8 25.1 - - + +
28A LYS* 3.9 11.7 + - - -
34A SER* 3.8 8.3 - - - -
35A GLU* 1.3 84.0 - - - +
37A ARG* 1.3 59.2 + - - +
83A SER* 3.3 5.4 + - - -
84A SER 2.8 48.3 + - - +
85A LYS* 3.6 35.2 + - + +
88A TYR* 3.7 26.0 - + + -
89A TYR* 3.9 18.6 + + - -
4D G 2.7 42.4 + - + -
5D C 3.9 8.1 + - - -
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Residues in contact with ARG 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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23A GLY 3.7 0.5 - - - +
24A LEU* 3.4 6.2 - - - -
25A TYR* 2.8 48.2 + - + +
27A LEU* 4.2 12.3 - - + +
29A TYR* 4.2 0.8 + - - -
35A GLU* 3.0 38.4 + - + +
36A TYR* 1.3 77.9 - - - +
38A VAL* 1.3 64.5 + - - +
39A VAL* 4.0 15.0 - - + -
79A GLU* 4.7 0.2 + - - -
81A ARG* 3.3 47.4 - - + +
82A VAL 3.6 3.6 - - - +
83A SER* 4.6 2.0 - - - +
88A TYR* 3.9 5.6 - - - -
17C T 3.4 17.9 + - - -
18C C 3.6 11.6 - - - +
7D G 2.7 29.7 + - - -
8D G 2.7 22.4 + - - -
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Residues in contact with VAL 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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18A ILE* 3.6 31.9 - - + -
23A GLY 3.7 2.9 - - - -
24A LEU* 3.8 10.3 - - + -
37A ARG* 1.3 71.4 - - - +
39A VAL* 1.3 60.9 + - - +
56A MET* 4.1 16.6 - - + -
80A LEU* 3.9 2.1 - - - +
81A ARG* 3.5 3.5 - - - -
82A VAL* 3.0 35.8 + - + +
84A SER 5.0 0.2 - - - +
87A LEU* 3.8 21.8 - - + +
88A TYR* 3.6 35.9 - - + +
91A PHE* 4.0 8.3 - - + -
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Residues in contact with VAL 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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18A ILE* 3.9 5.8 - - - -
22A GLY* 2.9 6.4 - - - -
23A GLY 2.8 37.9 + - - +
25A TYR* 3.5 32.5 - - + -
37A ARG* 4.1 12.3 - - + -
38A VAL* 1.3 80.2 - - - +
40A ILE* 1.3 69.8 + - - +
41A THR* 3.9 15.9 - - + -
79A GLU* 3.5 34.5 - - + +
80A LEU 3.4 10.1 - - - +
81A ARG* 4.2 4.7 - - + -
16C T 4.6 4.0 - - + -
17C T 5.9 0.2 - - + -
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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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14A LEU* 4.4 5.4 - - + +
17A LEU* 4.0 32.3 - - + +
18A ILE* 3.6 22.4 - - + +
21A ASP* 4.5 3.6 - - + -
22A GLY* 4.0 2.9 - - - -
38A VAL 4.4 0.2 + - - -
39A VAL* 1.3 80.0 - - - +
41A THR* 1.3 73.0 + - - +
48A ILE* 4.6 2.2 - - + +
52A ILE* 3.7 41.7 - - + -
56A MET* 4.0 24.7 - - + -
79A GLU 3.7 0.3 - - - -
80A LEU* 2.8 45.7 + - + +
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Residues in contact with THR 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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21A ASP* 2.6 39.5 + - - +
22A GLY* 4.2 1.1 - - - -
39A VAL* 3.9 16.8 - - + -
40A ILE* 1.3 81.0 - - - +
42A ALA* 1.3 65.1 + - - +
48A ILE* 4.7 0.2 - - - -
77A ARG* 3.6 30.1 - - + +
78A TYR 3.4 8.1 - - - -
79A GLU* 4.0 12.6 - - + -
14B A 3.4 31.4 - - - +
15C G 4.2 10.1 - - + -
16C T 4.8 1.1 - - + -
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Residues in contact with ALA 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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21A ASP* 5.6 1.1 - - - +
41A THR* 1.3 78.1 - - - +
43A LYS* 1.3 62.2 + - - +
44A SER 3.6 2.0 + - - +
47A LEU* 4.3 21.3 - - + -
48A ILE* 3.7 23.7 - - + +
52A ILE* 4.9 6.1 - - + -
77A ARG* 4.0 4.7 - - - +
78A TYR* 3.0 34.7 + - - +
14B A 3.4 12.8 + - - +
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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