Contacts of the strand formed by residues 23 - 31 (chain A) in PDB entry 2JC6
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 PHE 23 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A ILE* 2.8 33.8 + - + +
20A LYS* 3.0 26.0 - - - +
22A ILE* 1.3 92.5 - - + +
24A GLU* 1.3 58.6 + - - +
25A PHE* 3.8 20.6 + + + -
40A ALA* 4.2 14.8 - - + -
41A GLU 3.3 6.5 - - - +
42A GLU* 3.7 30.5 - - + -
43A LYS* 3.7 5.2 - - - -
49A PHE* 3.8 26.5 - + - -
51A VAL* 5.1 0.7 - - + -
86A ASP* 6.0 1.8 - - + -
88A TYR* 3.9 24.2 - + - -
97A VAL* 3.9 24.5 - - + -
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Residues in contact with GLU 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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23A PHE* 1.3 70.3 - - - +
25A PHE* 1.3 64.2 + - - +
26A LYS* 3.4 23.4 + - + +
40A ALA* 3.4 1.6 - - - -
41A GLU* 2.7 59.7 + - + +
43A LYS* 3.5 39.4 - - + +
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Residues in contact with PHE 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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19A ILE* 4.0 29.4 - - + -
20A LYS* 5.4 4.5 - - + -
23A PHE* 3.8 24.7 + - + -
24A GLU* 1.3 75.0 - - - +
26A LYS* 1.3 63.4 + - - +
38A VAL* 3.9 20.4 - - + -
39A LEU 3.8 2.9 - - - -
40A ALA* 3.9 15.7 - - + -
51A VAL* 4.0 22.2 - - + -
53A CYS* 4.1 20.0 - - - -
95A TYR* 4.4 8.1 - + - -
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Residues in contact with LYS 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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24A GLU* 3.5 29.2 - - + +
25A PHE* 1.3 77.4 - - - +
27A GLU* 1.3 69.2 + - + +
28A THR 3.8 0.3 + - - -
38A VAL* 4.0 5.2 - - - +
39A LEU* 2.8 35.8 + - + +
40A ALA 4.9 0.2 - - - -
41A GLU* 4.0 29.6 - - + +
48A LEU* 5.1 4.5 - - + -
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Residues in contact with GLU 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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26A LYS* 1.3 82.4 - - - +
28A THR* 1.3 63.8 + - - +
29A LEU* 3.9 23.5 - - + +
38A VAL* 3.5 2.4 - - - -
39A LEU* 2.7 50.0 + - + +
310A PHE* 6.2 0.3 - - - -
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Residues in contact with THR 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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26A LYS 3.8 1.4 + - - -
27A GLU* 1.3 80.4 - - - +
29A LEU* 1.3 64.1 + - - +
30A GLY* 3.6 16.2 - - - +
31A THR* 3.6 23.8 - - - +
36A GLU* 2.8 25.8 + - + -
37A VAL 3.7 6.3 - - - +
38A VAL* 3.7 4.5 - - - +
310A PHE* 5.0 7.8 - - - -
312A ALA* 5.8 2.7 - - + -
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Residues in contact with LEU 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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27A GLU* 3.5 28.5 + - + +
28A THR* 1.3 73.1 - - - +
30A GLY* 1.3 54.5 + - - +
37A VAL* 2.7 26.6 + - + +
39A LEU* 4.0 24.7 - - + +
50A ALA* 4.3 10.8 - - + -
100A LEU* 4.3 8.5 - - + -
310A PHE* 3.6 25.1 - - - -
1314A QPP 3.6 80.2 + - + +
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Residues in contact with GLY 30 (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 THR* 3.6 6.1 - - - +
29A LEU* 1.3 81.5 - - - +
31A THR* 1.3 65.3 + - - -
36A GLU* 3.5 1.4 - - - -
37A VAL* 2.9 29.4 + - - +
309A ALA* 3.3 18.4 - - - -
310A PHE* 4.1 1.3 - - - -
312A ALA* 5.5 0.2 - - - -
1314A QPP 3.8 14.1 - - - -
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Residues in contact with THR 31 (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 THR* 3.6 14.7 - - - +
30A GLY* 1.3 76.2 + - - -
32A GLY* 1.3 69.4 + - - +
35A SER 3.7 8.5 - - - +
36A GLU* 4.1 10.9 - - + +
308A GLN 4.7 0.3 - - - +
309A ALA* 2.8 28.2 + - - +
312A ALA* 3.9 23.5 - - - +
313A THR* 4.1 25.3 + - - +
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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