Contacts of the strand formed by residues 42 - 48 (chain A) in PDB entry 2JNG
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 42 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A ARG* 5.6 6.1 - - + -
28A VAL 3.4 7.9 - - - +
29A ARG* 3.1 38.7 + - + +
40A GLY 3.5 3.1 + - - +
41A ASP* 1.3 84.2 + - - +
43A GLY* 1.3 57.5 + - - +
59A TRP* 3.6 3.8 - - - -
60A GLU* 2.8 31.3 + - + +
61A SER* 3.8 2.7 + - - -
76A LEU* 3.3 22.3 - - + +
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Residues in contact with GLY 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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27A ARG* 3.1 12.2 - - - +
28A VAL* 2.7 38.7 + - - +
42A GLU* 1.3 75.3 - - - +
44A GLU* 1.3 55.9 + - - -
58A PHE* 3.0 15.9 - - - -
59A TRP* 3.6 8.5 - - - -
60A GLU* 3.8 7.6 - - - -
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Residues in contact with GLU 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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25A GLY* 4.2 20.6 - - - +
26A MET 3.9 11.0 - - - +
27A ARG* 4.2 10.0 + - + +
28A VAL* 4.3 1.1 - - - -
43A GLY* 1.3 75.2 - - - -
45A PHE* 1.3 68.6 + - - +
46A ARG* 2.7 38.1 + - - +
57A VAL* 3.2 6.5 - - - +
58A PHE* 2.8 39.3 + - + +
79A GLU* 4.3 15.6 - - - +
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Residues in contact with PHE 45 (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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22A LEU* 3.2 48.7 - - + -
23A GLN 3.4 16.8 - - - +
24A PRO* 3.1 17.5 - - + +
25A GLY 2.9 28.4 + - - -
26A MET 2.8 22.3 + - - +
28A VAL* 4.1 6.6 - - + +
44A GLU* 1.3 72.2 - - - +
46A ARG* 1.3 60.2 + - - +
47A GLN* 3.8 15.7 - - - -
48A SER* 3.3 26.5 - - - -
55A VAL* 3.3 29.8 - - + -
56A GLN 4.4 2.5 - - - -
57A VAL* 4.6 7.6 - - + -
70A TRP* 3.7 14.4 - + - -
73A LEU* 5.3 1.3 - - + -
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Residues in contact with ARG 46 (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 PRO* 3.2 26.7 - - - +
25A GLY* 5.5 2.2 - - - +
44A GLU* 2.7 40.1 + - - +
45A PHE* 1.3 77.3 + - - +
47A GLN* 1.3 73.3 + - + +
56A GLN* 3.3 15.0 + - + +
57A VAL 4.7 0.9 - - - -
58A PHE* 4.0 32.3 - - + +
65A THR* 5.0 4.5 - - + -
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Residues in contact with GLN 47 (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 PRO* 4.7 4.0 - - + -
45A PHE* 3.8 11.6 - - - -
46A ARG* 1.3 84.3 - - + +
48A SER* 1.3 67.2 + - - +
49A ASN* 5.8 3.0 - - - +
55A VAL* 3.6 2.6 - - - +
56A GLN* 2.8 53.7 + - + +
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Residues in contact with SER 48 (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 ARG* 4.7 6.6 - - - +
22A LEU 5.0 0.3 + - - -
45A PHE* 3.3 15.8 - - - -
47A GLN* 1.3 83.3 + - - +
49A ASN* 1.3 70.5 + - - +
50A ASN* 3.6 7.3 + - - +
55A VAL* 3.8 9.6 - - - +
56A GLN* 4.2 1.6 - - - +
70A TRP* 3.4 35.5 - - - -
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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