Contacts of the strand formed by residues 39 - 44 (chain A) in PDB entry 3JT0
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 39 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A GLU* 3.8 31.6 - - + -
34A ASP* 3.1 62.7 + - + +
37A GLY 3.6 0.6 - - - -
38A LYS* 1.3 81.8 - - + +
40A ILE* 1.3 75.7 + - - +
41A ARG* 3.9 14.6 - - - -
83A THR* 3.5 24.5 - - + -
84A ILE 3.0 14.1 - - - +
85A TRP* 3.3 34.8 - + + -
107A TRP* 3.7 5.7 - - - -
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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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30A ILE* 4.5 5.4 - - + -
32A GLU 3.4 9.6 - - - +
33A ILE* 4.6 4.0 - - + -
39A PHE* 1.3 82.3 - - - +
41A ARG* 1.3 62.7 + - - +
42A LEU* 4.3 10.0 - - + +
57A MSE 3.8 40.8 - - + -
59A ARG* 4.4 6.5 - - + -
82A VAL 3.9 0.7 - - - +
83A THR* 3.3 2.8 - - - +
84A ILE* 2.8 32.1 + - + +
101A TRP* 4.2 15.5 - - + -
107A TRP* 3.7 22.9 - - + -
115A VAL* 3.5 37.0 - - + -
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Residues in contact with ARG 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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30A ILE* 3.6 1.6 - - - +
31A GLU* 2.8 54.3 + - + +
32A GLU* 2.7 58.7 + - - +
39A PHE* 3.9 14.4 - - + -
40A ILE* 1.3 76.0 - - - +
42A LEU* 1.3 81.0 + - - +
81A THR* 3.9 16.8 - - - -
82A VAL 3.5 4.0 - - - +
83A THR* 3.6 23.5 + - + +
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Residues in contact with LEU 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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28A VAL* 4.2 8.5 - - + -
29A CYS 3.2 7.9 - - - +
30A ILE* 4.0 24.5 - - + -
31A GLU* 4.6 0.7 - - - -
40A ILE* 4.3 1.8 - - + -
41A ARG* 1.3 84.0 - - - +
43A LYS* 1.3 61.2 + - - +
52A MSE 3.7 22.0 - - + -
57A MSE 4.0 19.7 - - + -
70A TYR* 3.1 27.1 - - + +
76A LEU* 4.4 6.3 - - + -
81A THR* 3.1 27.4 - - - -
82A VAL* 3.0 22.9 + - + +
117A LEU* 4.1 21.3 - - + -
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Residues in contact with LYS 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 ASN 3.4 0.2 - - - +
28A VAL* 3.2 2.4 - - - -
29A CYS* 2.7 44.1 + - + +
31A GLU* 3.3 33.1 + - + +
42A LEU* 1.3 77.7 - - - +
44A ASN* 1.3 67.8 + - - +
45A THR* 3.4 21.5 + - + +
76A LEU* 4.2 4.5 - - - -
79A GLY* 3.7 24.7 + - - -
80A GLN 3.5 9.9 - - - +
81A THR* 3.8 16.4 - - + +
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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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27A ASN* 3.7 7.3 - - - +
28A VAL* 4.3 5.7 - - + +
43A LYS* 1.3 74.4 - - - +
45A THR* 1.3 55.9 + - - +
46A SER* 3.1 25.7 + - - -
48A GLN 3.0 23.4 + - - -
50A GLN* 3.5 16.5 - - - +
76A LEU* 2.8 35.7 + - + +
77A LYS 3.6 17.6 - - - +
78A ALA* 4.1 2.2 - - - -
79A GLY* 2.7 35.3 + - - -
80A GLN 3.0 10.2 + - - +
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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