Contacts of the strand formed by residues 39 - 44 (chain U) in PDB entry 3J7Y
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 THR 39 (chain U).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31U PRO* 5.0 5.9 - - - +
35U GLN* 3.4 28.1 - - - +
36U PRO* 2.7 43.9 + - + +
37U GLU 3.3 2.0 - - - +
38U ASP* 1.3 74.6 + - - +
40U VAL* 1.3 62.1 + - - +
41U GLN* 4.1 1.1 + - - -
69U ARG* 4.9 4.0 - - - +
96U TYR* 5.5 6.3 - - + -
97U VAL 3.4 9.4 - - - +
98U GLN* 3.4 34.8 - - + +
105U PHE* 5.2 6.0 - - - +
270s LYS 5.6 2.9 - - - +
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Residues in contact with VAL 40 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28U LEU* 3.9 25.8 - - + -
38U ASP 4.0 2.5 - - - +
39U THR* 1.3 74.6 - - - +
41U GLN* 1.3 62.5 - - - +
42U PHE* 3.5 31.5 + - + -
95U ALA 3.7 1.0 - - - +
96U TYR* 4.7 1.1 - - - -
97U VAL* 2.8 37.8 + - - +
99U LEU* 3.5 30.7 - - + -
105U PHE* 3.5 28.5 - - + -
64Y LEU* 3.7 7.6 - - + -
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Residues in contact with GLN 41 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2370A A 2.9 29.7 + - - -
28U LEU* 3.4 3.6 - - - +
29U VAL* 2.8 61.9 + - + +
31U PRO* 3.4 32.8 - - + +
35U GLN* 4.7 0.8 - - + +
39U THR 4.1 1.2 + - - -
40U VAL* 1.3 74.3 - - - +
42U PHE* 1.3 56.7 + - - +
43U ARG* 5.1 2.6 + - - +
92U TYR* 5.9 0.5 - - - -
94U VAL* 3.3 28.0 - - + +
95U ALA 3.1 16.6 - - - +
96U TYR* 3.5 21.4 + - + +
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Residues in contact with PHE 42 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26U ILE* 4.1 18.6 - - + -
27U GLN 3.4 4.9 - - - +
28U LEU* 3.2 39.3 - - + -
29U VAL* 4.6 2.0 - - - -
40U VAL* 3.5 24.0 - - + -
41U GLN* 1.3 73.5 - - - +
43U ARG* 1.3 61.3 - - - +
44U ILE* 3.7 15.9 - - + +
53U LEU* 4.5 5.6 - - + -
57U LEU* 3.8 25.8 - - + -
94U VAL* 3.5 5.1 - - - +
95U ALA* 2.8 33.7 + - + +
97U VAL* 3.7 34.8 - - + -
64Y LEU* 4.2 10.3 - - + -
67Y PHE* 3.8 20.6 - + - -
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Residues in contact with ARG 43 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2369A A 2.6 39.6 + - - -
26U ILE* 3.2 19.4 - - - +
27U GLN* 2.8 39.7 + - + +
29U VAL* 4.4 17.0 - - + +
41U GLN* 5.1 3.3 + - - +
42U PHE* 1.3 74.1 - - - +
44U ILE* 1.3 59.6 + - - +
45U PRO* 4.6 0.3 - - - +
92U TYR* 3.3 56.4 + - + -
93U LYS 3.5 4.3 - - - +
94U VAL* 5.4 0.9 - - + -
117Y GLN* 3.1 38.0 - - - +
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Residues in contact with ILE 44 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26U ILE* 3.4 12.3 - - + -
42U PHE* 3.7 11.2 - - + +
43U ARG* 1.3 79.2 - - - +
45U PRO* 1.3 88.2 - - + +
46U MET* 3.6 0.5 + - - +
48U MET* 3.5 28.9 - - + +
53U LEU* 3.3 41.1 - - + -
70U THR* 5.0 6.5 - - + -
92U TYR* 4.8 4.5 - - - +
93U LYS* 2.8 35.7 + - + +
94U VAL 5.1 0.2 - - - -
95U ALA* 3.3 15.5 - - + +
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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