Contacts of the strand formed by residues 40 - 49 (chain J) in PDB entry 1I5L
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 LEU 40 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9J LEU* 4.7 15.7 - - + -
19J VAL* 4.1 17.9 - - + -
31J LEU* 4.2 14.8 - - + -
33J GLY 3.9 4.0 - - - +
34J TYR* 4.0 17.5 - - + -
38J MET* 3.6 14.4 - - + +
39J ASN* 1.3 82.3 - - - +
41J VAL* 1.3 68.7 + - - +
42J LEU* 4.2 3.6 - - + -
61J VAL* 3.3 7.3 - - - +
62J ILE* 2.9 45.3 + - + +
67J VAL* 4.1 18.8 - - + -
70J VAL* 3.7 28.5 - - + -
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Residues in contact with VAL 41 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3I PRO* 4.7 0.7 - - + +
4I ARG 4.5 0.7 - - - -
5I PRO* 3.3 42.4 - - + +
8I VAL* 3.7 30.7 - - + -
31J LEU* 3.8 1.2 - - - -
32J ASP* 2.8 41.6 + - + +
33J GLY* 3.4 18.3 + - - +
40J LEU* 1.3 79.5 - - - +
42J LEU* 1.3 69.1 + - - +
43J LEU* 5.4 4.9 - - + -
59J SER* 5.6 1.6 - - - -
60J VAL 3.3 8.7 - - - +
61J VAL* 4.6 4.7 - - + -
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Residues in contact with LEU 42 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17J VAL* 3.9 18.8 - - + -
19J VAL* 4.1 12.3 - - + -
27J PHE* 4.0 22.2 - - + -
28J ARG 4.7 6.7 - - - +
29J GLY 4.4 1.6 - - - +
30J THR 3.2 17.7 - - - +
31J LEU* 3.8 21.3 - - + -
40J LEU* 5.0 3.1 - - + -
41J VAL* 1.3 77.8 - - - +
43J LEU* 1.3 64.0 + - - +
45J ALA* 4.1 15.7 - - + -
59J SER* 3.1 8.4 - - - -
60J VAL* 3.0 39.2 + - + +
62J ILE* 3.9 27.4 - - + -
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Residues in contact with LEU 43 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8I VAL* 6.6 0.2 - - + -
11I ARG* 5.9 5.2 - - - +
29J GLY* 3.9 0.7 - - - -
30J THR* 3.0 38.7 + - + +
32J ASP* 3.5 36.8 - - + +
41J VAL* 5.4 3.4 - - + -
42J LEU* 1.3 73.8 - - - +
44J ASP* 1.3 82.5 + - - +
45J ALA 3.2 2.6 + - - -
58J GLY 3.3 4.9 - - - +
59J SER* 3.4 23.8 - - - +
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Residues in contact with ASP 44 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28J ARG 4.2 0.2 - - - +
29J GLY* 4.0 7.1 - - - -
30J THR* 4.7 2.6 + - - +
43J LEU* 1.3 84.6 - - - +
45J ALA* 1.3 58.2 + - - +
46J GLU* 4.4 3.5 + - - +
57J VAL 3.7 4.9 - - - -
58J GLY* 2.7 25.1 + - - +
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Residues in contact with ALA 45 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27J PHE* 4.2 16.6 - - + -
28J ARG 2.9 19.7 - - - +
29J GLY* 4.1 4.9 - - - -
42J LEU* 4.1 20.4 - - + -
43J LEU 4.0 0.9 - - - -
44J ASP* 1.3 77.1 - - - +
46J GLU* 1.3 63.2 + - - +
56J LYS* 3.6 3.3 - - - +
57J VAL* 3.1 38.7 + - + +
60J VAL* 4.6 6.3 - - + -
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Residues in contact with GLU 46 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27J PHE* 3.2 10.4 - - - +
28J ARG* 2.9 50.6 + - + +
44J ASP 5.0 3.6 - - - +
45J ALA* 1.3 80.0 - - - +
47J GLU* 1.3 61.7 + - - +
48J ILE* 3.8 5.8 + - + +
53J VAL* 3.9 30.2 - - + +
55J ARG 4.1 9.4 - - - +
56J LYS* 2.6 38.5 + - + +
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Residues in contact with GLU 47 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20I ARG* 5.8 0.5 + - - -
69I PHE* 4.2 6.4 - - - -
25J ARG* 3.5 42.3 + - + +
26J GLU 3.6 8.1 - - - +
27J PHE* 4.0 29.6 - - + +
46J GLU* 1.3 72.6 - - - +
48J ILE* 1.4 58.2 + - - +
53J VAL* 4.1 1.9 - - - +
54J VAL* 2.9 53.0 + - + +
55J ARG* 4.0 37.8 + - + +
56J LYS 4.9 0.4 - - - +
57J VAL* 5.7 2.3 - - + +
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Residues in contact with ILE 48 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18J ILE* 5.9 2.7 - - + -
24J GLY 5.1 0.5 - - - +
25J ARG* 4.9 4.2 - - - -
26J GLU* 2.7 50.1 + - + +
27J PHE 4.7 2.2 - - - +
28J ARG* 3.2 53.2 - - + +
46J GLU* 4.0 18.8 - - + +
47J GLU* 1.4 75.6 - - - +
49J GLN* 1.3 66.0 + - - +
50J ASN 4.1 1.1 + - - +
51J GLY* 3.8 23.3 - - - +
52J GLU 3.3 16.8 - - - +
53J VAL* 5.2 6.3 - - + -
54J VAL* 4.2 2.0 - - - -
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Residues in contact with GLN 49 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D ARG* 2.8 46.7 + - - +
34E TYR* 4.7 0.6 + - - -
35E ASP* 3.8 14.7 - - + +
36E ILE* 2.8 49.8 - - + +
24J GLY 5.3 4.3 - - - +
25J ARG* 5.9 3.3 - - - -
48J ILE* 1.3 74.0 - - - +
50J ASN* 1.3 74.5 + - + +
51J GLY 3.3 0.9 - - - -
52J GLU 2.7 19.8 + - - -
54J VAL* 3.6 17.5 - - + -
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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