Contacts of the strand formed by residues 55 - 68 (chain J) in PDB entry 4M7D
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 55 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19C LYS* 4.0 14.0 + - - +
20C LEU 3.4 19.3 - - - +
21C ARG* 4.3 3.9 - - - -
22C GLY 3.6 10.0 + - - -
23C ALA* 3.4 13.8 + - - +
24C ARG 5.5 0.2 - - - +
74C THR* 6.1 3.9 - - - +
30D SER* 4.1 18.5 - - - +
32D LEU* 3.7 31.0 - - + -
56D TYR* 6.3 1.6 - - + -
50J GLN 3.7 0.2 - - - +
51J LEU* 3.2 8.4 - - - -
52J ASN* 2.9 34.3 + - - +
53J ASN 3.1 8.5 - - - +
54J GLU* 1.3 94.9 - - - +
56J LEU* 1.3 62.9 + - - +
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Residues in contact with LEU 56 (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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19C LYS* 5.9 0.3 + - - -
23C ALA* 4.5 10.9 - - + +
49C TYR* 3.9 29.8 - - + -
51C LEU* 5.3 2.7 - - + -
56C LEU* 3.8 37.5 - - + -
32D LEU* 4.7 7.6 - - - +
64D LEU* 4.6 6.2 - - - +
49J TYR* 4.3 22.2 - - + -
50J GLN 3.5 13.0 - - - +
51J LEU* 3.5 23.5 - - + +
55J GLU* 1.3 80.5 - - - +
57J SER* 1.3 64.8 + - - +
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Residues in contact with SER 57 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32D LEU* 5.0 0.9 - - - -
56D TYR* 3.7 44.0 - - - -
64D LEU* 4.1 9.2 - - - -
48J ILE 3.7 0.3 - - - +
49J TYR* 3.5 5.9 - - - -
50J GLN* 2.9 41.3 + - - +
52J ASN* 3.8 10.7 + - - -
56J LEU* 1.3 80.5 - - - +
58J GLU* 1.3 63.8 + - - +
59J SER* 4.3 1.6 + - - -
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Residues in contact with GLU 58 (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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56D TYR* 6.0 0.7 - - - +
62D LYS* 3.1 42.2 + - - +
63D LEU 5.0 0.9 - - - +
64D LEU* 3.5 27.1 - - + +
47J THR* 4.6 11.7 - - - -
48J ILE 3.2 7.4 - - - +
49J TYR* 2.7 43.2 + - + -
57J SER* 1.3 79.9 - - - +
59J SER* 1.3 67.7 + - - +
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Residues in contact with SER 59 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61D ASN* 6.6 0.4 - - - -
62D LYS* 4.5 6.1 - - - +
47J THR* 3.1 7.8 - - - -
48J ILE* 2.9 51.4 + - - +
50J GLN* 5.8 4.2 + - - +
57J SER* 4.3 2.0 - - - -
58J GLU* 1.3 76.7 - - - +
60J GLU* 1.3 67.5 + - - +
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Residues in contact with GLU 60 (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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62D LYS* 3.4 43.5 - - + +
45J VAL* 4.0 13.5 - - + +
46J GLU 3.3 11.4 - - - +
47J THR* 3.8 17.8 - - + +
48J ILE* 6.3 0.9 - - - -
58J GLU* 5.4 0.4 - - - +
59J SER* 1.3 82.5 + - - +
61J ARG* 1.3 66.2 + - - +
62J ARG* 3.1 29.0 + - - +
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Residues in contact with ARG 61 (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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16I VAL* 5.1 1.0 - - - +
18I GLU* 4.7 2.8 + - - -
24I GLU* 3.2 27.1 + - - -
50I LYS* 4.2 17.3 - - - +
71I TYR* 3.0 53.8 + - + +
44J ALA 3.9 0.7 - - - +
45J VAL* 3.3 4.4 - - - -
46J GLU* 2.8 58.8 + - + +
48J ILE* 5.8 3.4 - - + -
60J GLU* 1.3 78.1 - - - +
62J ARG* 1.3 71.2 + - - +
63J SER* 4.1 2.9 + - - -
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Residues in contact with ARG 62 (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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43J ASP 5.9 1.1 - - - -
44J ALA 3.4 13.0 - - - +
45J VAL* 4.0 25.5 - - + +
60J GLU* 3.1 28.4 + - - +
61J ARG* 1.3 81.2 + - - +
63J SER* 1.3 65.0 + - - +
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Residues in contact with SER 63 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71I TYR* 4.1 25.8 - - - -
26J LEU* 6.1 0.2 - - - +
43J ASP* 3.8 0.6 + - - -
44J ALA* 2.9 34.2 + - - +
61J ARG* 5.0 6.0 + - - -
62J ARG* 1.3 80.3 - - - +
64J GLU* 1.3 63.8 + - - +
65J MET* 3.3 2.6 + - - -
66J VAL* 3.5 26.0 - - - +
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Residues in contact with GLU 64 (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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72I LEU 4.1 7.4 - - - +
73I ASN* 3.1 28.2 - - - +
74I LYS* 3.5 37.5 + - + +
42J SER* 3.4 2.8 - - - -
43J ASP* 2.9 26.0 + - - +
63J SER* 1.3 73.6 - - - +
65J MET* 1.3 65.5 + - - +
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Residues in contact with MET 65 (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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6I PHE* 6.0 0.2 - - + -
71I TYR* 3.9 1.4 - - - +
72I LEU* 2.6 63.7 + - + +
73I ASN 4.2 5.2 - - - +
74I LYS* 4.3 10.8 - - - +
77I VAL* 3.6 30.7 - - + -
79I THR* 4.4 2.9 - - + -
31J GLN* 3.5 20.0 - - + -
40J VAL* 3.4 30.5 - - + -
41J LEU 3.3 11.4 - - - +
42J SER* 3.4 30.1 - - - -
63J SER* 3.3 3.2 + - - -
64J GLU* 1.3 78.8 + - - +
66J VAL* 1.3 60.6 + - - +
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Residues in contact with VAL 66 (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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69I TYR* 4.0 15.7 - - + -
70I VAL 3.5 5.4 - - - +
71I TYR* 3.7 27.1 - - + -
72I LEU* 4.3 1.8 - - - +
26J LEU* 4.9 9.9 - - + -
39J ILE 3.7 0.5 - - - +
40J VAL* 3.3 7.1 - - - -
41J LEU* 2.8 46.0 + - + +
44J ALA* 4.1 16.8 - - + -
63J SER* 3.5 21.5 - - - +
65J MET* 1.3 77.5 - - - +
67J PHE* 1.3 77.6 + - - +
68J ILE* 4.0 5.0 + - + +
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Residues in contact with PHE 67 (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 PHE* 3.2 37.5 - + - -
6I PHE* 5.6 2.2 - + + -
7I PHE* 3.8 18.6 - + + -
36I LEU* 3.4 25.6 - - + -
67I VAL* 5.2 5.4 - - + -
69I TYR* 3.1 8.6 - - - -
70I VAL* 2.8 64.0 + - + +
72I LEU* 4.4 11.6 - - + +
38J ASN* 3.9 6.3 - - + -
39J ILE 3.2 20.2 - - - -
40J VAL* 4.5 5.4 - - + +
66J VAL* 1.3 78.0 - - - +
68J ILE* 1.3 68.3 + - - +
69J ARG* 3.7 30.3 - - + -
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Residues in contact with ILE 68 (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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68I ARG 3.7 4.3 - - - +
69I TYR* 4.0 13.2 - - + -
18J ILE* 4.2 12.3 - - + -
20J LEU* 4.1 24.2 - - + -
26J LEU* 4.1 17.7 - - + -
37J SER 4.1 0.5 - - - +
38J ASN* 3.4 1.9 - - - -
39J ILE* 2.7 41.8 + - + +
41J LEU* 3.8 35.2 - - + -
66J VAL* 4.3 7.6 - - + +
67J PHE* 1.3 83.4 - - - +
69J ARG* 1.3 75.8 + - - +
70J GLY 3.3 0.7 + - - -
72J THR* 4.9 0.2 - - + -
73J VAL* 4.1 14.1 - - + -
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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