Contacts of the strand formed by residues 54 - 69 (chain F) in PDB entry 5IXM
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 54 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17F LEU* 5.3 2.2 - - - -
18F LEU* 3.7 23.8 - - + +
20F GLU* 5.3 16.8 + - - +
49F ARG 6.1 0.9 - - - +
52F ILE 3.9 9.0 - - - +
53F PRO* 1.3 79.8 - - - +
55F LEU* 1.3 61.0 + - - +
56F ARG* 5.3 0.3 + - - +
87F GLN 3.8 0.9 - - - +
88F VAL* 3.5 7.3 - - - +
89F LEU* 2.9 63.9 + - + +
91F PRO* 6.2 0.4 - - + -
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Residues in contact with LEU 55 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17F LEU* 4.4 12.8 - - + +
18F LEU 2.9 16.0 + - - +
19F LEU* 3.6 18.8 - - + +
20F GLU* 2.9 29.1 + - - +
32F ILE* 4.7 8.3 - - + -
36F LEU* 4.7 14.8 - - + -
54F THR* 1.3 73.4 - - - +
56F ARG* 1.3 60.5 + - - +
57F ILE* 3.9 11.2 - - + -
86F ALA* 4.4 10.8 - - + -
87F GLN 3.3 17.7 - - - +
88F VAL* 3.9 19.1 - - + -
135F LEU* 4.0 30.3 - - + -
139F LEU* 5.0 9.6 - - + -
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Residues in contact with ARG 56 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20F GLU* 3.4 33.6 + - + +
21F SER* 5.5 0.4 - - - +
54F THR* 4.0 1.5 - - - +
55F LEU* 1.3 72.5 - - - +
57F ILE* 1.3 71.6 + - - +
58F ILE* 3.5 8.7 + - + +
86F ALA* 3.4 2.7 - - - -
87F GLN* 2.9 59.3 + - + +
89F LEU* 3.7 40.7 - - + +
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Residues in contact with ILE 57 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19F LEU* 3.8 28.0 - - + -
20F GLU 2.9 14.6 + - - +
21F SER* 3.8 17.7 - - - +
22F SER* 3.2 21.7 + - - +
28F LEU* 4.7 15.9 - - + -
32F ILE* 3.6 29.2 - - + -
55F LEU* 3.9 15.0 - - + -
56F ARG* 1.3 78.4 - - - +
58F ILE* 1.3 63.7 + - - +
59F GLY* 4.0 17.5 - - - +
84F VAL* 4.9 3.6 - - + -
85F GLN 4.0 5.6 - - - +
86F ALA* 4.4 9.6 - - + +
135F LEU* 4.6 4.7 - - + -
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Residues in contact with ILE 58 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22F SER* 3.3 18.6 - - - -
56F ARG* 4.4 12.8 - - - +
57F ILE* 1.3 72.1 - - - +
59F GLY* 1.3 61.4 + - - +
85F GLN* 2.9 42.5 + - + +
86F ALA 4.5 2.2 - - - +
87F GLN* 3.5 41.1 - - + +
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Residues in contact with GLY 59 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22F SER* 4.7 7.4 - - - -
57F ILE* 3.5 8.9 - - - +
58F ILE* 1.3 85.7 - - - +
60F SER* 1.3 63.1 + - - -
84F VAL* 3.7 4.5 - - - +
85F GLN* 3.2 26.8 + - - +
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Residues in contact with SER 60 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28F LEU* 3.8 28.1 - - - +
59F GLY* 1.3 75.2 - - - -
61F SER* 1.3 61.9 + - - +
62F GLU* 5.9 0.9 - - - +
82F LEU* 4.2 8.8 - - - +
83F HIS 3.1 13.2 - - - -
84F VAL* 4.0 4.0 - - - -
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Residues in contact with SER 61 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60F SER* 1.3 76.7 - - - +
62F GLU* 1.3 66.1 + - - +
63F SER* 5.5 0.7 - - - -
81F VAL 3.7 0.5 - - - +
82F LEU* 3.4 5.1 - - - +
83F HIS* 2.9 57.4 + - - +
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Residues in contact with GLU 62 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60F SER* 5.8 0.9 - - - +
61F SER* 1.3 80.7 - - - +
63F SER* 1.3 66.8 + - - +
81F VAL 3.3 6.7 - - - +
82F LEU* 4.0 17.3 - - + +
124F ARG* 3.1 35.0 + - - +
128F ARG* 3.2 27.9 + - - +
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Residues in contact with SER 63 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553E GLN* 4.0 12.1 - - - -
61F SER* 5.0 0.9 + - - -
62F GLU* 1.3 81.4 + - - +
64F GLN* 1.3 64.3 + - - +
65F GLU* 5.8 0.7 - - - -
79F GLN 4.2 0.9 - - - -
80F LEU* 3.3 8.8 - - - +
81F VAL* 2.9 41.7 + - - +
83F HIS* 3.9 18.5 + - - -
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Residues in contact with GLN 64 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553E GLN* 4.4 0.4 - - - +
63F SER* 1.3 78.0 - - - +
65F GLU* 1.3 76.1 + - - +
78F ASN* 3.9 24.5 - - + +
79F GLN 3.3 7.6 - - - +
80F LEU* 3.5 24.8 - - + +
106F PHE* 3.7 22.0 - - - -
120F ALA* 5.7 1.9 - - - +
124F ARG* 5.4 3.3 + - - -
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Residues in contact with GLU 65 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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546E ASN* 4.9 8.6 + - - +
551E PRO* 3.4 32.3 - - + +
553E GLN* 3.3 35.1 - - + +
63F SER* 5.8 0.4 - - - -
64F GLN* 1.3 83.7 + - - +
66F THR* 1.3 65.5 + - - +
67F VAL* 3.8 0.6 + - + -
78F ASN* 3.4 6.8 - - - -
79F GLN* 2.9 33.5 + - - +
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Residues in contact with THR 66 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125E THR* 3.8 11.9 + - + -
126E ASP* 5.5 0.2 + - - -
549E ILE 3.9 15.5 + - - +
550E LEU* 3.4 19.4 - - + +
551E PRO* 4.0 5.9 - - - +
65F GLU* 1.3 77.5 + - - +
67F VAL* 1.3 60.3 + - - +
68F SER 3.2 29.4 - - - +
69F ILE* 4.0 11.7 - - + -
75F ALA* 3.6 22.3 - - + +
77F GLU 3.6 4.9 - - - +
78F ASN* 3.0 16.0 + - - -
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Residues in contact with VAL 67 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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429E ASN* 5.5 0.2 - - - +
431E ARG* 3.6 31.1 - - - +
456E GLN* 2.9 19.6 + - - -
476E TYR* 5.1 2.9 - - - -
550E LEU* 3.6 8.2 - - - +
551E PRO 6.1 0.7 - - - +
553E GLN* 4.3 5.6 - - + +
65F GLU* 3.8 2.0 + - + +
66F THR* 1.3 78.0 - - - +
68F SER* 1.3 61.0 + - - +
77F GLU* 2.9 30.2 + - + +
78F ASN 4.5 1.8 - - - +
79F GLN* 3.6 41.5 - - + +
105F THR* 4.8 1.6 - - + -
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Residues in contact with SER 68 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431E ARG* 4.3 3.1 - - - -
454E ILE* 4.3 14.6 - - - +
456E GLN* 3.4 18.6 - - - +
550E LEU* 3.7 2.6 - - - +
66F THR* 3.2 9.8 - - - +
67F VAL* 1.3 82.4 - - - +
69F ILE* 1.3 58.9 + - - +
76F ALA* 2.8 31.6 + - - +
77F GLU* 2.9 41.6 + - - +
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Residues in contact with ILE 69 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125E THR* 3.7 28.9 - - + -
454E ILE* 3.3 16.1 - - - +
456E GLN* 3.6 8.4 + - - +
478E ASP* 6.1 0.5 - - - -
485E ALA* 3.9 32.1 - - + +
508E ILE* 4.3 11.7 - - + -
549E ILE* 3.7 24.0 - - + -
550E LEU* 4.3 11.9 - - + -
66F THR* 4.0 8.3 - - + -
68F SER* 1.3 80.5 - - - +
70F PHE* 1.3 71.9 + - - +
73F GLY* 4.1 6.3 - - - +
74F VAL 3.3 12.6 - - - +
76F ALA* 3.8 7.9 - - - +
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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