Contacts of the strand formed by residues 47 - 56 (chain C) in PDB entry 1I8F
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 47 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B THR* 4.8 4.4 - - - +
12B LEU* 5.0 1.0 - - - +
16C LEU* 4.5 4.5 - - + -
26C VAL* 3.7 38.4 - - + -
38C LEU* 3.9 22.4 - - + -
40C SER 3.5 2.9 - - - -
41C PHE* 3.9 10.5 - - + -
45C VAL 3.5 13.2 - - - +
46C ASN* 1.3 83.9 - - - +
48C LEU* 1.3 60.8 + - - +
49C LEU* 4.0 12.1 - - + -
66C MET 3.8 0.2 - - - +
67C VAL* 3.2 6.9 - - - +
68C VAL* 2.9 47.8 + - + +
73C VAL* 4.9 2.2 - - + -
76C ILE* 3.8 27.6 - - + -
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Residues in contact with LEU 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B ALA 4.0 8.7 - - - +
11B THR* 4.0 8.7 - - - +
14B ALA* 6.1 2.7 - - + -
15B THR* 3.3 27.1 - - - +
38C LEU* 3.8 0.2 - - - -
39C ARG* 2.8 43.7 + - + -
40C SER* 2.9 34.4 + - - +
47C LEU* 1.3 75.1 - - - +
49C LEU* 1.3 69.4 + - - +
50C GLU* 5.1 7.4 - - + +
65C THR* 3.8 19.5 - - + -
66C MET 3.7 0.9 - - - +
67C VAL* 3.6 13.7 - - + +
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Residues in contact with LEU 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C VAL* 3.9 14.4 - - + -
26C VAL* 4.5 11.9 - - + -
34C ILE* 3.7 30.3 - - + -
36C GLY* 4.3 14.1 - - - +
37C ILE 3.2 12.6 - - - +
38C LEU* 3.8 21.5 - - + -
47C LEU* 4.4 12.3 - - + -
48C LEU* 1.3 83.5 - - - +
50C GLU* 1.3 64.7 + - - +
52C ALA* 4.0 14.1 - - + -
64C GLY 4.2 0.4 - - - -
65C THR* 3.3 5.5 - - - +
66C MET* 2.8 37.9 + - - +
68C VAL* 4.2 14.4 - - + -
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Residues in contact with GLU 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C GLY* 3.7 0.2 - - - -
37C ILE* 2.8 31.8 + - + +
39C ARG* 2.6 54.0 + - + +
48C LEU* 5.1 8.0 - - + +
49C LEU* 1.3 77.0 - - - +
51C ASP* 1.3 78.0 + - - +
52C ALA 3.0 2.8 + - - -
64C GLY 3.7 1.8 - - - -
65C THR* 4.0 19.3 + - + +
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Residues in contact with ASP 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C GLN* 5.4 3.1 + - - -
35C ARG 4.2 0.7 - - - +
36C GLY* 4.1 6.1 - - - -
37C ILE* 4.2 17.0 + - + +
39C ARG* 4.8 6.2 + - - -
50C GLU* 1.3 80.0 - - - +
52C ALA* 1.3 63.9 + - - +
53C GLU* 4.0 7.8 + - - +
64C GLY* 3.1 16.3 + - - -
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Residues in contact with ALA 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C ILE* 4.7 0.2 - - + -
35C ARG 3.1 11.7 - - - +
36C GLY* 3.8 2.2 - - - -
49C LEU* 4.0 17.0 - - + -
50C GLU 3.0 0.6 - - - -
51C ASP* 1.3 74.8 - - - +
53C GLU* 1.3 63.8 + - - +
62C LYS* 3.8 1.9 - - - +
63C ARG* 2.8 24.0 + - - -
64C GLY 2.7 24.1 + - - +
66C MET* 3.9 33.7 - - + -
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Residues in contact with GLU 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C GLN* 4.5 8.0 + - - -
34C ILE* 3.3 7.2 - - - +
35C ARG* 2.6 85.4 + - + +
51C ASP 4.8 6.6 - - - +
52C ALA* 1.3 77.3 - - - +
54C GLU* 1.3 65.0 + - - +
55C ILE* 3.9 4.9 - - + +
60C VAL* 4.9 9.4 - - + +
61C TYR 3.2 15.5 - - - +
62C LYS* 4.1 9.0 - - - +
63C ARG* 4.1 2.5 - - - +
66C MET* 5.0 0.4 - - - -
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Residues in contact with GLU 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B LYS* 2.6 35.2 + - - +
75B PHE* 3.6 27.3 - - + -
32C HIS* 4.4 6.9 + - - +
33C GLU 3.6 5.8 - - - +
34C ILE* 4.4 10.0 - - + +
53C GLU* 1.3 75.9 - - - +
55C ILE* 1.3 62.1 + - - +
56C ILE* 3.7 18.4 + - + +
59C ASN 3.6 0.7 - - - +
60C VAL* 3.3 5.0 - - - +
61C TYR* 2.8 37.4 + - + +
63C ARG* 2.8 42.4 + - + +
66C MET* 4.4 2.0 - - + -
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Residues in contact with ILE 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C SER 5.6 0.7 - - - +
33C GLU* 2.9 66.7 + - + +
35C ARG* 3.9 51.4 - - + +
53C GLU* 3.9 12.1 - - + +
54C GLU* 1.3 76.7 - - - +
56C ILE* 1.3 66.3 + - - +
57C ASP 4.2 0.2 - - - -
58C GLY* 4.1 24.2 - - - +
59C ASN 3.3 6.3 - - - +
60C VAL* 4.5 5.2 - - + -
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Residues in contact with ILE 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B LYS* 3.4 28.0 - - - +
32C HIS* 6.1 1.8 - - - +
54C GLU* 3.7 17.0 - - + +
55C ILE* 1.3 79.1 - - - +
57C ASP* 1.3 88.9 + - - +
59C ASN* 2.7 27.7 + - - +
61C TYR* 3.7 34.6 + - + +
63C ARG* 5.0 2.0 - - - +
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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