Contacts of the strand formed by residues 51 - 59 (chain C) in PDB entry 3IML
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 51 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94A LEU* 4.3 13.7 - - + -
51B LEU* 6.5 0.7 - - + -
46C LEU* 4.8 5.8 - - + -
47C CYS* 3.3 3.5 - - - -
48C ASN* 2.9 50.2 + - - +
49C THR 3.5 0.4 + - - -
50C GLY* 1.3 78.5 - - - +
52C VAL* 1.3 73.7 + - - +
53C VAL* 3.8 25.6 - - + -
91C CYS* 4.0 3.1 - - - +
92C ALA* 3.3 26.9 - - + +
94C LEU* 4.7 0.7 - - + -
53D VAL* 4.8 5.2 - - + -
55D ALA* 5.8 0.4 - - + -
94D LEU* 4.1 21.8 - - + -
96D ALA* 4.3 18.2 - - + -
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Residues in contact with VAL 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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24C ILE* 4.7 6.5 - - + -
45C THR* 4.1 9.4 - - + -
46C LEU 3.2 8.1 - - - +
47C CYS* 3.9 13.7 - - + -
48C ASN 5.6 0.4 - - - +
51C LEU* 1.3 80.4 - - - +
53C VAL* 1.3 67.1 + - - +
54C LEU* 3.6 28.9 - - + -
70C ALA* 5.0 6.1 - - + -
74C ILE* 4.3 16.4 - - + -
91C CYS* 4.3 20.4 - - - -
92C ALA 3.0 8.5 + - - +
93C VAL* 3.4 14.1 - - + +
94C LEU* 2.8 26.9 + - - +
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Residues in contact with VAL 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C GLU 3.8 0.3 - - - +
45C THR* 3.4 5.9 - - - -
46C LEU* 2.7 52.9 + - + +
51C LEU* 3.8 25.6 - - + -
52C VAL* 1.3 77.9 - - - +
54C LEU* 1.3 71.3 + - - +
55C ALA* 4.8 1.6 - - + -
94C LEU* 3.4 31.2 - - + +
96C ALA* 5.5 0.9 - - + -
46D LEU* 4.2 26.7 - - + +
51D LEU* 5.0 2.9 - - + -
53D VAL* 4.3 15.3 - - + -
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Residues in contact with LEU 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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24C ILE* 3.9 14.4 - - + -
28C ILE* 3.9 13.7 - - + -
44C GLU 3.6 2.5 - - - -
45C THR* 3.8 17.9 - - - +
52C VAL* 3.6 25.4 - - + -
53C VAL* 1.3 76.5 - - - +
55C ALA* 1.3 61.3 + - - +
66C TYR* 3.8 36.1 - - + +
70C ALA* 4.6 3.6 - - + -
93C VAL* 4.5 9.0 - - + -
94C LEU 2.7 14.0 + - - +
95C VAL* 4.0 13.7 - - + -
96C ALA* 2.8 29.3 + - - +
97C TYR* 3.5 18.1 + - + +
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Residues in contact with ALA 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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43C ALA* 3.7 0.2 - - - -
44C GLU* 2.8 34.9 + - + +
53C VAL* 4.1 2.2 - - + -
54C LEU* 1.3 75.9 - - - +
56C GLY* 1.3 59.6 + - - +
96C ALA* 3.9 20.0 - - + +
97C TYR* 3.1 19.0 - - - -
46D LEU* 4.3 18.1 - - + +
48D ASN* 4.4 4.9 - - - +
243D CYS* 3.9 19.7 - - - -
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Residues in contact with GLY 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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42C ALA 3.4 10.8 - - - -
44C GLU* 4.5 0.9 - - - -
55C ALA* 1.3 80.0 - - - +
57C GLU* 1.3 78.4 + - - +
96C ALA 4.2 2.2 + - - -
97C TYR* 3.4 6.8 - - - +
98C ASP* 2.9 26.3 + - - +
48D ASN* 5.3 1.0 - - - +
243D CYS* 3.9 12.3 - - - +
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Residues in contact with GLU 57 (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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40C ARG 4.0 1.1 - - - +
41C VAL* 3.6 1.6 - - - -
42C ALA* 2.8 51.3 + - + +
44C GLU* 5.9 0.5 - - - +
56C GLY* 1.3 88.5 - - - +
58C ILE* 1.3 63.6 + - - +
59C THR 4.4 0.2 - - - -
98C ASP* 3.6 15.6 - - + +
48D ASN* 5.8 0.5 - - - +
241D GLY 4.0 12.4 - - - +
242D ASP* 3.5 26.5 - - - +
243D CYS* 3.0 32.3 + - - +
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Residues in contact with ILE 58 (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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28C ILE* 4.9 0.2 - - + -
32C ILE* 4.2 23.1 - - + -
40C ARG 3.4 7.6 - - - +
41C VAL* 4.5 8.7 - - + -
42C ALA 4.8 0.2 - - - +
43C ALA* 4.8 4.7 - - + -
57C GLU* 1.3 82.7 - - - +
59C THR* 1.3 64.2 + - - +
60C THR* 3.7 28.0 + - + -
66C TYR* 4.1 13.2 - - + +
97C TYR* 3.4 52.0 - - + -
98C ASP 3.0 9.7 + - - +
99C LYS* 3.1 13.9 - - + -
100C GLN* 3.0 24.8 + - - +
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Residues in contact with THR 59 (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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39C SER* 3.4 4.2 - - - -
40C ARG* 2.8 53.8 + - + +
58C ILE* 1.3 72.7 + - - +
60C THR* 1.3 63.7 + - - +
100C GLN* 3.9 22.1 + - + +
101C SER* 3.7 27.4 - - - +
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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