Contacts of the strand formed by residues 78 - 87 (chain o) in PDB entry 4IL6
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 78 (chain o).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44o CYS* 3.2 4.0 - - - -
45o LEU* 2.6 46.0 + - + +
77o SER* 1.3 75.0 - - - +
79o ASP* 1.3 61.6 - - - +
81o ILE* 3.8 12.1 - - + -
101o ILE 3.4 9.2 - - - +
102o ASP 3.9 6.1 - - - +
103o PHE* 3.5 36.8 - - - +
104o GLN* 3.7 3.8 - - + +
120o PHE* 3.5 40.4 - - + +
121o THR* 4.0 4.5 - - - -
122o VAL* 3.7 37.2 - - + +
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Residues in contact with ASP 79 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343c ARG* 3.5 21.7 + - - +
349c ILE* 5.8 0.4 - - + -
373c ASN* 4.5 6.9 - - - +
16o ALA 5.5 2.4 - - - +
18o LYS 5.3 1.6 - - - +
42o ARG* 2.8 43.6 + - - +
43o LEU 3.5 4.9 - - - -
44o CYS* 3.4 20.5 - - - +
78o LEU* 1.3 74.4 - - - +
80o GLN* 1.3 97.9 + - + +
81o ILE* 3.1 5.1 + - - +
101o ILE* 3.0 35.5 + - + +
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Residues in contact with GLN 80 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349c ILE* 3.8 27.7 - - - +
373c ASN* 5.0 9.1 - - - +
375c LEU 3.8 7.5 + - - -
376c ASP* 3.8 7.6 - - - +
377c LEU* 2.8 55.2 + - + +
378c ASN* 4.4 5.2 + - - +
381c LYS* 6.0 0.2 + - - -
41o ALA 5.3 2.2 - - - +
42o ARG* 4.3 17.5 - - + +
43o LEU 3.6 1.4 + - - -
79o ASP* 1.3 100.0 + - - +
81o ILE* 1.3 61.7 + - - +
82o GLN* 3.8 7.4 + - - +
99o ASP 4.1 0.5 - - - +
100o GLY* 3.3 13.4 - - - -
101o ILE* 3.8 8.7 - - + +
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Residues in contact with ILE 81 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40o ILE* 4.2 1.0 - - - +
42o ARG* 3.3 7.3 - - - -
43o LEU* 2.7 60.9 + - + +
45o LEU* 4.3 7.6 - - + -
78o LEU* 3.8 29.2 - - + -
79o ASP 3.1 9.6 - - - +
80o GLN* 1.3 76.9 - - - +
82o GLN* 1.3 62.4 + - - +
95o PHE* 4.1 4.7 - - + -
97o GLU* 3.6 30.3 - - + -
99o ASP 3.3 5.6 - - - +
100o GLY* 3.9 2.5 - - - -
101o ILE 3.9 8.5 - - - +
102o ASP* 4.0 11.0 - - + -
122o VAL* 3.9 20.0 - - + -
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Residues in contact with GLN 82 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378c ASN* 3.8 20.4 + - - +
381c LYS* 4.4 17.6 + - - +
39o ARG* 2.8 23.7 + - - +
40o ILE 3.3 15.3 - - - +
41o ALA* 3.8 16.0 + - - +
80o GLN 4.7 5.9 + - - +
81o ILE* 1.3 75.7 - - - +
83o GLY* 1.3 58.8 + - - +
95o PHE* 4.1 7.2 - - - -
97o GLU* 4.1 1.4 - - - -
98o GLU* 3.0 24.8 + - + +
99o ASP* 2.9 31.4 + - + +
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Residues in contact with GLY 83 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39o ARG* 3.5 17.6 - - - +
40o ILE 2.9 27.8 + - - +
82o GLN* 1.3 78.3 - - - +
84o GLU* 1.3 63.1 + - - -
95o PHE* 3.6 8.6 - - - -
96o VAL 3.2 15.7 - - - -
98o GLU* 4.0 6.5 - - - -
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Residues in contact with GLU 84 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38o TYR 3.9 9.2 - - - +
39o ARG* 4.0 15.6 - - + +
83o GLY* 1.3 72.2 - - - -
85o LEU* 1.3 59.0 + - - +
86o LYS* 3.2 40.0 + - + +
94o THR 3.4 2.3 - - - +
95o PHE* 3.4 2.8 - - - -
96o VAL* 2.9 50.2 + - + +
98o GLU* 4.7 5.6 + - - +
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Residues in contact with LEU 85 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32o ILE* 5.1 2.0 - - + -
38o TYR* 3.1 42.8 + - + +
39o ARG* 4.3 7.9 - - - +
40o ILE* 4.4 8.3 - - + +
83o GLY 3.8 1.4 + - - -
84o GLU* 1.3 71.6 - - - +
86o LYS* 1.3 63.6 + - - +
87o VAL* 3.7 4.7 + - - +
93o LEU* 4.0 31.2 - - + -
94o THR 3.5 0.4 - - - -
95o PHE* 3.9 20.9 - - + +
136o ILE* 4.7 2.2 - - + -
142o PHE* 3.9 29.2 - - + -
243o ILE* 3.8 39.0 - - + -
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Residues in contact with LYS 86 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84o GLU* 3.2 38.1 + - - +
85o LEU* 1.3 74.4 - - - +
87o VAL* 1.3 61.0 + - - +
88o ASN* 3.9 14.4 - - - +
92o SER 3.9 0.2 - - - +
93o LEU* 3.2 7.8 - - - +
94o THR* 2.8 42.5 + - - +
96o VAL* 3.9 20.6 - - - +
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Residues in contact with VAL 87 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32o ILE* 3.9 22.4 - - + -
34o SER* 4.3 25.4 - - - +
36o GLN 4.3 10.1 - - - +
37o THR* 5.8 0.2 - - - -
38o TYR* 4.0 19.5 - - + +
85o LEU 4.3 2.5 - - - +
86o LYS* 1.3 76.9 - - - +
88o ASN* 1.3 71.1 + - - +
91o GLY* 4.8 9.4 - - - +
92o SER 3.8 3.1 - - - +
93o LEU* 3.9 23.3 - - + -
133o VAL 5.8 0.2 - - - +
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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