Contacts of the strand formed by residues 93 - 101 (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 93 (chain o).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32o ILE* 3.9 26.0 - - + -
38o TYR* 6.0 0.2 - - + -
85o LEU* 4.0 22.9 - - + -
86o LYS 3.2 8.3 - - - +
87o VAL* 3.9 35.7 - - + -
88o ASN* 4.0 0.2 - - - -
91o GLY 4.5 2.7 - - - +
92o SER* 1.3 75.8 - - - +
94o THR* 1.3 61.3 + - - +
95o PHE 4.2 0.4 - - - -
127o ALA 3.9 0.7 - - - +
128o SER* 3.2 4.0 - - - -
129o THR* 2.8 50.9 + - + +
133o VAL* 4.1 13.0 - - + +
136o ILE* 3.7 36.3 - - + -
142o PHE* 4.5 2.5 - - + -
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Residues in contact with THR 94 (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 3.4 2.3 - - - +
85o LEU* 4.1 2.7 - - - -
86o LYS* 2.8 47.3 + - - +
88o ASN* 2.9 31.5 + - - +
93o LEU* 1.3 70.8 - - - +
95o PHE* 1.3 63.6 + - - +
96o VAL* 3.7 11.5 + - + +
126o VAL* 3.8 25.4 - - + -
127o ALA 3.4 2.9 - - - +
128o SER* 2.7 23.8 + - - +
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Residues in contact with PHE 95 (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* 3.5 36.3 - - + -
43o LEU* 3.9 23.1 - - + -
81o ILE* 4.1 13.7 - - + -
82o GLN 4.2 0.2 - - - -
83o GLY* 3.6 31.0 - - - -
84o GLU 3.4 9.4 - - - -
85o LEU* 3.9 15.0 - - + +
93o LEU 4.2 0.4 - - - -
94o THR* 1.3 72.3 - - - +
96o VAL* 1.3 66.3 + - - +
97o GLU* 3.7 31.9 - - + -
125o LEU* 3.8 19.8 - - + +
126o VAL* 3.3 6.1 - - - -
127o ALA* 2.7 42.4 + - + +
142o PHE* 4.6 7.4 - - + -
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Residues in contact with VAL 96 (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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83o GLY* 3.2 19.6 - - - -
84o GLU* 2.9 28.8 + - + +
86o LYS* 3.9 29.8 - - - +
94o THR* 4.0 14.6 - - + +
95o PHE* 1.3 78.7 - - - +
97o GLU* 1.3 69.6 + - - +
98o GLU* 3.4 2.6 + - + +
125o LEU 3.8 2.5 - - - -
126o VAL* 4.5 17.5 - - + -
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Residues in contact with GLU 97 (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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81o ILE* 3.6 24.6 - - + +
95o PHE* 3.7 19.9 - - + -
96o VAL* 1.3 78.7 - - - +
98o GLU* 1.3 62.1 + - - +
99o ASP 3.7 15.6 + - - +
102o ASP* 2.7 36.4 - - + +
122o VAL* 4.0 13.0 - - + +
124o ASN* 2.9 31.0 + - - +
125o LEU* 2.9 28.8 + - + +
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Residues in contact with GLU 98 (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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327c ASN* 4.3 9.9 + - - +
39o ARG* 3.4 30.0 + - - +
82o GLN* 3.0 16.6 + - + +
83o GLY* 4.0 7.4 - - - -
84o GLU* 4.7 5.0 + - - +
96o VAL* 3.4 2.2 + - + +
97o GLU* 1.3 78.7 - - - +
99o ASP* 1.3 68.5 + - + +
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Residues in contact with ASP 99 (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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327c ASN* 3.4 31.7 + - - +
329c GLY 4.8 0.7 + - - -
330c SER* 3.0 29.0 + - - -
377c LEU* 5.1 1.1 - - - +
381c LYS* 2.8 37.9 + - - +
80o GLN 4.5 0.4 - - - -
81o ILE* 3.3 6.8 - - - +
82o GLN* 2.9 33.3 + - + +
97o GLU* 3.9 10.2 + - - -
98o GLU* 1.3 85.5 - - + +
100o GLY* 1.3 73.5 + - - +
102o ASP* 5.2 0.2 - - - -
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Residues in contact with GLY 100 (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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329c GLY 4.1 4.5 - - - -
330c SER* 3.3 23.9 - - - -
377c LEU* 3.9 10.5 - - - -
80o GLN 3.3 18.6 - - - -
81o ILE* 3.9 3.4 - - - -
99o ASP* 1.3 85.0 + - - +
101o ILE* 1.3 64.4 + - - -
102o ASP* 3.0 10.4 + - - +
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Residues in contact with ILE 101 (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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329c GLY* 3.7 18.6 - - - +
341c LEU* 5.6 11.0 - - + +
342c MET* 6.1 3.1 - - - -
343c ARG* 5.2 0.9 - - - +
349c ILE* 3.7 39.0 - - + -
377c LEU* 4.4 13.7 - - + -
77o SER 4.9 0.9 - - - +
78o LEU* 3.4 8.3 - - - +
79o ASP* 3.0 43.1 + - + +
80o GLN* 3.8 22.7 - - + +
81o ILE* 3.9 1.8 - - - +
100o GLY* 1.3 68.5 - - - -
102o ASP* 1.3 57.9 + - - +
103o PHE* 3.5 7.8 + - + +
104o GLN* 3.6 26.9 - - - +
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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