Contacts of the helix formed by residues 96 - 110 (chain C) in PDB entry 4I6J
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 ASP 96 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95C VAL* 1.3 76.4 - - - +
97C GLN* 1.3 57.7 + - - +
98C GLY* 3.0 5.1 + - - +
99C THR* 2.4 61.1 + - - -
100C LEU* 3.0 9.8 + - - -
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Residues in contact with GLN 97 (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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36B TRP* 3.2 37.5 + - + +
95C VAL 4.1 1.0 + - - -
96C ASP* 1.3 71.7 - - - +
98C GLY* 1.3 57.1 + - - +
100C LEU* 3.2 11.2 + - + +
101C PHE* 2.8 31.5 + - - +
126C MET* 6.0 5.6 - - + -
138C THR* 3.6 29.7 + - - +
139C PHE* 3.9 12.5 - - + +
140C ASN* 5.1 7.5 + - - +
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Residues in contact with GLY 98 (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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96C ASP* 2.8 9.8 + - - +
97C GLN* 1.3 77.2 + - - +
99C THR* 1.3 58.7 + - - +
101C PHE* 3.1 27.1 - - - +
102C GLU* 3.3 10.0 + - - +
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Residues in contact with THR 99 (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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53C ALA* 5.7 8.7 - - + -
95C VAL* 3.9 14.6 - - + -
96C ASP* 2.4 40.7 + - - -
98C GLY* 1.3 69.8 - - - +
100C LEU* 1.3 53.1 + - - +
102C GLU* 3.1 5.1 + - - +
103C LEU* 2.8 50.2 + - + +
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Residues in contact with LEU 100 (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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36B TRP* 4.4 11.7 - - + -
93C LEU* 4.4 20.6 - - + +
95C VAL* 3.8 9.8 - - + +
96C ASP 3.0 8.2 + - - +
97C GLN* 3.6 13.0 - - + +
99C THR* 1.3 77.6 - - - +
101C PHE* 1.3 64.2 + - - +
103C LEU* 3.4 7.8 + - + -
104C ILE* 3.2 23.2 + - + +
119C THR* 4.3 29.4 - - + +
122C THR* 4.3 10.1 - - + -
123C VAL* 4.1 18.6 - - + -
126C MET* 4.0 29.4 - - + -
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Residues in contact with PHE 101 (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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35B ASP* 2.8 51.4 - - - -
36B TRP* 3.7 38.3 - + + -
39B LEU* 4.0 13.0 - - + -
97C GLN 2.8 13.8 + - - +
98C GLY* 3.1 19.3 - - - +
100C LEU* 1.3 77.2 - - - +
102C GLU* 1.3 56.9 + - + +
104C ILE* 3.7 4.6 + - - +
105C LEU* 3.3 42.6 + - + +
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Residues in contact with GLU 102 (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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49C ASN* 4.2 16.7 + - - +
50C VAL* 4.8 4.8 - - - +
51C ASN* 5.2 8.3 + - - +
54C ILE* 5.8 0.2 - - - +
98C GLY 3.3 7.3 + - - +
99C THR* 3.1 8.4 + - - +
101C PHE* 1.3 75.1 - - + +
103C LEU* 1.3 59.1 + - - +
104C ILE 3.0 2.0 - - - -
105C LEU* 2.8 23.3 + - + +
106C ALA* 2.5 45.4 + - - +
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Residues in contact with LEU 103 (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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53C ALA* 3.9 22.4 - - + +
54C ILE* 4.5 19.8 - - + +
57C LYS* 5.6 0.2 - - + -
92C PHE* 4.4 15.7 - - + -
93C LEU* 4.2 19.5 - - + -
95C VAL* 4.1 14.6 - - + -
99C THR* 2.8 40.2 + - + +
100C LEU* 3.5 16.8 - - - +
102C GLU* 1.3 71.4 - - - +
104C ILE* 1.3 52.1 + - - +
106C ALA* 3.5 4.8 + - - +
107C ALA* 2.6 33.0 + - - +
119C THR* 4.3 13.9 - - + +
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Residues in contact with ILE 104 (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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36B TRP* 4.8 8.1 - - + -
39B LEU* 4.6 10.1 - - + -
43B ILE* 4.1 34.4 - - + +
47B VAL* 5.5 1.8 - - + -
100C LEU* 3.2 15.1 + - + +
101C PHE* 3.8 5.4 - - - +
102C GLU 3.0 0.6 - - - -
103C LEU* 1.3 76.2 - - - +
105C LEU* 1.3 63.9 + - - +
106C ALA 3.1 1.3 - - - -
107C ALA* 2.9 25.3 + - - +
108C ASN* 3.3 8.7 + - - +
116C LEU* 4.1 4.5 - - + +
119C THR* 2.9 46.2 - - - +
120C CYS* 4.2 9.6 - - - +
123C VAL* 3.9 18.8 - - + -
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Residues in contact with LEU 105 (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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39B LEU* 3.7 30.5 - - + +
40B LEU* 5.8 2.9 - - + -
43B ILE* 5.9 1.3 - - + -
101C PHE* 3.3 35.1 + - + +
102C GLU* 2.8 28.8 + - + +
104C ILE* 1.3 79.5 - - + +
106C ALA* 1.3 54.3 + - - +
108C ASN* 2.2 34.7 + - - +
109C TYR* 3.8 10.9 - - - -
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Residues in contact with ALA 106 (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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49C ASN 5.5 0.4 - - - -
50C VAL* 3.4 29.5 - - + +
54C ILE* 4.7 14.0 - - + +
102C GLU* 2.5 34.7 + - - +
103C LEU* 3.8 6.1 - - - +
105C LEU* 1.3 71.9 - - - +
107C ALA* 1.3 66.4 + - - +
108C ASN 3.1 1.1 + - - -
109C TYR* 3.3 23.6 - - - +
110C LEU* 3.8 3.5 + - - +
112C ILE* 5.6 0.3 - - - +
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Residues in contact with ALA 107 (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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54C ILE* 6.3 1.1 - - - -
103C LEU 2.6 21.1 + - - +
104C ILE* 2.9 20.4 + - - +
106C ALA* 1.3 73.0 - - - +
108C ASN* 1.3 63.0 + - - +
110C LEU 3.2 17.0 - - - +
111C ASP 4.1 0.2 + - - -
112C ILE* 4.0 18.3 + - + +
115C LEU 4.1 7.4 - - - +
116C LEU* 3.5 34.0 - - + +
119C THR* 4.2 0.2 - - - +
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Residues in contact with ASN 108 (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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40B LEU* 4.2 21.6 - - + +
43B ILE* 4.7 15.0 - - + +
26C THR* 4.5 0.2 + - - -
104C ILE 3.3 6.3 + - - +
105C LEU* 2.2 41.1 + - - +
107C ALA* 1.3 70.4 - - - +
109C TYR* 1.3 76.0 + - - +
110C LEU 2.3 21.4 + - - -
111C ASP* 2.8 17.7 + - - +
116C LEU* 4.6 6.4 - - + +
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Residues in contact with TYR 109 (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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26C THR* 3.1 28.8 - - - +
47C LEU* 5.4 1.8 - - + -
48C PRO* 3.8 29.9 - - + +
49C ASN* 4.1 24.5 + - + +
50C VAL* 4.2 21.3 - - + -
105C LEU 3.8 15.7 - - - -
106C ALA* 3.3 14.6 - - - +
108C ASN* 1.3 91.9 + - - +
110C LEU* 1.3 59.7 + - + +
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Residues in contact with LEU 110 (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 3.8 7.2 - - - +
24C SER* 4.3 6.3 - - - +
25C VAL 3.3 23.8 - - - +
26C THR* 3.7 14.4 - - - +
27C ILE* 3.5 40.8 - - + -
47C LEU* 6.2 0.2 - - + -
58C VAL* 6.1 3.8 - - + -
106C ALA 3.8 2.2 + - - +
107C ALA 3.2 7.0 + - - +
108C ASN 2.3 11.4 + - - -
109C TYR* 1.3 75.0 - - + +
111C ASP* 1.3 83.9 + - - +
112C ILE* 2.9 21.8 - - + +
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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