Contacts of the helix formed by residues 100 - 119 (chain C) in PDB entry 4DAJ
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 THR 100 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92C PHE* 4.0 1.6 - - - -
97C GLN 3.8 5.7 + - - -
98C LEU 3.2 2.5 + - - -
99C LYS* 1.3 81.9 + - - +
101C VAL* 1.3 69.5 + - + +
102C ASN* 3.2 26.9 - - - +
103C ASN* 3.0 26.1 + - - +
104C TYR* 2.7 34.9 + - - +
181C THR* 4.6 12.8 - - - +
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Residues in contact with VAL 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100C THR* 1.3 77.9 - - + +
102C ASN* 1.3 65.6 + - - +
104C TYR* 2.9 18.5 + - - +
105C PHE* 3.0 36.9 + - + -
164C ASP* 4.2 1.3 - - - +
175C TYR* 5.5 0.9 - - - +
179C ARG* 3.1 50.9 - - + +
180C THR* 4.1 25.1 - - - +
181C THR* 4.6 4.8 - - + +
183C ARG* 6.4 0.2 - - + -
184C ALA* 4.4 11.0 - - + +
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Residues in contact with ASN 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100C THR* 3.2 22.4 - - - +
101C VAL* 1.3 75.1 - - - +
103C ASN* 1.3 62.2 + - - +
105C PHE* 3.1 18.3 + - - +
106C LEU* 3.0 31.3 + - + +
161C ILE* 5.9 0.2 - - - +
164C ASP* 3.8 2.6 - - - +
165C ARG* 2.9 45.0 + - - +
179C ARG* 3.3 26.6 + - - +
490C GLN* 5.5 1.8 - - - +
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Residues in contact with ASN 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C PHE* 3.6 14.4 - - + -
97C GLN 4.6 1.4 + - - -
98C LEU* 2.7 42.1 + - + +
100C THR* 3.0 24.9 + - - +
101C VAL 3.2 0.6 - - - -
102C ASN* 1.3 76.9 - - - +
104C TYR* 1.3 59.3 + - - +
106C LEU* 3.7 21.7 - - - +
107C LEU* 2.9 27.2 + - - +
490C GLN* 5.0 1.7 + - - -
547C ASN* 4.4 14.5 + - - +
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Residues in contact with TYR 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C PHE* 3.9 24.9 - + - -
100C THR 2.7 13.0 + - - +
101C VAL* 3.0 14.4 - - - +
103C ASN* 1.3 74.5 - - - +
105C PHE* 1.3 63.2 + - - +
107C LEU* 3.0 17.0 + - + +
108C SER* 3.0 20.8 + - - -
181C THR* 4.0 28.2 + - + -
184C ALA* 3.5 21.3 - - + -
185C GLY* 3.3 30.4 - - - -
188C ILE* 3.9 12.3 - - + +
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Residues in contact with PHE 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101C VAL* 3.0 35.4 + - + -
102C ASN* 3.2 14.6 - - - +
104C TYR* 1.3 75.8 - - - +
106C LEU* 1.3 63.5 + - - +
108C SER* 2.9 14.4 + - - -
109C LEU* 3.0 10.4 + - - +
157C ASN* 3.5 10.4 - - - +
160C VAL* 4.0 24.7 - - + -
161C ILE* 3.6 32.8 - - + -
164C ASP* 3.4 37.7 - - + -
165C ARG* 5.4 0.2 - - - -
175C TYR* 5.1 2.5 - - - -
179C ARG* 4.3 0.2 - - - -
184C ALA* 3.8 26.5 - - + -
187C MET* 5.6 6.1 - - + -
188C ILE* 4.0 20.2 - - + -
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Residues in contact with LEU 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C VAL* 5.1 0.9 - - + -
102C ASN* 3.0 18.7 + - + +
103C ASN* 3.8 23.8 - - - +
104C TYR 3.3 0.2 - - - -
105C PHE* 1.3 75.0 - - - +
107C LEU* 1.3 64.1 + - - +
109C LEU* 3.2 3.9 + - + -
110C ALA* 2.9 13.0 + - - +
161C ILE* 3.8 26.0 - - + -
165C ARG* 5.5 5.4 - - - +
490C GLN* 5.6 2.9 - - - +
491C THR* 4.4 23.8 - - + +
495C ILE* 5.1 2.7 - - + -
543C TYR* 2.7 57.9 + - + +
547C ASN* 5.6 2.0 - - - +
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Residues in contact with LEU 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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88C VAL* 4.7 4.9 - - - +
89C ILE* 4.0 26.5 - - + +
92C PHE* 3.3 48.2 - - + -
93C LYS* 6.1 1.1 - - + -
103C ASN 2.9 15.3 + - - +
104C TYR* 3.1 19.1 - - + +
106C LEU* 1.3 75.9 - - - +
108C SER* 1.3 58.6 + - - +
110C ALA* 2.8 24.4 + - - +
111C CYS* 2.9 30.5 + - - -
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Residues in contact with SER 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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104C TYR 3.0 4.4 + - - -
105C PHE 2.9 7.2 + - - -
107C LEU* 1.3 78.2 - - - +
109C LEU* 1.3 63.2 + - - +
111C CYS* 2.8 23.7 + - - +
112C ALA* 3.0 13.0 + - - +
157C ASN* 2.7 28.1 + - - -
188C ILE* 3.4 38.1 - - - +
192C TRP* 3.6 10.4 + - - -
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Residues in contact with LEU 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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105C PHE 3.0 7.5 + - - +
106C LEU* 3.4 7.6 - - + +
108C SER* 1.3 75.3 - - - +
110C ALA* 1.3 52.2 + - - +
112C ALA* 3.4 4.6 + - - +
113C ASP* 2.7 43.5 + - - +
154C SER* 3.7 17.7 - - - +
157C ASN* 3.2 36.3 - - + +
158C LEU* 3.5 25.6 - - + -
161C ILE* 3.5 27.1 - - + -
495C ILE* 4.4 10.8 - - + -
539C ASN* 5.1 6.7 - - - +
543C TYR* 3.1 25.6 - - + +
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Residues in contact with ALA 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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85C ASN* 3.6 13.1 - - - +
88C VAL* 3.4 39.5 - - + -
89C ILE* 4.4 9.7 - - + +
106C LEU 2.9 7.3 + - - +
107C LEU* 2.8 12.7 + - - +
109C LEU* 1.3 73.8 - - - +
111C CYS* 1.3 58.4 + - - +
113C ASP* 3.9 7.6 - - - -
114C LEU* 2.9 28.8 + - - +
543C TYR* 4.0 5.3 + - + -
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Residues in contact with CYS 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C ILE* 4.1 13.2 - - + -
107C LEU* 2.9 37.6 + - - -
108C SER* 2.8 15.9 + - - +
110C ALA* 1.3 74.5 - - - +
112C ALA* 1.3 66.3 + - - +
114C LEU* 3.0 8.1 + - - +
115C ILE* 2.9 24.3 + - - +
192C TRP* 4.5 11.9 - - + -
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Residues in contact with ALA 112 (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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108C SER 3.0 10.9 + - - +
109C LEU* 3.7 8.7 - - - +
111C CYS* 1.3 75.2 - - - +
113C ASP* 1.3 65.0 + - - +
115C ILE* 3.0 13.9 - - - +
116C ILE* 2.9 25.0 + - - +
150C ALA* 4.0 22.1 - - - +
153C ALA* 5.4 0.7 - - + -
154C SER* 4.2 19.1 - - - +
157C ASN* 6.1 1.3 - - - +
192C TRP* 4.2 16.0 - - + -
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Residues in contact with ASP 113 (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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81C THR* 3.7 1.9 - - - +
85C ASN* 3.2 28.7 + - - +
109C LEU* 2.7 29.2 + - - +
110C ALA* 3.9 3.3 + - - +
112C ALA* 1.3 74.8 - - - +
114C LEU* 1.3 57.2 + - - +
116C ILE* 2.9 23.2 - - - +
117C GLY* 3.0 10.6 + - - -
154C SER* 4.2 9.5 + - - -
536C SER* 2.7 38.3 + - - +
539C ASN* 3.2 30.8 + - - +
543C TYR* 5.0 0.9 + - - -
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Residues in contact with LEU 114 (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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82C ILE* 4.7 10.0 - - + +
85C ASN* 3.3 17.5 - - + +
86C ILE* 3.7 33.7 - - + +
89C ILE* 3.8 23.1 - - + -
110C ALA 2.9 19.6 + - - +
111C CYS* 3.0 7.4 + - - +
113C ASP* 1.3 76.6 - - - +
115C ILE* 1.3 62.6 + - + +
117C GLY* 3.2 1.8 + - - -
118C VAL* 2.9 38.7 + - + +
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Residues in contact with ILE 115 (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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111C CYS 2.9 14.6 + - - +
112C ALA* 3.0 24.5 - - - +
114C LEU* 1.3 77.7 - - + +
116C ILE* 1.3 65.3 + - - +
118C VAL* 3.2 11.7 - - + +
119C ILE* 3.2 29.1 + - + +
120C SER* 4.1 0.7 + - - -
146C ILE* 3.8 32.7 - - + +
150C ALA* 4.0 17.3 - - + -
192C TRP* 4.4 14.8 - - + -
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Residues in contact with ILE 116 (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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81C THR* 5.3 0.9 - - + -
112C ALA 2.9 15.6 + - - +
113C ASP* 2.9 28.7 - - - +
115C ILE* 1.3 77.3 - - - +
117C GLY* 1.3 62.1 + - - +
120C SER* 3.3 34.2 + - - +
121C MET* 3.2 15.0 + - + +
146C ILE* 6.3 0.7 - - - -
147C ASP* 4.1 10.8 - - - +
150C ALA* 5.0 9.4 - - + -
151C SER* 5.3 10.5 - - - -
503C TRP* 6.5 1.1 - - + -
532C CYS 4.8 3.8 - - - +
533C TYR* 3.6 33.0 - - + -
536C SER* 4.0 23.6 - - - +
2000C 0HK 5.3 2.7 - - - -
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Residues in contact with GLY 117 (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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78C ALA* 4.3 4.5 - - - +
81C THR* 4.2 4.7 - - - -
82C ILE* 3.7 15.9 - - - +
113C ASP 3.0 17.0 + - - -
114C LEU 3.6 3.4 - - - -
116C ILE* 1.3 79.1 - - - +
118C VAL* 1.3 61.3 + - - +
121C MET* 3.4 38.2 - - - +
122C ASN* 4.4 3.5 + - - -
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Residues in contact with VAL 118 (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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82C ILE* 3.9 11.4 - - + +
114C LEU* 2.9 29.1 + - + +
115C ILE* 3.2 21.1 - - + +
117C GLY* 1.3 77.4 - - - +
119C ILE* 1.3 74.6 + - + +
122C ASN* 2.7 27.8 + - - +
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Residues in contact with ILE 119 (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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115C ILE* 3.2 13.8 + - + +
118C VAL* 1.3 97.8 - - + +
120C SER* 1.3 73.7 + - - +
121C MET 3.4 1.6 - - - -
122C ASN* 2.9 13.0 + - - +
123C LEU* 3.1 44.4 - - + +
143C TRP* 4.2 5.4 - - + -
146C ILE* 4.0 35.2 - - + -
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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
------------------------------------------------------------
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