Contacts of the helix formed by residues 100 - 119 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92D PHE* 4.0 1.4 - - - -
97D GLN 4.3 5.0 + - - -
98D LEU 3.3 5.1 + - - -
99D LYS* 1.3 77.6 + - - +
101D VAL* 1.3 70.9 + - + +
102D ASN* 2.9 29.8 - - - +
103D ASN* 3.2 19.5 + - - +
104D TYR* 2.7 23.6 + - - +
179D ARG* 5.0 1.3 - - - +
181D THR* 4.2 8.6 - - - +
2001D PO4 4.2 14.4 - - - +
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Residues in contact with VAL 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D THR* 1.3 75.4 - - + +
102D ASN* 1.3 61.5 + - - +
104D TYR* 3.0 9.8 - - - +
105D PHE* 3.0 35.8 + - + -
164D ASP* 3.5 24.7 - - - +
179D ARG* 3.1 43.1 - - + +
180D THR* 3.9 27.8 - - - +
181D THR* 4.1 7.2 - - + +
184D ALA* 4.4 7.6 - - + -
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Residues in contact with ASN 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D THR* 2.9 38.6 - - - +
101D VAL* 1.3 73.8 - - - +
103D ASN* 1.3 63.6 + - - +
105D PHE* 2.9 26.1 + - - +
106D LEU* 3.0 16.7 + - + +
161D ILE* 6.0 0.2 - - - +
165D ARG* 3.1 45.7 + - - +
179D ARG* 3.6 15.4 + - - +
490D GLN* 4.0 17.7 + - + +
2001D PO4 4.5 5.8 + - - -
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Residues in contact with ASN 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92D PHE* 3.5 12.0 - - + -
97D GLN 4.7 1.0 + - - -
98D LEU* 2.9 37.2 + - - +
100D THR* 3.2 21.7 + - - +
102D ASN* 1.3 82.5 - - - +
104D TYR* 1.3 57.1 + - - +
106D LEU* 3.6 18.2 - - - +
107D LEU* 2.9 26.9 + - - +
547D ASN* 4.0 6.6 + - - +
550D PHE* 3.2 35.5 - - + -
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Residues in contact with TYR 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92D PHE* 4.1 22.9 - + - -
100D THR 2.7 11.9 + - - +
101D VAL* 3.0 17.3 - - - +
103D ASN* 1.3 75.7 - - - +
105D PHE* 1.3 59.1 + - - +
107D LEU* 2.9 31.8 + - + +
108D SER 3.0 10.2 + - - -
181D THR* 3.7 40.2 + - + -
184D ALA* 3.9 11.4 - - + -
185D GLY* 4.1 17.9 - - - -
188D ILE* 3.7 22.0 - - + +
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Residues in contact with PHE 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101D VAL* 3.0 27.4 + - + -
102D ASN* 2.9 11.7 + - - +
104D TYR* 1.3 77.2 - - - +
106D LEU* 1.3 57.3 + - - +
108D SER* 3.1 6.3 + - - -
109D LEU* 3.0 33.2 + - - +
157D ASN* 4.8 1.8 - - - +
160D VAL* 3.8 22.7 - - + -
161D ILE* 3.6 35.0 - - + -
164D ASP* 2.9 42.2 - - + -
165D ARG* 4.8 2.2 - - - -
184D ALA* 3.7 33.7 - - + -
187D MET* 4.6 10.8 - - + -
188D ILE* 3.9 18.8 - - + -
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Residues in contact with LEU 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88D VAL* 4.3 2.0 - - - +
102D ASN* 3.0 17.9 + - + +
103D ASN* 3.6 31.4 - - + +
104D TYR 3.2 0.2 - - - -
105D PHE* 1.3 75.1 - - - +
107D LEU* 1.3 56.7 + - - +
109D LEU* 3.8 2.9 - - + -
110D ALA* 2.9 26.2 + - - +
161D ILE* 4.0 22.4 - - + -
165D ARG* 5.5 3.8 - - - +
491D THR* 4.0 28.3 - - + +
495D ILE* 5.1 3.6 - - + -
543D TYR* 3.3 50.4 + - + +
547D ASN* 5.1 1.8 - - - +
550D PHE* 4.5 12.6 - - + -
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Residues in contact with LEU 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88D VAL* 4.9 3.1 - - - -
89D ILE* 4.5 25.4 - - + +
92D PHE* 3.4 45.8 - - + -
93D LYS* 5.8 2.0 - - + -
103D ASN 2.9 12.1 + - - +
104D TYR* 2.9 25.4 + - + +
106D LEU* 1.3 76.0 - - - +
108D SER* 1.3 64.7 + - - +
110D ALA* 3.2 7.1 + - - +
111D CYS* 2.9 36.2 + - - -
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Residues in contact with SER 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104D TYR* 3.0 6.7 + - - -
105D PHE 3.2 2.7 - - - -
107D LEU* 1.3 77.3 - - - +
109D LEU* 1.3 57.9 + - - +
111D CYS* 2.8 27.3 + - - +
112D ALA* 3.0 13.0 + - - +
157D ASN* 2.6 38.8 + - - -
188D ILE* 3.1 40.1 - - - +
192D TRP* 3.8 5.4 + - - +
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Residues in contact with LEU 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105D PHE 3.0 16.7 + - - +
106D LEU* 3.7 2.0 - - + +
108D SER* 1.3 75.1 - - - +
110D ALA* 1.3 64.2 + - - +
111D CYS 3.1 0.3 + - - -
112D ALA* 3.1 7.9 + - - +
113D ASP* 2.9 30.1 + - - +
154D SER* 4.9 9.0 - - - +
157D ASN* 2.9 47.6 - - + +
158D LEU* 4.3 13.5 - - + -
161D ILE* 3.6 21.3 - - + -
495D ILE* 4.2 24.0 - - + -
539D ASN* 4.3 16.6 - - - +
543D TYR* 3.2 23.8 - - - +
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Residues in contact with ALA 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85D ASN* 3.5 18.2 - - - +
88D VAL* 3.5 32.3 - - + -
89D ILE* 4.1 13.6 - - + +
106D LEU 2.9 16.0 + - - +
107D LEU 3.2 10.1 + - - +
109D LEU* 1.3 75.6 - - - +
111D CYS* 1.3 56.7 + - - +
113D ASP* 4.4 0.7 - - - -
114D LEU* 2.9 30.7 + - - +
539D ASN* 6.5 0.2 - - - -
540D PRO* 5.5 0.4 - - - -
543D TYR* 4.4 3.2 + - + -
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Residues in contact with CYS 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89D ILE* 4.6 12.8 - - - -
107D LEU* 2.9 39.1 + - - -
108D SER* 2.8 16.2 + - - +
110D ALA* 1.3 74.1 - - - +
112D ALA* 1.3 63.8 + - - +
114D LEU* 3.1 5.7 + - - +
115D ILE* 3.0 27.7 + - - +
192D TRP* 4.3 12.6 - - + -
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Residues in contact with ALA 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108D SER 3.0 10.9 + - - +
109D LEU* 3.1 10.7 + - - +
111D CYS* 1.3 74.0 - - - +
113D ASP* 1.3 60.8 + - - +
115D ILE* 3.1 11.1 - - - +
116D ILE* 2.9 30.6 + - - +
150D ALA* 4.5 11.6 - - - +
151D SER* 5.7 0.2 - - - -
153D ALA 5.3 0.4 - - - -
154D SER* 4.2 28.9 - - - +
157D ASN* 5.8 1.6 - - - +
192D TRP* 3.8 16.3 - - + +
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Residues in contact with ASP 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81D THR* 3.8 1.0 - - - +
85D ASN* 3.1 32.8 + - - +
109D LEU* 2.9 19.7 + - - +
110D ALA* 4.4 0.2 - - - -
112D ALA* 1.3 80.7 - - - +
114D LEU* 1.3 57.6 + - - +
116D ILE* 2.9 22.5 - - - +
117D GLY* 2.9 11.1 + - - -
154D SER* 4.5 5.9 + - - -
536D SER* 2.8 37.4 + - - +
539D ASN* 2.7 37.4 + - - +
540D PRO* 4.0 0.2 - - - +
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Residues in contact with LEU 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82D ILE* 4.3 13.0 - - + +
85D ASN* 3.3 10.9 - - + +
86D ILE* 3.9 32.1 - - + +
89D ILE* 3.5 26.9 - - + -
110D ALA 2.9 18.3 + - - +
111D CYS* 3.7 5.2 - - - +
113D ASP* 1.3 76.6 - - - +
115D ILE* 1.3 62.9 + - + +
117D GLY* 3.0 2.1 + - - -
118D VAL* 2.9 43.5 + - + +
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Residues in contact with ILE 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111D CYS 3.0 19.5 + - - +
112D ALA* 3.1 21.5 - - - +
114D LEU* 1.3 79.9 - - + +
116D ILE* 1.3 60.0 + - - +
118D VAL* 3.6 7.6 - - + +
119D ILE* 3.5 38.7 + - + +
120D SER* 5.0 0.3 + - - -
146D ILE* 4.3 25.4 - - + +
150D ALA* 4.4 10.5 - - + -
192D TRP* 3.9 24.5 - - + -
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Residues in contact with ILE 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81D THR* 5.1 0.7 - - + -
112D ALA 2.9 12.7 + - - +
113D ASP* 2.9 32.5 - - - +
115D ILE* 1.3 78.5 - - + +
117D GLY* 1.3 58.2 + - - +
120D SER* 3.2 28.3 + - - +
121D MET* 3.3 13.7 + - + +
146D ILE* 6.2 0.9 - - - -
147D ASP* 4.1 11.0 - - - +
150D ALA* 5.2 7.0 - - + -
151D SER* 4.4 21.8 - - - -
503D TRP* 5.7 0.4 - - + -
532D CYS 4.7 4.3 - - - +
533D TYR* 3.7 35.2 - - + +
536D SER* 3.4 27.8 - - - +
2000D 0HK 4.8 1.3 - - - -
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Residues in contact with GLY 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78D ALA* 4.1 1.7 - - - +
81D THR* 4.0 8.1 - - - -
82D ILE* 3.6 10.2 - - - +
113D ASP 2.9 15.3 + - - -
114D LEU 3.0 2.7 + - - -
116D ILE* 1.3 75.8 - - - +
118D VAL* 1.3 62.9 + - - +
119D ILE 3.2 2.7 + - - -
121D MET* 3.5 35.8 - - - +
122D ASN* 3.5 12.0 + - - +
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Residues in contact with VAL 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82D ILE* 3.3 21.5 - - + +
114D LEU* 2.9 28.9 + - + +
115D ILE* 3.6 9.9 - - + +
117D GLY* 1.3 75.7 - - - +
119D ILE* 1.3 77.2 + - + +
122D ASN* 2.5 23.1 + - - +
123D LEU* 5.0 2.3 - - - +
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Residues in contact with ILE 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115D ILE* 3.5 24.5 + - + +
117D GLY 3.2 0.4 - - - -
118D VAL* 1.3 95.7 - - + +
120D SER* 1.3 70.4 + - - +
121D MET 3.5 1.1 - - - -
122D ASN* 3.2 4.2 + - - +
123D LEU* 3.1 38.8 + - + +
143D TRP* 3.7 22.0 - - + -
146D ILE* 3.8 36.1 - - + -
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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