Contacts of the helix formed by residues 100 - 119 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A PHE* 4.1 1.6 - - - -
97A GLN 3.9 6.8 + - - -
98A LEU 3.3 3.8 + - - -
99A LYS* 1.3 77.7 + - - +
101A VAL* 1.3 72.4 + - + +
102A ASN* 3.1 32.7 + - - +
103A ASN* 3.8 15.5 + - - -
104A TYR* 2.9 28.6 + - - +
179A ARG* 5.5 0.9 - - - +
181A THR* 3.7 14.7 - - - +
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Residues in contact with VAL 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A THR* 1.3 79.7 - - + +
102A ASN* 1.3 57.2 + - - +
104A TYR* 2.8 31.7 + - - +
105A PHE* 3.0 35.3 + - + -
164A ASP* 4.2 2.5 - - - +
179A ARG* 3.1 42.8 - - + +
180A THR* 3.8 33.2 - - - +
181A THR* 4.1 5.4 - - + +
184A ALA* 4.0 9.4 - - + -
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Residues in contact with ASN 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A THR* 3.1 33.7 - - - +
101A VAL* 1.3 73.5 - - - +
103A ASN* 1.3 68.4 + - - +
105A PHE* 3.2 16.3 + - - +
106A LEU* 3.0 33.8 + - + +
161A ILE* 5.3 0.6 - - - +
164A ASP* 5.2 2.9 - - - +
165A ARG* 3.8 32.5 + - + +
179A ARG* 3.5 18.0 + - - +
490A GLN* 5.0 5.9 + - - +
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Residues in contact with ASN 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A PHE* 3.2 16.6 - - + -
97A GLN 4.3 1.8 + - - -
98A LEU* 2.8 46.5 + - - +
100A THR* 3.8 15.1 + - - +
101A VAL 3.3 0.4 - - - -
102A ASN* 1.3 87.9 + - - +
104A TYR* 1.3 56.5 + - - +
106A LEU* 3.3 15.3 + - - +
107A LEU 2.9 21.8 + - - -
490A GLN* 5.3 2.6 - - - +
547A ASN* 4.7 6.4 + - - +
550A PHE* 4.0 25.4 - - + -
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Residues in contact with TYR 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A PHE* 4.0 20.4 - + - -
93A LYS* 6.0 3.6 - - - -
99A LYS* 6.4 0.2 - - - -
100A THR 2.9 13.8 + - - +
101A VAL* 2.8 18.9 + - - +
103A ASN* 1.3 74.6 - - - +
105A PHE* 1.3 62.2 + - - +
107A LEU* 3.0 26.8 + - + +
108A SER 3.0 9.7 + - - -
181A THR* 3.8 34.2 + - + -
184A ALA* 4.0 12.6 - - + -
185A GLY* 3.6 28.4 - - - -
188A ILE* 3.7 19.3 - - + +
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Residues in contact with PHE 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A VAL* 3.0 35.7 + - + -
102A ASN* 3.2 13.0 + - - +
104A TYR* 1.3 75.4 - - - +
106A LEU* 1.3 58.7 + - - +
108A SER* 3.0 6.1 + - - -
109A LEU* 2.9 25.6 + - - +
157A ASN* 3.3 8.0 - - - +
160A VAL* 3.7 25.1 - - + -
161A ILE* 3.5 34.8 - - + -
164A ASP* 3.6 27.8 - - + -
184A ALA* 3.6 32.5 - - + -
187A MET* 4.7 9.4 - - + -
188A ILE* 3.4 28.9 - - + -
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Residues in contact with LEU 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A VAL* 4.9 1.3 - - + -
102A ASN* 3.0 20.1 + - + +
103A ASN* 3.6 21.8 - - - +
104A TYR 3.1 0.2 - - - -
105A PHE* 1.3 76.0 - - - +
107A LEU* 1.3 57.6 + - - +
109A LEU* 4.1 4.0 - - + -
110A ALA* 3.0 17.0 + - - +
161A ILE* 3.9 23.3 - - + -
165A ARG* 6.0 4.0 - - - +
490A GLN* 5.9 1.6 - - - +
491A THR* 4.5 16.4 - - + +
495A ILE* 5.1 6.5 - - + -
543A TYR* 2.7 65.8 + - + +
547A ASN* 5.7 2.2 - - - +
550A PHE* 4.8 13.2 - - + -
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Residues in contact with LEU 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A VAL* 4.7 6.0 - - + +
89A ILE* 5.1 10.7 - - + +
92A PHE* 3.5 42.2 - - + -
93A LYS* 3.6 30.5 - - + +
103A ASN 2.9 14.2 + - - +
104A TYR* 3.0 24.0 + - + +
106A LEU* 1.3 73.2 - - - +
108A SER* 1.3 73.4 + - - +
110A ALA* 3.2 7.9 + - - +
111A CYS* 2.9 35.4 + - - +
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Residues in contact with SER 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A TYR 3.0 5.7 + - - -
105A PHE 3.0 10.4 + - - -
107A LEU* 1.3 82.2 - - - +
109A LEU* 1.3 63.5 + - - +
111A CYS* 2.9 17.7 + - - +
112A ALA* 3.0 12.2 + - - +
157A ASN* 2.6 32.0 + - - -
188A ILE* 3.3 33.5 - - - +
192A TRP* 3.7 9.1 + - - +
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Residues in contact with LEU 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A PHE 2.9 8.0 + - - +
106A LEU* 3.7 4.0 - - + +
107A LEU 3.2 0.2 - - - -
108A SER* 1.3 75.4 - - - +
110A ALA* 1.3 65.7 + - - +
112A ALA* 2.9 17.8 + - + +
113A ASP* 2.9 23.0 + - - +
154A SER* 3.7 40.2 - - - +
157A ASN* 3.9 19.1 - - + +
158A LEU* 3.6 27.4 - - + -
161A ILE* 3.9 14.1 - - + -
495A ILE* 4.2 11.2 - - + -
539A ASN* 5.5 7.4 - - + +
543A TYR* 3.1 23.6 - - + +
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Residues in contact with ALA 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A ASN* 3.4 27.1 - - - +
88A VAL* 3.4 45.5 - - + -
89A ILE* 4.9 5.4 - - + -
106A LEU 3.0 11.9 + - - +
107A LEU 3.6 4.0 - - - +
109A LEU* 1.3 75.6 - - - +
111A CYS* 1.3 56.8 + - - +
113A ASP* 4.2 3.6 + - - -
114A LEU* 2.9 23.4 + - - +
540A PRO* 5.6 0.2 - - - -
543A TYR* 4.0 4.9 + - + -
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Residues in contact with CYS 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A ILE* 4.0 23.3 - - - -
107A LEU* 2.9 29.7 + - - +
108A SER* 2.9 16.8 + - - +
110A ALA* 1.3 75.2 - - - +
112A ALA* 1.3 64.3 + - - +
114A LEU* 3.0 8.5 + - - +
115A ILE* 2.9 25.9 + - - +
192A TRP* 4.8 7.9 - - + -
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Residues in contact with ALA 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A SER 3.0 8.5 + - - +
109A LEU* 2.9 14.7 + - - +
111A CYS* 1.3 71.1 - - - +
113A ASP* 1.3 60.8 + - - +
115A ILE* 3.0 14.1 - - - +
116A ILE* 2.9 32.0 + - - +
150A ALA* 4.4 9.0 - - - +
153A ALA 5.4 0.2 - - - -
154A SER* 4.3 27.1 - - - +
157A ASN* 6.5 0.2 - - + -
192A TRP* 4.0 20.2 - - + -
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Residues in contact with ASP 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A THR* 3.6 2.4 - - - +
85A ASN* 3.0 34.2 + - - +
109A LEU* 2.9 23.0 + - - +
110A ALA* 3.6 3.0 - - - +
112A ALA* 1.3 80.3 - - - +
114A LEU* 1.3 57.4 + - - +
116A ILE* 2.9 8.3 - - - +
117A GLY* 2.9 24.1 + - - -
154A SER* 4.7 6.6 + - - -
535A ASN* 4.3 1.6 - - - +
536A SER* 2.8 34.0 + - - +
539A ASN* 3.2 32.7 + - - +
540A PRO* 4.1 0.2 - - - +
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Residues in contact with LEU 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A ILE* 4.3 11.5 - - + +
85A ASN* 3.7 11.2 - - + +
86A ILE* 3.6 33.9 - - + +
89A ILE* 3.4 29.6 - - + -
110A ALA 2.9 17.2 + - - +
111A CYS* 3.0 7.6 + - - +
113A ASP* 1.3 73.4 - - - +
115A ILE* 1.3 73.9 + - + +
116A ILE 3.1 1.6 - - - -
117A GLY* 2.9 1.4 + - - -
118A VAL* 2.9 37.4 + - + +
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Residues in contact with ILE 115 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111A CYS 2.9 14.1 + - - +
112A ALA* 3.0 25.1 - - - +
114A LEU* 1.3 85.1 - - + +
116A ILE* 1.3 58.5 + - - +
118A VAL* 4.0 4.0 - - - -
119A ILE* 3.3 39.3 + - + +
146A ILE* 3.8 26.2 - - + +
150A ALA* 4.5 9.0 - - + -
192A TRP* 4.1 23.3 - - + -
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Residues in contact with ILE 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A ALA 2.9 27.2 + - - +
113A ASP* 2.9 27.4 - - - +
115A ILE* 1.3 81.1 - - + +
117A GLY* 1.3 56.1 + - - +
118A VAL 3.5 0.2 - - - -
120A SER* 3.1 39.7 + - - +
121A MET* 3.3 10.2 + - + +
146A ILE* 6.2 1.1 - - - -
147A ASP* 4.4 9.6 - - - +
150A ALA* 5.0 9.4 - - + -
151A SER* 5.0 15.5 - - - +
503A TRP* 6.4 0.4 - - + -
532A CYS 4.7 4.5 - - - +
533A TYR* 3.6 28.5 - - + -
536A SER* 3.3 24.2 - - - +
2000A 0HK 5.2 1.3 - - - -
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Residues in contact with GLY 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A ALA* 3.7 11.8 - - - +
81A THR* 4.0 4.0 - - - -
82A ILE* 3.3 18.0 - - - +
113A ASP 2.9 19.3 + - - -
114A LEU 2.9 1.1 + - - -
116A ILE* 1.3 78.9 - - - +
118A VAL* 1.3 57.7 + - - +
119A ILE 3.4 0.4 - - - -
121A MET* 3.6 21.0 - - - +
122A ASN* 3.4 17.2 - - - +
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Residues in contact with VAL 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A ILE* 3.3 20.2 - - + +
114A LEU* 2.9 29.1 + - + +
115A ILE* 3.7 8.7 - - - +
117A GLY* 1.3 75.8 - - - +
119A ILE* 1.3 78.2 + - + +
122A ASN* 2.8 25.6 + - - +
123A LEU* 5.3 1.0 - - - +
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Residues in contact with ILE 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A ILE* 3.3 34.1 + - + +
117A GLY 3.4 1.2 - - - -
118A VAL* 1.3 95.7 - - + +
120A SER* 1.3 71.7 + - - +
121A MET 3.5 0.7 - - - -
122A ASN* 3.3 2.4 + - - +
123A LEU* 3.1 40.0 + - + +
143A TRP* 4.2 16.8 - - + -
146A ILE* 4.6 28.7 - - + -
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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