Contacts of the helix formed by residues 100 - 119 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92B PHE* 4.5 0.2 - - - -
97B GLN 3.7 8.7 - - - +
98B LEU 3.6 2.6 + - - -
99B LYS* 1.3 81.2 - - - +
101B VAL* 1.3 59.8 + - - +
102B ASN* 3.7 11.0 + - - -
103B ASN* 2.8 41.5 + - - +
104B TYR* 2.9 29.6 + - - +
181B THR* 4.3 12.7 - - - +
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Residues in contact with VAL 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B THR* 1.3 74.1 - - - +
102B ASN* 1.3 58.3 + - - +
104B TYR* 2.8 32.8 + - - +
105B PHE* 3.0 23.4 + - + -
164B ASP* 3.8 9.0 - - - +
175B TYR* 5.7 0.2 - - - +
179B ARG* 3.1 51.1 - - + +
180B THR* 4.7 18.2 - - - +
181B THR* 4.6 4.6 - - + +
184B ALA* 4.1 12.6 - - + +
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Residues in contact with ASN 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B THR* 4.0 11.3 + - - -
101B VAL* 1.3 76.7 - - - +
103B ASN* 1.3 68.1 + - - +
105B PHE* 3.1 15.0 + - - +
106B LEU* 3.0 31.2 + - + +
161B ILE* 6.0 0.2 - - - +
164B ASP* 4.0 3.1 - - - +
165B ARG* 3.1 47.6 + - - +
179B ARG* 3.6 22.1 + - - +
490B GLN* 5.4 1.8 - - - +
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Residues in contact with ASN 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B PHE* 3.3 14.2 - - + -
97B GLN 3.4 12.9 + - - -
98B LEU* 2.8 47.3 + - + +
100B THR* 2.8 25.9 + - - +
102B ASN* 1.3 81.6 - - - +
104B TYR* 1.3 56.8 + - - +
106B LEU* 3.7 15.6 - - - +
107B LEU* 2.9 22.3 + - - +
490B GLN* 5.6 3.5 + - - -
547B ASN* 5.7 1.7 - - - +
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Residues in contact with TYR 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B PHE* 4.0 25.4 - + - -
99B LYS* 6.2 0.2 - - + -
100B THR 2.9 14.0 + - - +
101B VAL* 2.8 16.7 + - - +
103B ASN* 1.3 74.7 - - - +
105B PHE* 1.3 57.8 + - - +
107B LEU* 2.9 31.4 + - + +
108B SER 3.0 5.9 + - - -
181B THR* 4.1 25.7 + - + -
184B ALA* 3.9 14.4 - - + -
185B GLY* 3.4 29.2 - - - -
188B ILE* 3.3 28.9 - - + +
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Residues in contact with PHE 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B VAL* 3.0 26.3 + - + -
102B ASN* 3.1 13.0 + - - +
104B TYR* 1.3 78.1 - - - +
106B LEU* 1.3 56.6 + - - +
108B SER 3.2 2.0 + - - +
109B LEU* 3.0 23.6 + - - +
157B ASN* 3.0 17.5 + - - +
160B VAL* 4.0 22.2 - - + -
161B ILE* 3.6 37.5 - - + -
164B ASP* 3.1 42.8 - - + -
165B ARG* 5.8 0.2 - - - -
175B TYR* 5.1 2.7 - - - -
184B ALA* 3.4 36.1 - - + -
187B MET* 5.3 4.9 - - + -
188B ILE* 4.3 14.4 - - + -
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Residues in contact with LEU 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B VAL* 5.0 2.7 - - + -
102B ASN* 3.0 25.1 + - + +
103B ASN* 3.8 14.6 - - - +
105B PHE* 1.3 72.5 - - - +
107B LEU* 1.3 59.6 + - - +
109B LEU* 3.8 18.6 - - + -
110B ALA* 2.9 26.0 + - - +
161B ILE* 4.4 10.3 - - + -
165B ARG* 5.9 4.0 - - - +
490B GLN* 6.1 1.6 - - - +
491B THR* 4.0 22.7 - - + -
495B ILE* 4.5 12.3 - - + -
543B TYR* 3.0 44.7 + - + -
547B ASN* 5.8 1.1 - - - +
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Residues in contact with LEU 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B VAL* 4.8 4.7 - - + -
89B ILE* 4.9 17.7 - - + +
92B PHE* 3.3 48.7 - - + -
103B ASN 2.9 13.8 + - - +
104B TYR* 2.9 24.2 + - + +
106B LEU* 1.3 73.6 - - - +
108B SER* 1.3 60.7 + - - +
110B ALA* 2.7 25.8 + - - +
111B CYS* 2.9 31.7 + - - -
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Residues in contact with SER 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B TYR 3.0 6.5 + - - -
105B PHE 3.6 6.1 - - - -
107B LEU* 1.3 81.0 - - - +
109B LEU* 1.3 63.9 + - - +
111B CYS* 3.0 9.5 + - - +
112B ALA* 2.9 22.0 + - - +
157B ASN* 2.7 26.1 + - - -
188B ILE* 3.7 31.5 - - - +
192B TRP* 3.3 19.4 + - - -
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Residues in contact with LEU 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B PHE 3.0 7.9 + - - +
106B LEU* 3.6 20.6 - - + +
107B LEU 3.2 0.2 - - - -
108B SER* 1.3 74.9 + - - +
110B ALA* 1.3 58.0 + - - +
112B ALA* 3.1 6.4 + - - +
113B ASP* 2.9 38.4 + - - +
154B SER* 3.6 24.9 - - - +
157B ASN* 3.2 26.2 - - + +
158B LEU* 3.6 27.1 - - + -
161B ILE* 3.5 28.0 - - + -
495B ILE* 4.4 7.4 - - + -
539B ASN* 5.0 9.2 - - - +
543B TYR* 3.4 13.9 - - - +
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Residues in contact with ALA 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B ASN* 3.3 23.2 - - - +
88B VAL* 3.3 41.1 - - + -
89B ILE* 4.6 7.2 - - + -
106B LEU 2.9 8.8 + - - +
107B LEU* 2.7 18.5 + - - +
109B LEU* 1.3 73.5 - - - +
111B CYS* 1.3 53.9 + - - -
113B ASP* 4.5 0.4 - - - -
114B LEU* 2.9 29.0 + - - +
543B TYR* 3.8 4.9 + - + -
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Residues in contact with CYS 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B ILE* 4.0 19.1 - - - -
107B LEU* 2.9 30.2 + - - -
108B SER* 3.0 11.6 + - - +
110B ALA* 1.3 74.5 - - - +
112B ALA* 1.3 66.9 + - - +
114B LEU* 3.1 9.4 + - - +
115B ILE* 2.9 26.5 + - - +
192B TRP* 4.7 10.8 - - + -
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Residues in contact with ALA 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B SER 2.9 11.3 + - - +
109B LEU* 3.4 11.2 - - - +
111B CYS* 1.3 77.6 - - - +
113B ASP* 1.3 66.2 + - - +
115B ILE* 3.0 10.9 - - - +
116B ILE* 2.9 24.4 + - - +
150B ALA* 4.0 22.4 - - - +
154B SER* 4.3 18.4 - - - +
157B ASN* 6.0 0.7 - - - +
192B TRP* 4.1 15.1 - - + -
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Residues in contact with ASP 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B THR* 3.5 4.5 - - - +
85B ASN* 3.0 30.3 + - - +
109B LEU* 2.9 18.0 + - - +
110B ALA* 4.5 0.5 - - - -
112B ALA* 1.3 77.5 - - - +
114B LEU* 1.3 60.0 + - - +
116B ILE* 2.7 25.9 - - - +
117B GLY 3.0 5.2 + - - -
154B SER* 4.5 8.3 + - - -
535B ASN* 5.2 0.3 - - - +
536B SER* 2.6 39.4 + - - +
539B ASN* 3.2 33.7 + - - +
543B TYR* 4.7 0.3 + - - -
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Residues in contact with LEU 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B THR* 5.1 0.9 - - - -
82B ILE* 4.5 11.0 - - + +
85B ASN* 3.0 14.0 - - + +
86B ILE* 4.5 23.6 - - + +
89B ILE* 3.5 30.7 - - + -
110B ALA 2.9 18.9 + - - +
111B CYS* 3.1 8.5 + - - +
113B ASP* 1.3 75.5 - - - +
115B ILE* 1.3 66.1 + - + +
117B GLY* 3.0 4.5 + - - -
118B VAL* 2.9 35.9 + - + +
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Residues in contact with ILE 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B CYS 2.9 14.7 + - - +
112B ALA* 3.0 21.3 - - - +
114B LEU* 1.3 78.5 - - + +
116B ILE* 1.3 65.2 + - - +
118B VAL* 3.1 29.6 - - + +
119B ILE* 3.4 17.5 + - + +
120B SER* 4.2 0.9 + - - -
146B ILE* 4.6 22.0 - - + +
150B ALA* 4.0 20.2 - - + -
192B TRP* 4.6 13.7 - - + -
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Residues in contact with ILE 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B THR* 4.9 0.9 - - + -
112B ALA 2.9 10.1 + - - +
113B ASP* 2.7 37.9 - - - +
115B ILE* 1.3 77.9 - - - +
117B GLY* 1.3 60.8 + - - +
120B SER* 3.2 17.3 + - - +
121B MET* 3.1 27.3 + - + +
146B ILE* 6.2 0.4 - - - -
147B ASP* 3.9 14.6 - - - +
150B ALA* 4.8 11.2 - - + -
151B SER* 5.4 9.2 - - - -
503B TRP* 6.1 2.0 - - + -
532B CYS 4.7 3.1 - - - +
533B TYR* 3.3 41.5 - - + -
536B SER* 3.6 24.7 - - - +
2000B 0HK 4.9 4.9 - - - -
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Residues in contact with GLY 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B ALA* 4.5 3.6 - - - +
81B THR* 4.2 6.1 - - - -
82B ILE* 4.0 10.3 - - - +
113B ASP 3.0 14.3 + - - -
114B LEU 3.4 4.0 - - - -
116B ILE* 1.3 78.9 - - - +
118B VAL* 1.3 63.4 + - - +
119B ILE 3.2 0.7 + - - -
121B MET* 3.4 37.8 + - - +
122B ASN* 4.2 8.3 + - - -
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Residues in contact with VAL 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B ILE* 3.9 13.8 - - + +
114B LEU* 2.9 19.5 + - + +
115B ILE* 3.1 30.7 - - + +
117B GLY* 1.3 75.5 - - - +
119B ILE* 1.3 75.8 + - + +
122B ASN* 3.2 20.1 + - - +
123B LEU* 5.3 0.5 - - - +
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Residues in contact with ILE 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B ILE* 3.4 13.1 + - + +
118B VAL* 1.3 99.6 - - + +
120B SER* 1.3 66.5 + - - +
121B MET 3.5 1.3 - - - -
122B ASN* 3.0 4.1 + - - +
123B LEU* 2.9 61.4 + - + +
143B TRP* 4.1 9.9 - - + -
146B ILE* 4.2 33.4 - - + -
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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