Contacts of the helix formed by residues 108 - 127 (chain A) in PDB entry 3TW4
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 TRP 108 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A SER 4.4 11.2 - - - -
106A ASN* 3.9 15.5 + - - +
107A CYS* 1.3 77.5 - - - +
109A GLN* 1.3 88.2 + - + +
110A PRO* 3.0 4.1 - - - +
111A VAL* 2.8 31.7 + - + +
112A ILE* 2.9 25.4 + - + +
156A LEU* 5.3 8.3 - - + -
159A GLU* 3.1 45.8 - - + -
160A PHE* 4.1 14.8 - - + -
163A ARG* 4.6 15.5 - - + -
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Residues in contact with GLN 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A ASN* 6.0 3.4 - - + -
107A CYS* 5.1 1.3 - - - -
108A TRP* 1.3 93.2 - - + +
110A PRO* 1.3 69.1 - - + +
112A ILE* 3.1 13.5 + - + -
113A ASP* 2.7 28.7 + - + +
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Residues in contact with PRO 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A VAL* 4.6 11.2 - - + +
107A CYS* 3.5 19.3 - - + -
108A TRP 3.0 13.0 - - - +
109A GLN* 1.3 95.2 - - + +
111A VAL* 1.3 61.1 + - - +
113A ASP* 4.1 3.6 - - + +
114A TYR* 3.2 20.8 + - - +
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Residues in contact with VAL 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A MET* 5.3 17.2 - - + +
37A VAL* 6.0 5.2 - - + -
74A VAL* 5.3 4.9 - - - +
95A THR* 6.1 3.6 - - + -
108A TRP* 2.8 19.1 + - + +
110A PRO* 1.3 71.6 - - - +
112A ILE* 1.3 73.3 + - + +
114A TYR* 2.9 9.7 + - - +
115A ILE* 2.9 25.4 + - + +
164A LEU* 5.9 3.1 - - + -
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Residues in contact with ILE 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 TRP* 2.9 30.0 + - + +
109A GLN* 3.3 16.8 - - + +
111A VAL* 1.3 76.0 - - + +
113A ASP* 1.3 61.8 + - + +
115A ILE* 2.8 31.0 + - + +
116A ASP* 2.9 29.2 + - - +
163A ARG* 5.1 4.9 - - + +
164A LEU* 4.0 31.2 - - + +
167A LYS* 4.4 19.7 - - + -
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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
----------------------------------------------------------
109A GLN* 2.7 20.7 + - + +
110A PRO* 4.3 3.8 - - + +
112A ILE* 1.3 78.2 - - + +
114A TYR* 1.3 55.6 + - - +
116A ASP* 4.7 4.7 - - - +
117A SER* 2.9 27.3 + - - +
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Residues in contact with TYR 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A MET* 4.7 17.3 - - + -
74A VAL* 4.3 25.8 - - + -
76A GLN* 2.9 39.4 + - - -
93A VAL* 4.5 12.7 - - + +
110A PRO 3.2 13.3 + - - +
111A VAL* 2.9 11.6 + - - +
112A ILE 2.8 1.0 + - - -
113A ASP* 1.3 75.2 - - - +
115A ILE* 1.3 76.7 + - + +
117A SER* 3.0 12.6 + - - -
118A LYS* 2.9 27.3 + - + +
137A ASN* 5.0 7.8 + - - +
139A VAL* 4.7 17.5 - - + -
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Residues in contact with ILE 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A MET* 4.7 14.6 - - + -
111A VAL* 2.9 23.5 + - + +
112A ILE* 2.8 14.8 + - + +
114A TYR* 1.3 77.3 - - + +
116A ASP* 1.3 69.2 + - - +
118A LYS* 2.9 22.4 + - - +
119A PHE* 2.9 33.1 + - + -
139A VAL* 3.3 33.2 - - + -
164A LEU* 6.1 2.9 - - + -
167A LYS* 3.6 33.2 - - + +
168A VAL* 4.7 8.7 - - + -
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Residues in contact with ASP 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A ILE* 2.9 24.5 + - - +
113A ASP* 4.7 4.3 - - - +
115A ILE* 1.3 83.7 - - - +
117A SER* 1.3 64.5 + - - +
119A PHE* 3.8 14.8 - - - +
120A GLU* 3.0 29.9 + - - +
167A LYS* 3.3 32.7 - - - +
290A TYR* 4.1 17.2 + - + +
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Residues in contact with SER 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A ASP 2.9 19.5 + - - -
114A TYR* 3.0 21.0 + - - -
116A ASP* 1.3 77.7 - - - +
118A LYS* 1.3 68.6 + - - +
120A GLU* 3.9 8.0 - - - +
121A ASP* 2.9 27.1 + - - +
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Residues in contact with LYS 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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114A TYR* 2.9 12.9 + - + +
115A ILE* 2.9 15.9 + - - +
117A SER* 1.3 78.9 + - - +
119A PHE* 1.3 65.9 + - + +
121A ASP* 3.7 5.7 - - - +
122A TYR* 3.0 21.1 + - - +
137A ASN* 4.0 38.5 - - + +
138A ARG* 4.2 9.2 + - - -
139A VAL* 5.0 5.4 - - + -
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Residues in contact with PHE 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A ILE* 2.9 42.9 + - + +
116A ASP* 3.9 13.0 - - - +
118A LYS* 1.3 71.4 - - + +
120A GLU* 1.3 57.4 + - - +
122A TYR* 2.6 30.3 + - - +
123A LEU* 2.9 11.8 + - - -
138A ARG* 4.1 25.6 - - + -
139A VAL* 4.9 6.1 - - + -
167A LYS* 3.9 19.1 - - + -
282A THR* 4.8 9.9 - - + -
286A HIS* 4.4 14.6 - - + -
287A TYR* 4.2 25.9 - + + -
290A TYR* 3.1 47.8 - + + -
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Residues in contact with GLU 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A ASP 3.0 18.1 + - - +
117A SER* 4.9 6.2 - - - +
119A PHE* 1.3 76.7 - - - +
121A ASP* 1.3 59.4 + - - +
123A LEU* 3.8 9.0 - - + +
124A ASN* 2.9 33.1 + - + +
290A TYR* 2.8 29.6 + - - +
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Residues in contact with ASP 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A SER* 2.9 20.4 + - - +
118A LYS* 3.7 6.7 - - - +
120A GLU* 1.3 80.4 - - - +
122A TYR* 1.3 58.2 + - - +
124A ASN* 3.6 5.2 + - - +
125A ALA* 3.0 27.2 + - - +
137A ASN* 6.0 3.6 - - + +
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Residues in contact with TYR 122 (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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118A LYS 3.0 14.3 + - - +
119A PHE* 2.6 16.9 + - + +
121A ASP* 1.3 68.6 - - - +
123A LEU* 1.3 59.4 + - - +
125A ALA* 3.0 9.0 - - - +
126A GLU* 2.9 37.3 + - + +
134A MET* 5.4 11.7 - - + -
135A PRO 4.5 6.3 - - - -
136A ASP* 3.1 41.5 - - + -
137A ASN 5.1 2.9 - - - +
138A ARG* 5.8 4.5 - - + +
283A ASN* 6.1 1.2 - - + +
287A TYR* 3.1 44.9 - + - -
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Residues in contact with LEU 123 (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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119A PHE 2.9 12.4 + - - +
120A GLU* 3.8 17.9 - - + +
122A TYR* 1.3 70.3 - - - +
124A ASN* 1.3 73.0 + - + +
125A ALA 2.6 5.7 + - - -
126A GLU* 2.4 36.3 + - + +
127A SER* 3.0 21.8 + - - +
287A TYR* 3.2 26.5 - - + +
290A TYR* 5.0 7.0 - - + +
291A ARG* 4.8 19.1 - - + -
295A LEU* 5.3 11.2 - - + -
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Residues in contact with ASN 124 (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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120A GLU* 2.9 26.9 + - + +
121A ASP* 3.8 5.8 - - - +
123A LEU* 1.3 81.4 - - + +
125A ALA* 1.3 58.1 + - - +
127A SER* 4.2 5.9 - - - +
128A ARG* 3.4 38.7 + - - +
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Residues in contact with ALA 125 (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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121A ASP 3.0 14.5 + - - +
122A TYR* 3.0 16.2 - - - +
123A LEU 2.6 4.6 + - - -
124A ASN* 1.3 72.8 - - - +
126A GLU* 1.3 57.1 + - - +
127A SER 3.1 2.5 - - - -
128A ARG* 2.9 29.4 + - - +
131A ARG* 4.2 10.2 - - - +
134A MET* 4.4 22.7 - - + -
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Residues in contact with GLU 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A TYR* 2.9 26.1 + - + +
123A LEU* 2.4 30.4 + - + +
125A ALA* 1.3 69.0 - - - +
127A SER* 1.3 62.3 + - - +
128A ARG 3.4 0.2 - - - -
131A ARG* 2.7 53.4 + - + +
287A TYR* 4.1 17.4 + - - +
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Residues in contact with SER 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A LEU* 3.0 23.0 + - - +
124A ASN* 4.5 5.4 - - - -
126A GLU* 1.3 86.6 + - - +
128A ARG* 1.3 67.7 + - - +
129A VAL* 4.7 0.2 - - - -
131A ARG* 4.7 7.0 - - - +
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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
------------------------------------------------------------
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