Contacts of the helix formed by residues 106 - 125 (chain A) in PDB entry 1VJZ
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 ASP 106 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101A THR* 4.0 19.8 - - - +
102A ASN* 2.9 22.9 + - + +
103A LEU 3.8 0.8 + - - -
105A LYS* 1.3 76.1 - - + +
107A GLU* 1.3 65.5 + - - +
108A THR* 3.1 15.2 + - - -
109A ALA* 3.1 27.2 + - + +
110A GLN* 3.0 24.4 + - - +
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Residues in contact with GLU 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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105A LYS 3.5 6.5 + - - +
106A ASP* 1.3 71.5 + - - +
108A THR* 1.3 59.7 + - - +
110A GLN* 3.4 12.1 + - - +
111A GLU* 2.9 45.3 + - + +
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Residues in contact with THR 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A PRO* 4.8 9.6 - - + -
57A PHE* 3.9 23.2 - - + -
106A ASP* 3.1 10.2 + - - -
107A GLU* 1.3 78.5 - - - +
109A ALA* 1.3 60.5 + - - +
111A GLU* 3.1 13.7 + - - +
112A ALA* 2.9 28.5 + - - +
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Residues in contact with ALA 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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56A PRO* 5.7 2.5 - - - -
89A PRO* 3.9 16.7 - - - +
101A THR* 4.0 16.2 - - + +
103A LEU* 3.7 27.0 - - - +
106A ASP* 3.1 25.3 + - + +
108A THR* 1.3 74.9 - - - +
110A GLN* 1.3 52.6 + - - +
112A ALA* 3.3 8.2 + - - +
113A PHE* 2.8 34.7 + - - +
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Residues in contact with GLN 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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103A LEU* 3.0 34.9 + - - +
104A TRP* 3.3 20.6 + - - +
105A LYS 3.9 6.8 + - - +
106A ASP 3.0 13.0 + - - +
107A GLU* 3.6 12.4 - - - +
109A ALA* 1.3 74.5 - - - +
111A GLU* 1.3 65.2 + - - +
113A PHE* 3.3 2.4 + - - +
114A ILE* 3.0 30.3 + - - +
152A ASP* 5.0 2.4 + - - +
155A SER* 5.9 0.6 + - - -
156A LEU* 3.6 26.7 - - + +
159A ARG* 2.4 40.1 + - - +
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Residues in contact with GLU 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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57A PHE* 3.8 19.8 - - + -
107A GLU* 2.9 38.5 + - + +
108A THR* 3.1 14.4 + - - +
110A GLN* 1.3 75.9 - - - +
112A ALA* 1.3 57.5 + - - +
114A ILE* 3.4 8.3 + - - +
115A HIS* 2.9 28.8 + - - +
159A ARG* 5.6 4.2 - - - +
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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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56A PRO* 3.7 39.7 - - + +
57A PHE* 3.4 21.0 - - + -
89A PRO* 3.8 5.8 - - + -
108A THR 2.9 13.0 + - - +
109A ALA 3.4 8.3 - - - +
111A GLU* 1.3 74.0 - - - +
113A PHE* 1.3 59.9 + - - +
115A HIS* 3.2 1.7 + - - +
116A HIS* 2.9 37.2 + - - -
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Residues in contact with PHE 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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85A LEU* 4.1 2.5 - - + -
88A ALA* 3.5 30.3 - - + -
89A PRO* 4.4 8.6 - - + +
103A LEU* 3.6 20.6 - - + -
109A ALA 2.8 20.3 + - - +
110A GLN 3.4 4.5 - - - +
112A ALA* 1.3 71.6 - - - +
114A ILE* 1.3 56.7 + - - +
116A HIS* 3.3 5.5 + - - +
117A TRP* 3.0 40.7 + + - -
136A LEU* 3.4 36.8 - - + -
137A ILE* 4.1 14.8 - - + -
156A LEU* 4.0 23.1 - - + -
157A ILE* 5.3 3.8 - - + -
160A THR* 3.3 35.2 - - + -
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Residues in contact with ILE 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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110A GLN 3.0 18.1 + - - +
111A GLU* 3.8 6.7 - - - +
113A PHE* 1.3 74.0 - - + +
115A HIS* 1.3 55.8 - - - +
117A TRP* 3.2 6.2 + - - +
118A SER* 2.7 39.5 + - - -
156A LEU* 4.4 3.6 - - + -
159A ARG* 3.5 48.0 - - + +
160A THR* 3.6 23.3 - - + +
163A GLU* 3.5 35.4 - - + +
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Residues in contact with HIS 115 (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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57A PHE* 3.0 55.3 + + + -
59A ILE* 3.6 21.3 - - + +
111A GLU 2.9 18.5 + - - +
112A ALA 3.3 7.6 - - - +
114A ILE* 1.3 77.1 - - - +
116A HIS* 1.3 63.5 + + - +
118A SER* 3.4 6.9 + - - -
119A PHE* 3.1 22.3 + - - +
122A ARG* 5.3 6.1 + - - -
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Residues in contact with HIS 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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47A HIS* 4.4 4.7 - + + -
50A TRP* 2.8 37.2 + + + +
51A SER* 3.4 20.9 + - - -
56A PRO 2.6 27.6 + - - -
57A PHE* 4.4 0.8 - - - -
58A ILE 3.4 10.7 + - - -
59A ILE* 3.6 14.4 - - + +
85A LEU* 4.7 14.8 - - + -
89A PRO* 4.0 14.4 - - + +
112A ALA 2.9 30.8 + - - +
113A PHE* 3.7 4.9 - - - +
115A HIS* 1.3 78.8 - + - +
117A TRP* 1.3 65.4 + - - +
119A PHE* 3.2 4.5 + - - +
120A ILE* 3.1 32.2 + - + +
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Residues in contact with TRP 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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45A MSE 5.2 0.4 - - + -
83A ILE* 3.7 25.8 - - + -
84A SER 4.9 0.2 - - - -
85A LEU* 3.5 25.7 - - + +
113A PHE* 3.0 42.2 + + - +
114A ILE 3.9 3.6 - - - +
116A HIS* 1.3 76.2 - - - +
118A SER* 1.3 56.7 + - - +
120A ILE* 3.3 30.3 + - + +
121A ALA* 2.8 31.5 + - - +
134A PHE* 3.4 42.6 - + + -
135A ASN 3.3 20.2 - - - -
136A LEU* 2.9 30.8 + - + +
160A THR* 3.9 22.2 - - + -
164A ILE* 4.0 11.5 - - + +
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Residues in contact with SER 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 ILE* 2.7 25.4 + - - -
115A HIS* 3.6 8.5 - - - -
116A HIS 3.1 0.2 - - - -
117A TRP* 1.3 72.2 - - - +
119A PHE* 1.3 59.1 + - - +
121A ALA* 3.3 2.2 + - - +
122A ARG* 2.9 42.2 + - - +
163A GLU* 5.4 6.5 + - - +
164A ILE* 5.1 2.9 - - - +
167A ILE* 3.1 26.3 - - - +
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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
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50A TRP* 5.9 0.9 - - - -
59A ILE* 3.5 40.6 - - + -
61A GLU* 3.6 38.8 - - + -
64A PHE* 3.5 35.0 - + - -
115A HIS 3.1 7.6 + - - +
116A HIS 3.5 4.5 - - - +
118A SER* 1.3 75.5 - - - +
120A ILE* 1.3 69.8 + - + +
122A ARG* 3.3 33.1 + - - +
123A ARG* 2.9 50.0 + - + +
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Residues in contact with ILE 120 (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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45A MSE 4.1 22.0 - - + -
50A TRP* 4.6 3.8 - - + -
64A PHE* 4.1 22.9 - - + -
83A ILE* 3.6 28.3 - - + -
85A LEU* 4.6 9.6 - - + -
116A HIS* 3.1 18.9 + - + +
117A TRP* 3.7 36.6 - - + +
118A SER 3.2 0.2 - - - -
119A PHE* 1.3 81.8 - - + +
121A ALA* 1.3 64.9 + - - +
123A ARG* 3.1 4.5 + - - +
124A TYR* 3.0 33.6 + - + +
134A PHE* 3.8 6.7 - - + -
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Residues in contact with ALA 121 (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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117A TRP 2.8 18.2 + - - +
118A SER 3.5 4.7 - - - +
120A ILE* 1.3 76.0 - - - +
122A ARG* 1.3 57.7 + - - +
124A TYR 3.8 0.5 - - - -
125A LYS* 3.0 31.0 + - - +
134A PHE* 3.8 14.0 - - + -
164A ILE* 4.1 26.9 - - + +
167A ILE* 3.8 24.4 - - + +
168A ASP* 4.7 5.9 - - + +
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Residues in contact with ARG 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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59A ILE* 5.9 0.2 - - - +
115A HIS* 5.3 5.9 + - - -
118A SER* 2.9 25.7 + - - +
119A PHE* 3.5 39.6 + - - +
120A ILE 3.2 0.2 - - - -
121A ALA* 1.3 77.2 - - - +
123A ARG* 1.3 63.6 + - - +
124A TYR 3.4 0.2 + - - -
125A LYS* 3.7 13.4 + - - +
167A ILE* 3.8 28.7 - - + -
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Residues in contact with ARG 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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61A GLU* 3.8 31.1 + - - +
64A PHE* 3.4 20.7 - - - +
65A GLU* 3.7 22.4 - - - +
68A ASP* 2.8 38.1 + - - -
119A PHE* 2.9 33.6 + - + +
120A ILE* 3.1 6.0 + - - +
122A ARG* 1.3 79.2 - - - +
124A TYR* 1.3 85.8 + - + +
125A LYS 3.8 2.1 + - - +
127A ILE* 5.5 0.2 - - - +
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Residues in contact with TYR 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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64A PHE* 3.6 10.4 + + - -
67A ILE* 3.4 20.9 - - + +
68A ASP* 2.5 35.7 + - - -
71A ILE* 3.4 26.2 - - + -
83A ILE* 4.2 10.1 - - + -
120A ILE* 3.0 40.0 + - + +
121A ALA 3.8 0.4 - - - -
123A ARG* 1.3 97.4 + - + +
125A LYS* 1.3 67.5 + - - +
127A ILE* 3.0 34.0 + - + +
132A LEU* 3.4 20.2 - - + -
134A PHE* 4.5 2.9 - - + -
171A ARG* 2.9 22.5 + - - +
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Residues in contact with LYS 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 ALA 3.0 16.9 + - - +
122A ARG* 3.8 11.2 - - + +
123A ARG 3.5 3.7 - - - +
124A TYR* 1.3 79.3 - - - +
126A GLY* 1.3 63.4 + - - +
127A ILE* 4.7 1.4 - - - +
166A LYS 5.2 0.8 + - - -
167A ILE* 2.9 40.7 + - + +
168A ASP* 3.6 15.9 - - - +
169A PRO* 6.1 0.4 - - - -
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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
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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