Contacts of the helix formed by residues 120 - 136 (chain A) in PDB entry 2VBJ
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 120 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119A PRO* 1.3 81.0 - - - +
121A LYS* 1.3 57.9 + - + +
122A PHE 3.7 1.1 - - - +
123A LEU* 3.9 17.1 - - - +
124A GLU* 3.2 23.7 + - - +
149A ARG* 5.5 4.2 + - - -
151A VAL* 5.7 1.2 - - - +
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Residues in contact with LYS 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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111A GLN* 3.1 43.0 + - - +
114A SER* 3.8 31.4 + - - +
115A ALA* 4.1 4.5 - - - -
118A SER* 3.7 16.8 - - - +
119A PRO 2.8 7.1 + - - -
120A ASP* 1.3 72.0 - - + +
122A PHE* 1.3 65.9 + - - +
123A LEU 3.3 0.7 - - - -
124A GLU* 3.4 25.1 + - - +
125A VAL* 3.1 27.2 + - + +
128A TRP* 5.1 2.5 - - + -
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Residues in contact with PHE 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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35A PHE* 3.7 36.1 - + + -
37A HIS* 3.9 34.5 - - + -
38A ARG* 5.1 0.2 - - - -
39A LEU* 4.0 33.2 - - + -
115A ALA* 3.7 23.0 + - + +
116A LYS* 5.6 1.1 - - - -
118A SER 3.1 19.0 + - - +
119A PRO* 4.8 3.4 - - + -
121A LYS* 1.3 74.0 - - - +
123A LEU* 1.3 66.4 + - + +
125A VAL* 3.1 7.8 + - + +
126A CYS* 3.0 42.5 + - - -
148A VAL* 3.9 21.3 - - + -
151A VAL* 5.6 2.5 - - + -
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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 PRO* 5.3 0.2 - - - +
120A ASP* 3.9 22.6 - - - +
121A LYS 3.3 0.2 - - - -
122A PHE* 1.3 79.6 - - + +
124A GLU* 1.3 63.6 + - - +
126A CYS* 3.2 7.8 + - + +
127A THR* 3.2 29.9 + - + +
145A SER* 3.7 17.0 - - - +
146A GLU* 5.2 0.9 - - - +
148A VAL* 3.3 45.1 - - + +
149A ARG* 3.4 47.6 - - + +
151A VAL* 5.4 9.2 - - + -
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Residues in contact with GLU 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 ASP 3.2 19.4 + - - +
121A LYS* 3.4 31.5 + - + +
122A PHE 3.1 0.6 - - - -
123A LEU* 1.3 79.5 - - - +
125A VAL* 1.3 61.5 + - - +
127A THR* 2.7 28.0 + - - +
128A TRP* 3.4 37.2 + - + +
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Residues in contact with VAL 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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39A LEU* 3.5 29.4 - - + -
108A ILE* 3.7 27.8 - - + +
111A GLN* 4.3 11.0 - - + -
112A LEU* 4.9 2.2 - - + -
115A ALA* 4.1 17.0 - - + -
121A LYS* 3.1 21.0 + - + +
122A PHE* 3.1 8.5 + - - +
124A GLU* 1.3 75.8 - - - +
126A CYS* 1.3 53.6 + - - +
128A TRP* 2.8 47.2 + - + +
129A VAL* 3.1 11.4 + - + +
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Residues in contact with CYS 126 (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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27A ILE* 3.9 15.8 - - + +
39A LEU* 4.0 14.1 - - - -
122A PHE* 3.0 48.6 + - - -
123A LEU* 3.4 12.6 - - + +
124A GLU 3.1 0.4 - - - -
125A VAL* 1.3 77.1 - - - +
127A THR* 1.3 56.3 + - - +
129A VAL* 3.3 12.0 + - - +
130A ASP* 2.9 29.5 + - - +
145A SER* 3.7 19.0 - - - -
148A VAL* 4.1 8.5 - - - -
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Residues in contact with THR 127 (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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123A LEU* 3.2 18.7 + - + +
124A GLU* 2.7 23.2 + - - +
126A CYS* 1.3 76.5 - - - +
128A TRP* 1.3 70.1 + - - +
130A ASP* 3.3 12.3 - - - +
131A GLN* 3.2 26.5 + - - +
145A SER* 3.9 16.4 - - - +
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Residues in contact with TRP 128 (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 LEU* 4.1 11.6 - - + +
107A LYS* 3.2 54.4 - - + +
108A ILE* 3.8 28.3 - - + -
111A GLN* 3.5 40.2 - - + -
121A LYS* 5.1 2.9 - - - -
124A GLU* 3.5 47.2 + - + +
125A VAL* 2.8 20.5 + - + +
127A THR* 1.3 83.6 + - - +
129A VAL* 1.3 64.5 + - - +
131A GLN* 3.4 22.3 + - - +
132A ILE* 3.2 24.1 + - - +
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Residues in contact with VAL 129 (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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25A ALA* 3.4 42.0 - - + +
26A GLN 4.0 2.5 - - - +
27A ILE* 3.9 13.7 - - + -
39A LEU* 4.2 25.6 - - + -
41A LEU* 5.1 2.7 - - + -
108A ILE* 3.9 16.8 - - + -
125A VAL 3.1 11.7 + - - +
126A CYS* 3.3 9.2 - - - +
128A TRP* 1.3 73.2 - - - +
130A ASP* 1.3 65.5 + - - +
132A ILE* 3.1 4.3 + - - +
133A ALA* 3.0 20.6 + - - +
141A ARG* 3.6 15.7 - - - +
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Residues in contact with ASP 130 (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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126A CYS 2.9 14.6 + - - +
127A THR* 3.3 16.6 - - - +
129A VAL* 1.3 73.9 - - - +
131A GLN* 1.3 57.9 + - + +
133A ALA* 3.3 5.4 + - - +
134A ALA* 2.9 26.4 + - - +
141A ARG* 2.8 31.8 + - - +
144A THR* 3.7 7.0 - - - -
145A SER* 2.5 40.7 + - - -
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Residues in contact with GLN 131 (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 LEU* 3.9 25.8 - - + +
107A LYS* 5.3 2.1 + - - -
127A THR 3.2 10.2 + - - +
128A TRP* 3.4 29.8 - - - +
129A VAL 3.2 0.2 - - - -
130A ASP* 1.3 77.3 - - + +
132A ILE* 1.3 65.9 + - - +
134A ALA* 3.3 8.9 + - - +
135A LEU* 3.2 27.9 + - + +
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Residues in contact with ILE 132 (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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23A ILE 3.6 24.7 - - - +
25A ALA* 3.5 32.8 - - + +
101A GLN* 3.9 13.7 - - + +
104A LEU* 3.4 37.5 - - + -
105A VAL* 3.7 17.7 - - + -
108A ILE* 3.7 18.6 - - + -
128A TRP 3.2 4.4 + - - +
129A VAL 3.1 7.2 + - - +
131A GLN* 1.3 75.8 - - - +
133A ALA* 1.3 65.0 + - - +
135A LEU* 3.0 17.4 + - - +
136A ASN* 3.1 17.1 + - - +
17C G 5.2 0.2 - - - +
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Residues in contact with ALA 133 (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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25A ALA 5.3 1.7 + - - +
129A VAL 3.0 7.3 + - - +
130A ASP 3.5 7.0 - - - +
132A ILE* 1.3 78.3 - - - +
134A ALA* 1.3 59.8 + - - +
136A ASN* 3.3 10.0 + - - +
138A SER* 3.3 22.3 - - - -
141A ARG* 3.4 45.3 - - - +
17C G 3.5 21.1 - - - +
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Residues in contact with ALA 134 (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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130A ASP 2.9 13.2 + - - +
131A GLN* 3.5 13.5 - - - +
132A ILE 3.2 0.4 - - - -
133A ALA* 1.3 76.1 - - - +
135A LEU* 1.3 63.8 + - + +
136A ASN 3.4 6.4 - - - +
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Residues in contact with LEU 135 (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 LYS* 3.6 49.6 - - + +
101A GLN* 3.6 31.1 + - + +
104A LEU* 3.8 18.8 - - + -
131A GLN* 3.2 16.1 + - + +
132A ILE 3.0 7.3 + - - +
134A ALA* 1.3 75.8 - - + +
136A ASN* 1.3 63.1 - - - +
137A ASP* 5.0 1.6 - - - +
50B GLN* 5.4 5.0 + - - -
51B ARG* 5.3 4.7 + - - -
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Residues in contact with ASN 136 (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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22A SER* 4.9 0.4 + - - -
23A ILE* 3.0 26.0 + - - +
24A ILE* 4.5 2.6 - - - +
98A LYS* 4.8 1.4 + - - +
101A GLN* 2.8 28.4 + - - +
132A ILE* 3.1 18.8 + - - +
133A ALA 3.4 7.7 - - - +
134A ALA 3.3 6.7 - - - +
135A LEU* 1.3 81.6 - - - +
137A ASP* 1.3 63.2 + - - +
138A SER 3.1 8.1 + - - +
51B ARG* 5.8 0.2 - - - -
16C G 3.6 29.8 + - - +
17C G 2.9 27.8 + - - +
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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