Contacts of the helix formed by residues 118 - 136 (chain B) 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 SER 118 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35B PHE* 3.6 3.8 - - - -
114B SER 3.6 10.6 + - - -
115B ALA 3.4 6.7 + - - +
116B LYS 3.8 0.4 - - - -
117B GLU* 1.3 86.5 + - - +
119B PRO* 1.3 68.1 - - - +
120B ASP* 4.0 9.6 - - - -
121B LYS* 3.9 14.6 - - - +
122B PHE* 2.8 26.2 + - - +
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Residues in contact with PRO 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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35B PHE* 3.6 33.4 - - + -
117B GLU 4.6 1.1 - - - +
118B SER* 1.3 85.8 - - - +
120B ASP* 1.3 62.9 + - + +
122B PHE* 3.5 2.6 + - + +
123B LEU* 3.0 34.6 + - - +
152B LEU* 4.1 13.2 - - + -
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Residues in contact with ASP 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B SER* 4.0 10.7 - - - -
119B PRO* 1.3 82.9 - - + +
121B LYS* 1.3 70.8 + - - +
123B LEU* 3.6 7.2 + - + +
124B GLU* 3.0 26.9 + - - +
149B ARG* 6.0 2.2 - - - +
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Residues in contact with LYS 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B GLN* 3.3 28.9 - - + +
114B SER* 3.1 43.0 + - - +
115B ALA* 3.6 7.4 - - - -
118B SER* 3.2 16.2 + - - +
120B ASP* 1.3 83.0 + - - +
122B PHE* 1.3 65.0 + - - +
124B GLU* 3.3 24.7 + - - +
125B VAL* 3.1 30.9 + - + +
128B TRP* 4.9 1.3 - - - -
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Residues in contact with PHE 122 (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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35B PHE* 3.6 37.0 - + + -
37B HIS* 3.7 35.4 - - + -
38B ARG* 4.9 1.3 - - - -
39B LEU* 4.1 27.8 - - + -
115B ALA* 3.6 27.0 + - + +
116B LYS* 5.5 6.3 - - + -
118B SER 2.8 19.6 + - - +
119B PRO 3.6 4.9 - - - +
121B LYS* 1.3 71.3 - - - +
123B LEU* 1.3 60.9 + - + +
125B VAL* 3.1 5.7 + - - +
126B CYS* 2.9 49.0 + - - -
148B VAL* 3.8 20.9 - - + -
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Residues in contact with LEU 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B PRO 3.0 26.1 + - - +
120B ASP* 3.6 8.5 - - - +
121B LYS 3.3 0.2 - - - -
122B PHE* 1.3 77.4 - - + +
124B GLU* 1.3 58.2 + - - +
126B CYS* 3.1 6.3 + - + +
127B THR* 2.9 34.4 + - + +
145B SER* 3.4 33.7 - - - +
148B VAL* 3.7 14.6 - - + -
149B ARG* 3.7 44.4 - - + +
152B LEU* 3.5 26.2 - - + -
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Residues in contact with GLU 124 (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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120B ASP 3.0 18.2 + - - +
121B LYS* 3.6 30.1 + - + +
122B PHE 3.3 0.2 - - - -
123B LEU* 1.3 72.4 - - - +
125B VAL* 1.3 66.7 + - - +
127B THR* 2.6 28.9 + - - +
128B TRP* 3.3 40.6 + - + +
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Residues in contact with VAL 125 (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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39B LEU* 3.6 19.3 - - + -
108B ILE* 3.6 35.4 - - + -
111B GLN* 4.0 10.8 - - + -
112B LEU* 4.8 3.6 - - + -
115B ALA* 4.1 12.6 - - + -
121B LYS* 3.1 27.2 + - + +
122B PHE* 3.6 7.2 - - - +
124B GLU* 1.3 76.6 - - - +
126B CYS* 1.3 61.9 + - - +
128B TRP* 3.0 39.6 + - + +
129B VAL* 3.2 10.6 + - - +
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Residues in contact with CYS 126 (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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27B ILE* 3.8 13.5 - - + +
39B LEU* 4.1 9.4 - - - -
122B PHE* 2.9 50.1 + - - -
123B LEU* 3.1 10.5 + - + +
125B VAL* 1.3 76.4 - - - +
127B THR* 1.3 62.8 + - - +
129B VAL* 3.2 12.5 + - - +
130B ASP* 3.1 23.6 + - - +
145B SER* 3.7 17.5 - - - -
148B VAL* 4.0 16.8 - - - -
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Residues in contact with THR 127 (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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123B LEU* 2.9 19.1 + - + +
124B GLU* 2.6 21.4 + - - +
126B CYS* 1.3 78.2 - - - +
128B TRP* 1.3 69.0 + - - +
130B ASP* 3.2 13.5 - - - +
131B GLN* 3.1 31.3 + - - +
145B SER* 3.7 16.4 - - - +
149B ARG* 6.1 4.3 - - - +
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Residues in contact with TRP 128 (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 LEU* 4.0 14.1 - - + +
107B LYS* 3.2 47.5 - - + +
108B ILE* 3.8 32.5 - - + -
111B GLN* 3.6 33.4 - - + -
121B LYS* 4.9 1.1 - - - -
124B GLU* 3.5 49.8 + - + +
125B VAL* 3.0 23.0 + - + +
127B THR* 1.3 80.6 + - - +
129B VAL* 1.3 66.3 + - - +
131B GLN* 3.2 25.3 + - - +
132B ILE* 3.0 25.6 + - - +
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Residues in contact with VAL 129 (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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25B ALA* 3.5 39.9 - - + +
26B GLN* 4.1 4.3 - - - +
27B ILE* 3.9 13.5 - - + -
39B LEU* 4.2 26.2 - - + -
41B LEU* 5.2 3.1 - - + -
108B ILE* 4.0 14.8 - - + -
125B VAL 3.2 12.1 + - - +
126B CYS* 3.2 9.4 + - - +
128B TRP* 1.3 78.2 - - - +
130B ASP* 1.3 63.3 + - - +
132B ILE* 3.2 5.2 + - - +
133B ALA* 3.1 20.8 + - - +
141B ARG* 3.8 15.3 - - - +
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Residues in contact with ASP 130 (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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126B CYS 3.1 13.3 + - - +
127B THR* 3.2 13.5 - - - +
129B VAL* 1.3 77.2 - - - +
131B GLN* 1.3 57.6 + - + +
133B ALA* 3.3 2.6 + - - +
134B ALA* 2.9 28.8 + - - +
141B ARG* 2.6 42.2 + - - +
144B THR* 3.7 2.4 - - - -
145B SER* 2.4 44.3 + - - -
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Residues in contact with GLN 131 (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 LEU* 3.6 25.5 - - + +
127B THR* 3.1 20.8 + - - +
128B TRP* 3.2 25.5 + - - +
130B ASP* 1.3 74.5 - - + +
132B ILE* 1.3 65.3 + - - +
134B ALA* 3.2 8.8 + - - +
135B LEU* 3.1 30.4 + - + +
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Residues in contact with ILE 132 (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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23B ILE* 3.6 25.6 - - + +
25B ALA* 3.5 32.3 - - + +
101B GLN* 4.0 15.0 - - + +
104B LEU* 3.5 25.6 - - + -
105B VAL* 3.7 19.3 - - + -
108B ILE* 3.7 24.9 - - + -
128B TRP 3.0 10.0 + - - +
129B VAL 3.2 6.7 + - - +
131B GLN* 1.3 75.2 - - - +
133B ALA* 1.3 62.5 + - - +
135B LEU* 3.0 10.4 + - - +
136B ASN* 3.0 25.6 + - - +
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Residues in contact with ALA 133 (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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25B ALA 5.2 4.9 - - - +
129B VAL 3.1 10.2 + - - +
130B ASP 3.7 6.3 - - - +
132B ILE* 1.3 76.6 - - - +
134B ALA* 1.3 61.6 + - - +
136B ASN* 3.2 16.3 + - - +
138B SER* 3.3 15.9 - - - +
141B ARG* 3.4 40.2 - - - +
17E A 3.5 22.9 - - - +
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Residues in contact with ALA 134 (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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130B ASP 2.9 14.3 + - - +
131B GLN* 3.5 13.5 - - - +
132B ILE 3.1 0.2 - - - -
133B ALA* 1.3 78.3 - - - +
135B LEU* 1.3 61.2 + - + +
136B ASN 3.6 5.0 - - - +
138B SER* 5.5 0.2 - - - -
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Residues in contact with LEU 135 (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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50A GLN* 5.5 4.3 + - - -
51A ARG* 5.2 5.0 + - - -
100B LYS* 3.7 50.0 - - + +
101B GLN* 3.5 28.5 + - + +
104B LEU* 3.8 18.6 - - + -
131B GLN* 3.1 16.5 + - + +
132B ILE 3.0 6.4 + - - +
134B ALA* 1.3 77.2 - - + +
136B ASN* 1.3 61.7 + - - +
137B ASP* 5.0 1.6 - - - +
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Residues in contact with ASN 136 (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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50A GLN* 6.0 0.3 + - - -
22B SER* 4.8 0.2 + - - -
23B ILE 2.9 27.0 + - - +
24B ILE* 4.5 3.0 - - - +
98B LYS* 4.9 1.6 + - - -
101B GLN* 2.8 28.6 + - - +
132B ILE* 3.0 18.1 + - - +
133B ALA 3.2 10.5 + - - +
134B ALA 3.6 5.9 - - - +
135B LEU* 1.3 80.9 - - - +
137B ASP* 1.3 62.1 + - - +
138B SER 3.0 8.7 + - - +
16E A 3.6 30.5 + - - +
17E A 3.0 28.3 + - - +
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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