Contacts of the strand formed by residues 123 - 134 (chain B) in PDB entry 1VWJ
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 123 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109B LEU* 4.1 24.0 - - + -
110B LEU 3.3 4.3 - - - +
111B THR* 3.4 25.4 + - - +
120B TRP 5.2 0.8 + - - -
121B LYS* 3.4 4.7 - - - +
122B SER* 1.3 90.4 + - - +
124B LEU* 1.3 75.2 + - - +
125B VAL* 5.6 1.4 - - - +
93D SER 5.4 0.6 + - - +
94D GLY* 5.8 0.2 - - - -
107D GLN* 4.8 20.7 - - + +
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Residues in contact with LEU 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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108B TRP* 3.8 16.3 - - + -
109B LEU* 3.3 5.0 - - - -
110B LEU* 2.8 56.0 + - + +
122B SER 5.6 1.3 - - - +
123B THR* 1.3 81.9 - - - +
125B VAL* 1.3 62.9 + - - +
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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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107B GLN* 4.6 10.1 - - - +
108B TRP* 3.3 20.9 - - - +
109B LEU* 4.0 16.4 - - + -
123B THR 5.6 1.3 - - - +
124B LEU* 1.3 77.2 - - - +
126B GLY* 1.3 67.5 + - - +
109D LEU* 5.4 7.6 - - + -
125D VAL* 6.4 1.1 - - + -
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Residues in contact with GLY 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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107B GLN* 3.2 14.0 + - - -
108B TRP* 2.9 47.0 + - - +
125B VAL* 1.3 78.8 - - - +
127B HIS* 1.3 70.3 + - - -
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Residues in contact with HIS 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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24B GLN* 3.8 6.4 + - - -
106B THR 3.2 16.8 - - - +
107B GLN* 3.7 17.5 - - - +
108B TRP* 3.3 6.0 + - - +
126B GLY* 1.3 81.4 - - - +
128B ASP* 1.3 70.0 + - - +
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Residues in contact with ASP 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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23B ASN* 3.3 22.3 + - + +
24B GLN* 2.9 27.6 + - - +
25B LEU* 4.5 8.3 - - - +
43B TYR* 4.0 1.0 + - - -
92B TRP* 3.1 23.6 + - - -
104B ILE 3.8 1.2 - - - +
106B THR* 2.8 38.8 + - - +
108B TRP* 3.5 16.7 + - - -
127B HIS* 1.3 79.0 - - - +
129B THR* 1.3 65.7 + - - +
130B PHE* 3.7 18.1 - - + -
5M GLN* 4.5 4.7 + - - +
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Residues in contact with THR 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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23B ASN* 3.2 12.3 - - - -
24B GLN* 3.1 20.4 + - - +
103B ARG* 4.2 23.6 - - + -
104B ILE 3.4 4.9 - - - +
105B ASN* 3.1 28.0 + - - +
128B ASP* 1.3 77.3 + - - +
130B PHE* 1.3 64.6 + - - +
131B THR* 5.0 2.2 + - - +
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Residues in contact with PHE 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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21B TRP* 3.7 20.3 - - + -
22B TYR* 3.1 13.0 - - - +
23B ASN* 3.6 19.3 - - + -
27B SER 5.3 1.8 - - - -
29B PHE* 4.2 21.1 - + + -
43B TYR* 3.5 34.5 - + - -
75B TRP* 3.9 24.2 - + - -
92B TRP* 3.8 13.2 - + - -
103B ARG* 3.3 11.7 - - - -
104B ILE* 2.9 45.3 + - + +
106B THR* 3.8 15.9 - - + -
128B ASP* 3.7 21.5 - - + -
129B THR* 1.3 77.5 - - - +
131B THR* 1.3 62.3 + - - +
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Residues in contact with THR 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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21B TRP* 3.2 4.3 - - - -
22B TYR* 2.9 35.8 + - - +
102B ALA 4.1 4.5 - - - -
103B ARG* 3.6 35.0 + - - +
129B THR* 5.0 3.6 + - - +
130B PHE* 1.3 74.9 - - - +
132B LYS* 1.3 72.3 + - - +
133B VAL* 3.7 0.7 + - + +
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Residues in contact with LYS 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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15B ALA 3.5 3.8 + - - -
16B GLY* 2.7 34.7 + - - +
18B THR 2.8 27.2 + - - -
19B GLY* 4.1 0.9 - - - -
20B THR 3.5 10.3 - - - +
21B TRP* 3.3 32.4 - - + -
102B ALA* 3.7 17.2 + - + +
131B THR* 1.3 83.9 - - - +
133B VAL* 1.3 64.8 + - - +
134B LYS 3.5 19.5 - - - +
135B PRO* 4.4 7.0 - - - +
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Residues in contact with VAL 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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20B THR* 2.8 30.5 + - + +
22B TYR* 3.2 39.0 - - + -
131B THR 3.7 0.6 + - - +
132B LYS* 1.3 77.4 - - - +
134B LYS* 1.3 86.9 + - + +
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Residues in contact with LYS 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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19B GLY* 3.2 2.6 - - - -
20B THR* 2.8 37.9 + - + +
22B TYR* 4.0 11.3 + - - -
132B LYS* 3.5 10.3 - - - -
133B VAL* 1.3 109.2 - - + +
135B PRO* 1.3 74.7 - - + +
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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