Contacts of the strand formed by residues 103 - 112 (chain D) 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 ARG 103 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B GLU* 6.3 0.6 - - - +
21D TRP* 3.9 2.5 - - - -
95D GLN 4.0 0.9 - - - +
96D TYR* 3.5 2.9 - - - -
97D VAL* 2.9 60.0 + - - +
101D GLU* 3.3 38.1 + - + +
102D ALA* 1.3 77.4 - - - +
104D ILE* 1.3 68.1 + - - +
105D ASN* 3.1 28.2 + - - +
129D THR* 4.3 15.3 - - + -
130D PHE 3.3 13.2 - - - +
131D THR* 4.5 8.7 - - + -
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Residues in contact with ILE 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D ILE* 4.5 15.7 - - + -
21D TRP* 3.7 40.8 - - + +
29D PHE* 4.0 19.5 - - + -
73D LEU* 4.1 22.0 - - + -
75D TRP* 4.2 6.7 - - + -
95D GLN 3.4 10.5 - - - +
96D TYR* 4.1 9.2 - - + -
103D ARG* 1.3 79.9 - - - +
105D ASN* 1.3 62.4 - - - +
106D THR* 3.7 22.4 + - + -
128D ASP 3.9 0.7 - - - +
129D THR* 3.5 2.6 - - - -
130D PHE* 2.9 36.4 + - + -
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Residues in contact with ASN 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94D GLY* 3.1 3.6 - - - -
95D GLN* 2.9 39.9 + - + +
97D VAL* 4.6 8.8 - - - +
103D ARG* 3.1 31.8 + - - +
104D ILE* 1.3 73.0 - - - +
106D THR* 1.3 60.7 + - - +
128D ASP 4.0 1.6 - - - -
129D THR* 3.3 33.1 + - - +
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Residues in contact with THR 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75D TRP* 4.0 18.8 - - + -
92D TRP* 3.4 24.4 - - + -
93D SER 3.4 13.9 - - - +
94D GLY* 4.3 3.8 - - - -
104D ILE* 3.7 23.8 - - + +
105D ASN* 1.3 80.9 - - - +
107D GLN* 1.3 67.3 + - - +
127D HIS* 3.1 8.7 - - - +
128D ASP* 2.8 53.1 + - - +
130D PHE* 3.9 2.2 - - + -
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Residues in contact with GLN 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B LEU* 3.6 22.4 - - + +
123B THR* 4.8 21.3 - - + +
92D TRP* 3.5 2.3 - - - -
93D SER 3.0 30.7 + - - +
106D THR* 1.3 75.9 - - - +
108D TRP* 1.3 61.1 + - - +
125D VAL* 4.2 13.5 - - + +
126D GLY* 2.8 37.7 + - - -
127D HIS* 3.8 13.1 - - + +
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Residues in contact with TRP 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B LEU* 4.1 2.9 - - - -
25D LEU* 6.3 2.5 - - + -
90D THR* 4.0 6.7 - - + -
91D THR 3.1 14.4 - - - +
92D TRP* 3.8 17.9 - + + -
107D GLN* 1.3 75.3 - - - +
109D LEU* 1.3 64.5 + - - +
110D LEU* 3.8 25.4 - - + -
124D LEU* 3.9 17.0 - - + -
125D VAL* 3.2 19.3 - - - +
126D GLY* 2.8 57.4 + - - -
127D HIS* 3.4 14.5 + - - +
128D ASP* 3.4 35.6 + - - -
5P GLN* 3.4 26.2 - - - -
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Residues in contact with LEU 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B THR 4.9 0.2 - - - +
93B SER* 3.3 22.5 + - - +
107B GLN* 3.5 42.2 - - + +
108B TRP* 4.1 3.8 - - - +
109B LEU* 3.8 30.7 - - + +
125B VAL* 5.4 5.6 - - + -
90D THR* 3.2 3.3 - - - -
91D THR* 3.0 35.4 + - - +
108D TRP* 1.3 74.5 - - - +
110D LEU* 1.3 59.1 + - - +
123D THR* 4.1 17.0 - - + -
124D LEU 3.4 2.9 - - - +
125D VAL* 3.9 29.2 - - + -
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Residues in contact with LEU 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79D TRP* 3.9 5.8 - - - +
88D SER* 3.7 28.9 - - - +
89D ALA 3.4 10.5 - - - +
90D THR* 3.2 20.4 - - - +
108D TRP* 3.8 18.6 - - + -
109D LEU* 1.3 72.4 - - - +
111D THR* 1.3 61.4 - - - +
112D SER* 4.9 4.9 + - - +
122D SER 3.6 1.9 - - - +
123D THR* 3.3 2.2 - - - -
124D LEU* 2.9 52.5 + - + +
3P HIS* 3.9 21.3 - - + +
5P GLN* 3.7 17.3 - - + +
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Residues in contact with THR 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B ALA* 3.7 3.0 - - - +
73B LEU 5.4 0.7 - - - -
93B SER* 2.8 29.8 + - - -
94B GLY* 3.6 29.6 - - - +
95B GLN* 3.7 18.8 - - + -
88D SER* 3.1 4.6 - - - -
89D ALA* 3.0 32.0 + - - -
110D LEU* 1.3 74.8 - - - +
112D SER* 1.3 65.7 + - - +
122D SER* 3.3 10.5 - - - +
123D THR* 3.3 26.8 + - - +
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Residues in contact with SER 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B ALA* 4.4 0.9 - - - -
95B GLN* 3.2 22.1 - - - +
87D HIS 3.5 8.7 - - - -
88D SER* 3.8 10.0 - - - -
110D LEU* 4.9 5.9 - - - +
111D THR* 1.3 77.1 - - - +
113D GLY* 1.3 67.4 + - - +
114D THR* 3.3 13.5 + - - +
122D SER* 2.9 14.6 + - - -
124D LEU* 6.2 0.3 - - - +
3P HIS* 5.9 0.7 - - - -
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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