Contacts of the strand formed by residues 88 - 97 (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 SER 88 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61B ASP* 3.1 8.5 + - - +
72B ALA* 3.6 6.5 - - - -
78D ALA* 3.7 1.0 - - - -
79D TRP* 3.0 29.9 + - - +
86D ALA 3.1 10.9 + - - -
87D HIS* 1.3 79.1 - - - +
89D ALA* 1.3 64.1 + - - +
110D LEU* 3.7 11.9 - - - -
111D THR 3.1 15.5 - - - -
112D SER* 3.8 10.5 - - - -
3P HIS* 3.0 26.2 + - - -
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Residues in contact with ALA 89 (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* 4.1 3.6 - - + +
73B LEU* 3.9 38.6 - - - +
74B GLY* 4.6 1.6 - - - +
93B SER* 4.0 4.5 + - - -
94B GLY 5.7 0.2 - - - +
76D THR* 4.7 3.6 - - + -
77D VAL 3.2 13.9 - - - +
78D ALA* 4.0 8.5 - - + -
79D TRP* 3.7 2.0 - - - -
88D SER* 1.3 77.9 - - - +
90D THR* 1.3 62.9 + - - +
91D THR* 5.8 0.2 - - - -
109D LEU 3.7 1.2 - - - +
110D LEU* 3.4 2.1 - - - +
111D THR* 3.0 31.0 + - - +
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Residues in contact with THR 90 (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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76D THR* 3.2 4.7 - - - +
77D VAL 2.8 31.7 + - - -
79D TRP* 2.8 17.0 + - - +
89D ALA* 1.3 72.4 - - - +
91D THR* 1.3 65.7 + - - +
92D TRP* 3.6 33.8 - - + -
108D TRP* 4.0 10.8 - - + -
109D LEU 3.2 11.4 - - - +
110D LEU* 3.2 10.6 - - - +
5P GLN* 2.6 35.8 + - - +
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Residues in contact with THR 91 (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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74B GLY* 3.8 9.4 - - - -
75B TRP 4.1 1.3 - - - +
91B THR* 3.4 25.9 + - - -
92B TRP 3.4 23.3 - - - +
93B SER* 3.4 22.2 + - - +
109B LEU* 4.9 0.7 - - - +
75D TRP 3.1 5.8 - - - -
76D THR* 3.4 22.0 - - + +
89D ALA 5.8 0.2 - - - -
90D THR* 1.3 76.5 - - - +
92D TRP* 1.3 63.4 + - - +
93D SER 4.2 0.2 + - - -
108D TRP* 3.1 4.5 - - - +
109D LEU* 3.0 33.7 + - - +
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Residues in contact with TRP 92 (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* 3.4 3.1 - - - +
43D TYR* 3.5 34.1 - + - -
74D GLY* 2.9 25.1 - - - -
75D TRP* 2.9 58.5 + + + -
77D VAL* 3.7 15.9 - - + -
79D TRP* 3.8 15.5 - + - -
90D THR* 3.6 44.0 - - + -
91D THR* 1.3 75.1 - - - +
93D SER* 1.3 60.2 - - - +
106D THR* 3.4 26.5 - - - -
107D GLN 3.5 4.9 - - - -
108D TRP* 3.8 13.8 - + + -
128D ASP* 3.1 20.6 + - - -
130D PHE* 3.9 11.2 - + - -
5P GLN* 4.3 11.0 - - - -
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Residues in contact with SER 93 (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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89B ALA 3.8 5.0 + - - -
91B THR* 3.4 23.6 - - - +
109B LEU* 3.3 33.3 + - - -
111B THR* 2.8 28.9 + - - -
123B THR* 5.4 0.5 + - - -
73D LEU 3.7 6.5 + - - -
91D THR 4.2 0.2 - - - -
92D TRP* 1.3 73.3 - - - +
94D GLY* 1.3 57.4 + - - +
106D THR* 3.4 3.4 - - - -
107D GLN* 3.0 29.6 + - - +
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Residues in contact with GLY 94 (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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111B THR* 3.5 20.5 + - - +
72D ALA* 3.5 3.8 - - - -
73D LEU* 3.0 35.0 + - - +
93D SER* 1.3 77.1 + - - +
95D GLN* 1.3 64.8 + - - +
105D ASN 3.1 13.9 - - - -
106D THR* 4.2 3.6 - - - -
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Residues in contact with GLN 95 (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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111B THR* 4.5 5.6 - - + -
112B SER 3.9 6.3 - - - +
113B GLY* 3.5 2.6 - - - -
114B THR* 3.0 53.1 + - - +
119B ALA* 4.4 8.8 - - - +
122B SER* 3.8 15.6 + - - -
70D GLY* 3.5 13.7 - - - -
71D THR 3.1 17.5 - - - +
72D ALA* 4.3 2.2 - - - +
73D LEU* 4.3 1.9 - - - +
94D GLY* 1.3 77.2 - - - +
96D TYR* 1.3 63.0 + - - +
97D VAL* 4.6 10.9 - - + +
103D ARG 4.0 0.7 - - - +
104D ILE* 3.4 5.9 - - - -
105D ASN* 2.9 38.8 + - + +
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Residues in contact with TYR 96 (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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13D ALA 2.7 46.7 + - - -
14D GLU 5.0 0.7 - - - -
16D GLY* 3.8 20.6 + - - -
17D ILE* 3.6 20.0 - - + -
21D TRP* 3.9 23.3 - + - -
70D GLY* 3.1 6.8 - - - -
71D THR* 2.8 48.7 + - - +
73D LEU* 3.9 18.3 - - + +
95D GLN* 1.3 73.9 - - - +
97D VAL* 1.3 70.6 + - - +
98D GLY* 3.3 21.0 - - - -
99D GLY 4.7 0.2 + - - -
102D ALA* 4.1 5.4 - - + +
103D ARG 3.5 10.5 - - - -
104D ILE* 4.1 7.9 - - + +
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Residues in contact with VAL 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B THR 6.0 0.2 - - - +
70D GLY* 4.4 12.8 - - - +
95D GLN* 4.6 13.7 - - + +
96D TYR* 1.3 83.3 - - - +
98D GLY* 1.3 72.5 + - - +
102D ALA* 3.2 4.0 - - - +
103D ARG* 2.9 58.4 + - - +
105D ASN* 4.6 11.9 - - - +
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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