Contacts of the strand formed by residues 53 - 60 (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 53 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42D THR* 3.6 23.6 - - + +
43D TYR 3.4 4.0 - - - -
44D GLU* 3.9 24.7 - - + +
48D GLY 5.5 0.2 - - - +
50D ALA* 2.6 37.8 + - - +
51D GLU* 2.9 40.6 + - - +
52D SER* 1.3 81.4 - - - +
54D TYR* 1.3 64.8 - - - +
81D ASN* 3.2 18.9 + - - +
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Residues in contact with TYR 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42D THR* 3.3 7.8 - - - +
43D TYR* 2.8 34.5 + - - +
45D SER* 4.4 1.1 - - - -
51D GLU 4.6 1.0 + - - -
52D SER* 3.2 30.7 - - - -
53D ARG* 1.3 74.8 - - - +
55D VAL* 1.3 63.4 + - - +
77D VAL* 3.6 21.3 - - + -
78D ALA 3.9 4.0 - - - +
79D TRP* 3.7 38.3 + + - -
80D LYS 3.6 22.7 - - - -
81D ASN* 3.5 27.1 + - - -
84D ARG* 3.7 24.1 - - - +
4P PRO* 3.6 34.2 - - + +
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Residues in contact with VAL 55 (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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59B ARG* 3.9 44.7 + - - +
41D GLY 3.7 9.6 - - - +
42D THR* 4.6 1.8 - - + +
54D TYR* 1.3 78.9 - - - +
56D LEU* 1.3 73.5 + - - +
57D THR* 5.5 1.1 - - - -
77D VAL* 3.9 19.2 - - - +
78D ALA 4.5 2.5 + - - +
80D LYS 5.4 1.4 + - - -
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Residues in contact with LEU 56 (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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59B ARG* 5.0 0.7 - - - -
29D PHE* 3.1 37.9 - - + -
31D VAL* 3.6 23.8 - - + -
39D LEU* 4.6 2.9 - - + +
40D THR* 3.8 5.2 - - - +
41D GLY 3.0 32.3 + - - +
42D THR 3.7 23.3 - - - +
43D TYR* 4.1 6.5 - - + +
55D VAL* 1.3 81.5 - - - +
57D THR* 1.3 69.9 + - - +
75D TRP* 4.1 16.6 - - + -
76D THR 3.3 13.2 - - - +
77D VAL* 3.6 12.1 - - + -
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Residues in contact with THR 57 (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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57B THR* 2.7 29.3 + - - +
58B GLY* 3.3 37.5 - - - +
59B ARG* 3.7 14.6 - - + -
76B THR* 4.8 0.3 + - - -
39D LEU 3.4 10.2 + - - -
40D THR* 4.8 6.8 - - - +
55D VAL* 5.5 1.6 - - - -
56D LEU* 1.3 76.7 - - - +
58D GLY* 1.3 59.3 + - - +
75D TRP* 3.3 4.4 - - - -
76D THR* 2.9 26.3 + - - +
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Residues in contact with GLY 58 (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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57B THR* 3.1 16.9 - - - +
76B THR* 4.5 3.8 - - - -
38D ALA* 3.8 1.6 - - - +
39D LEU* 2.8 34.3 + - - +
57D THR* 1.3 77.3 + - - +
59D ARG* 1.3 69.4 + - - -
74D GLY 3.4 14.6 - - - -
75D TRP* 3.8 2.7 - - - -
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Residues in contact with ARG 59 (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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55B VAL* 3.8 46.9 + - - +
57B THR* 3.7 17.9 - - + -
76B THR* 3.9 25.1 - - + +
78B ALA* 3.8 25.6 + - + +
80B LYS 5.5 4.9 + - - -
36D ASP* 3.3 21.2 + - - +
37D GLY* 3.0 15.7 - - - -
38D ALA* 3.3 29.2 - - - +
39D LEU* 3.8 5.7 - - - +
58D GLY* 1.3 85.9 - - - +
60D TYR* 1.3 62.7 + - - +
73D LEU* 3.3 3.5 - - - +
74D GLY 3.2 28.7 + - - +
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Residues in contact with TYR 60 (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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78B ALA* 3.5 13.1 - - - +
80B LYS* 5.8 0.7 - - - +
14D GLU* 4.8 17.8 + - + +
15D ALA* 5.6 1.9 - - - +
17D ILE* 4.0 22.0 - - + -
33D ALA* 3.7 19.8 - - + +
34D GLY 2.8 29.3 + - - -
35D ALA* 4.0 9.4 + - - -
37D GLY* 2.9 42.4 + - - -
38D ALA 3.7 1.6 - - - -
39D LEU* 3.5 21.1 - - + -
59D ARG* 1.3 75.0 - - - +
61D ASP* 1.3 70.5 + - - +
62D SER* 3.9 20.9 + - - -
71D THR* 4.0 5.4 - - + -
72D ALA 3.3 7.2 - - - +
73D LEU* 3.6 16.8 - - + +
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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