Contacts of the strand formed by residues 60 - 66 (chain D) in PDB entry 3V5I
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 ILE 60 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D ARG* 3.6 36.3 - - - +
30D ILE* 4.1 14.6 - - + -
48D LEU* 4.3 11.7 - - + +
51D LEU* 3.7 38.1 - - + -
59D ASP* 1.3 72.8 - - - +
61D TYR* 1.3 69.8 + - - +
62D LEU* 5.3 0.2 - - + -
84D ILE* 3.8 28.9 - - + -
86D PRO* 3.9 10.1 - - + -
87D ASP 2.9 9.5 + - - +
88D VAL* 3.5 11.2 - - + -
89D GLN* 2.7 35.7 + - - +
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Residues in contact with TYR 61 (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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27D ASP 4.4 8.3 - - - -
28D ARG* 2.9 18.1 + - + +
29D ILE* 3.4 24.6 - - + +
30D ILE* 2.7 33.4 + - - +
59D ASP* 3.7 30.4 + - - -
60D ILE* 1.3 74.4 - - - +
62D LEU* 1.3 57.1 + - - +
63D TYR* 3.9 6.4 + + + -
89D GLN* 3.5 40.7 + - + -
91D ILE* 4.3 17.5 - - + -
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Residues in contact with LEU 62 (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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30D ILE* 3.5 36.8 - - + +
32D LEU* 4.4 14.4 - - + -
44D ILE* 4.6 10.8 - - + -
48D LEU* 5.8 2.7 - - + -
60D ILE* 4.0 1.7 + - + -
61D TYR* 1.3 71.0 - - - +
63D TYR* 1.3 67.8 + - - +
64D ILE* 3.7 17.7 + - + +
77D ILE* 5.0 9.0 - - + -
81D ILE* 4.1 26.2 - - + -
88D VAL* 4.0 11.7 - - + -
89D GLN 2.7 17.4 + - - +
90D THR* 3.4 16.0 - - + -
91D ILE* 3.0 23.4 + - - +
103D LEU* 5.5 3.1 - - + -
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Residues in contact with TYR 63 (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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45C VAL* 5.6 1.3 - - + -
49C LEU* 3.8 31.7 - - + +
83C HIS* 5.6 4.0 - - - -
29D ILE* 3.7 36.0 - - + +
30D ILE 3.0 7.4 + - - +
31D MET* 3.8 26.9 - - + -
32D LEU* 2.9 31.1 + - - +
61D TYR* 4.4 9.3 - - + -
62D LEU* 1.3 73.2 - - - +
64D ILE* 1.3 59.8 + - - +
65D ASN 4.2 0.4 - - - -
91D ILE* 3.3 49.9 - - + +
93D ILE* 4.1 24.9 - - + -
115D LEU* 6.1 1.3 - - + -
190D MET* 5.4 6.1 - - + +
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Residues in contact with ILE 64 (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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32D LEU* 3.7 14.1 - - + -
62D LEU* 3.8 18.8 - - + +
63D TYR* 1.3 78.8 - - - +
65D ASN* 1.3 62.3 + - - +
66D SER* 4.3 17.3 - - - +
90D THR* 4.0 17.7 - - + -
91D ILE 2.8 12.1 + - - +
92D CYS* 3.5 7.6 - - + -
93D ILE* 3.1 25.4 + - - +
95D MET 3.9 2.9 - - - +
96D ALA* 4.1 20.2 - - + -
100D GLY 4.1 8.1 - - - +
103D LEU* 4.0 12.1 - - + -
104D LEU* 3.7 35.4 - - + +
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Residues in contact with ASN 65 (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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38C ASP* 3.6 36.7 + - - +
41C ALA* 4.7 4.0 - - - +
42C ASN* 5.4 4.4 - - - +
72C THR* 4.9 1.9 + - - -
73C ALA* 4.6 5.3 - - - +
76C ALA* 4.2 16.0 - - - +
32D LEU 2.8 11.8 + - - +
33D GLY* 3.2 30.5 + - - +
64D ILE* 1.3 71.1 - - - +
66D SER* 1.3 59.6 + - - +
93D ILE* 3.1 26.4 - - + +
94D GLY* 3.8 2.2 - - - -
95D MET* 3.0 27.8 + - - +
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Residues in contact with SER 66 (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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38C ASP* 5.0 0.2 - - - -
32D LEU* 4.3 11.7 - - - -
34D SER 3.0 21.2 + - - -
36D ILE* 3.8 9.9 - - - +
64D ILE* 4.0 15.6 - - - +
65D ASN* 1.3 76.2 + - - +
67D PRO* 1.3 64.7 - - - +
68D GLY* 3.0 18.4 + - - -
95D MET* 2.8 16.3 + - - +
96D ALA* 3.5 0.9 - - - -
97D ALA 3.0 24.6 + - - +
100D GLY* 4.4 5.6 - - - -
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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