Contacts of the strand formed by residues 64 - 69 (chain D) in PDB entry 2Q2U
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 64 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34D VAL* 3.1 6.5 - - - +
35D LYS* 2.7 35.1 + - - +
60D LEU* 3.5 21.3 - - - +
61D PRO* 3.1 25.1 + - - +
63D GLY* 1.3 78.1 - - - +
65D ASP* 1.3 60.4 + - - +
95D TYR* 3.5 5.6 + - - -
97D TRP* 3.0 37.4 + - - +
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Residues in contact with ASP 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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3D ILE* 5.4 1.1 - - + -
7D LEU* 4.7 0.7 - - - +
32D ARG* 2.5 49.5 + - - -
33D SER 4.2 0.7 - - - -
34D VAL* 3.3 16.7 - - + +
63D GLY 4.0 1.3 + - - +
64D SER* 1.3 73.6 - - - +
66D GLY* 1.3 62.3 + - - +
95D TYR* 3.3 4.3 - - - -
97D TRP* 3.3 4.4 - - - -
98D PHE* 3.0 33.9 + - - -
99D ASP* 3.1 29.6 + - + +
101D VAL* 6.1 0.4 - - + -
166D ARG* 5.3 0.3 + - - -
172D TYR* 3.0 24.3 + - + +
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Residues in contact with GLY 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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32D ARG* 3.4 7.3 - - - -
33D SER 2.8 24.7 + - - +
65D ASP* 1.3 79.6 + - - +
67D GLU* 1.3 60.7 + - - -
95D TYR* 2.9 16.0 + - - -
96D TYR 2.9 15.3 - - - -
98D PHE* 3.3 15.5 - - - -
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Residues in contact with GLU 67 (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 LYS* 3.4 18.3 + - - -
28D ILE* 3.1 24.0 - - + +
30D GLY 2.9 36.0 + - - +
31D ILE 3.2 4.0 - - - +
32D ARG* 3.6 30.5 + - - +
66D GLY* 1.3 79.7 - - - +
68D ILE* 1.3 65.2 + - - +
69D SER* 3.8 0.9 + - - -
94D SER 3.9 0.2 - - - +
95D TYR* 3.3 5.9 - - - -
96D TYR* 2.8 40.1 + - + +
98D PHE* 3.9 15.1 - - + -
31L C 5.4 0.3 + - - +
32L C 4.5 6.4 + - - -
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Residues in contact with ILE 68 (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 GLY* 3.3 2.9 - - - -
31D ILE* 2.7 37.7 + - + +
33D SER* 3.8 26.5 - - - +
47D ILE* 4.3 12.6 - - + -
52D MET* 3.8 21.5 - - + -
56D LEU* 4.0 16.8 - - + -
67D GLU* 1.3 72.5 - - - +
69D SER* 1.3 64.4 + - - +
78D THR* 3.9 5.2 - - + +
82D VAL* 3.7 41.3 - - + -
93D PHE* 4.1 6.5 - - + -
94D SER 3.6 9.4 - - - +
95D TYR* 3.8 19.1 - - + -
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Residues in contact with SER 69 (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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28D ILE* 3.7 28.2 - - - +
29D ASP 5.1 1.6 + - - -
30D GLY* 4.1 5.0 - - - -
67D GLU 3.8 0.4 + - - -
68D ILE* 1.3 76.4 - - - +
70D ILE* 1.3 72.3 + - - +
71D GLU* 3.5 5.0 + - - +
78D THR* 3.7 8.1 + - - -
94D SER* 3.0 36.2 + - - +
96D TYR* 4.3 15.2 - - - -
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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