Contacts of the strand formed by residues 47 - 55 (chain A) in PDB entry 2YRZ
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 LEU 47 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A PRO* 3.6 29.4 - - + -
40A GLU* 3.6 29.6 - - + +
41A PRO* 4.7 2.2 - - + -
43A CYS* 3.5 27.1 - - + -
45A ARG 3.4 0.4 + - - -
46A PRO* 1.3 77.1 - - - +
48A GLN* 1.3 62.9 + - - +
49A GLY 4.4 4.9 - - - +
50A TYR* 2.9 32.1 - - + +
70A PRO* 2.9 29.4 - - + +
92A ALA* 4.2 6.1 - - + -
93A GLN 3.4 15.3 - - - +
94A SER* 4.0 4.5 - - - +
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Residues in contact with GLN 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A PRO* 4.1 7.9 - - - +
47A LEU* 1.3 78.0 - - - +
49A GLY* 1.3 58.0 + - - +
67A ILE 4.1 3.3 - - - +
68A PRO* 4.2 6.2 - - - +
70A PRO* 3.5 17.8 - - - +
93A GLN* 2.9 26.1 + - - +
94A SER 4.2 2.9 - - - -
95A GLN* 4.0 30.1 - - - +
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Residues in contact with GLY 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A LEU* 3.6 2.4 - - - +
48A GLN* 1.3 82.5 - - - +
50A TYR* 1.3 78.6 + - - -
67A ILE 3.0 15.0 - - - -
70A PRO* 3.8 11.4 - - - +
93A GLN* 3.5 26.7 + - - +
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Residues in contact with TYR 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A PRO* 5.7 1.1 - - + -
38A TRP* 3.0 45.1 - + + -
40A GLU* 3.5 9.9 - - - +
41A PRO* 3.3 18.7 - - + +
47A LEU* 2.9 28.9 - - + +
49A GLY* 1.3 86.9 - - - -
51A SER* 1.3 59.9 + - - +
66A ASN* 3.5 4.9 - - - +
67A ILE* 2.7 48.8 + - + +
69A ASN 4.3 2.7 - - - -
70A PRO* 3.4 24.9 - - + -
72A GLN 4.0 9.6 - - - -
73A THR* 4.5 6.3 - - + -
90A VAL* 4.5 0.9 - - + -
91A ARG 3.2 21.5 - - - +
92A ALA* 3.4 22.0 - - + +
98A TRP* 4.3 7.3 - - - -
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Residues in contact with SER 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A TYR* 1.3 74.3 - - - +
52A VAL* 1.3 63.7 + - - +
53A GLU* 3.6 12.2 + - - -
64A ARG* 3.4 29.5 + - - +
65A LEU 3.2 4.6 + - - -
66A ASN* 4.0 2.0 + - - -
89A ARG 3.6 2.6 - - - +
90A VAL* 3.4 3.1 - - - +
91A ARG* 2.7 46.9 + - - +
98A TRP* 3.4 27.6 - - - -
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Residues in contact with VAL 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A VAL* 4.6 3.6 - - + -
38A TRP* 3.5 36.1 - - + -
51A SER* 1.3 75.7 - - - +
53A GLU* 1.3 61.3 + - - +
54A TYR 3.9 0.3 + - - -
63A HIS 3.5 1.9 - - - +
65A LEU* 2.8 51.3 + - + +
67A ILE* 4.6 5.2 - - + -
75A VAL* 3.6 23.6 - - + -
77A VAL* 4.8 0.2 - - + -
88A PHE* 4.1 25.4 - - + -
89A ARG 4.0 2.2 - - - -
90A VAL* 4.1 17.5 - - + +
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Residues in contact with GLU 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A SER* 3.6 11.9 + - - -
52A VAL* 1.3 72.7 - - - +
54A TYR* 1.3 58.3 + - - +
62A LEU* 3.8 22.1 - - + +
63A HIS 3.4 2.7 - - - -
64A ARG* 3.6 35.1 + - + +
87A VAL 3.2 2.3 - - - +
88A PHE* 3.5 1.4 - - - -
89A ARG* 2.8 55.4 + - + +
91A ARG* 3.5 28.2 + - - +
101A GLU* 4.8 7.8 - - - +
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Residues in contact with TYR 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A VAL 4.5 0.7 - - - -
53A GLU* 1.3 72.1 - - - +
55A GLN* 1.3 64.3 + - - +
62A LEU* 3.3 2.1 - - - +
63A HIS* 2.9 79.6 + + + +
65A LEU* 4.0 22.9 - - + -
77A VAL* 3.5 25.1 - - + -
78A GLU 4.2 11.6 + - - -
79A ASP* 4.9 4.7 + - - +
80A LEU* 3.7 17.4 - - + +
86A TYR* 4.0 17.3 - + + -
87A VAL 3.3 5.8 - - - +
88A PHE* 3.2 37.9 - + + -
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Residues in contact with GLN 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A TYR* 1.3 77.5 - - - +
56A LEU* 1.3 73.7 + - - +
59A GLY* 5.4 3.0 - - - -
60A GLY 4.4 13.2 + - - +
61A GLU 3.0 21.8 - - - +
62A LEU* 3.4 31.4 - - + +
86A TYR* 3.2 10.0 - - - -
87A VAL* 2.9 36.0 + - + +
89A ARG* 4.0 21.3 + - - -
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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