Contacts of the strand formed by residues 45 - 49 (chain A) in PDB entry 2CRY
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 45 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A PRO 3.4 0.2 - - - -
44A ASP* 1.3 82.9 - - + +
46A ILE* 1.3 75.4 + - - +
47A ALA* 5.7 0.7 - - + -
56A GLU* 5.8 8.5 - - + +
96A ALA 3.5 0.2 - - - -
97A TRP* 2.7 74.7 + - + +
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Residues in contact with ILE 46 (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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37A ILE* 4.1 14.6 - - + -
43A PRO* 3.5 24.9 - - + +
44A ASP 5.6 0.2 - - - -
45A ARG* 1.3 86.7 - - - +
47A ALA* 1.3 66.1 + - - +
48A TRP* 4.3 4.5 - - + -
56A GLU* 3.4 27.4 - - - +
65A VAL* 5.9 1.3 - - + -
67A THR* 3.8 33.7 - - + +
74A VAL* 5.4 0.7 - - + -
76A SER* 4.2 11.0 - - - +
94A CYS* 3.7 28.0 - - - -
95A THR 3.7 6.7 - - - +
96A ALA* 3.7 11.0 - - + -
97A TRP* 4.3 2.0 - - - -
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Residues in contact with ALA 47 (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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45A ARG* 5.7 0.7 - - + -
46A ILE* 1.3 78.8 - - - +
48A TRP* 1.3 65.4 + - - +
49A SER* 3.8 2.6 + - - +
54A VAL* 3.7 24.7 - - + -
55A LEU 3.8 4.5 - - - -
56A GLU* 4.2 10.8 - - + +
94A CYS* 3.7 2.1 - - - -
95A THR* 2.9 33.2 + - - -
97A TRP* 3.8 21.8 - - + -
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Residues in contact with TRP 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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20A THR* 4.1 10.8 - - + -
33A ILE* 3.8 34.3 - - + -
35A CYS* 3.9 6.7 - - + -
46A ILE* 4.3 4.0 - - + -
47A ALA* 1.3 74.6 - - - +
49A SER* 1.3 55.8 + - - +
50A TRP* 2.6 34.7 - - + -
55A LEU 2.9 31.5 + - - +
65A VAL* 4.0 27.3 - - + +
76A SER* 2.8 47.4 + - - -
78A LEU* 3.8 25.9 - - + +
92A TYR* 4.1 20.6 - + + -
93A ASN 3.6 12.1 - - - -
94A CYS* 3.6 32.0 - - + -
107A ILE* 4.7 4.0 - - + -
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Residues in contact with SER 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 ALA* 3.8 2.3 + - - -
48A TRP* 1.3 75.3 - - - +
50A TRP* 1.3 63.2 + - - +
51A LYS 5.9 1.3 - - - -
53A ASN 3.0 19.1 - - - -
54A VAL* 3.6 20.0 - - - -
93A ASN* 2.8 42.3 + - - +
95A THR* 4.6 9.4 + - - -
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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