Contacts of the strand formed by residues 92 - 97 (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 TYR 92 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A ILE* 3.3 29.2 - - + -
48A TRP* 4.1 15.5 - + + -
50A TRP* 3.8 35.0 - + + -
63A TYR* 3.7 23.7 + + - -
78A LEU* 4.3 12.3 - - + -
80A ILE* 3.5 18.9 - - + +
87A ASP* 3.6 34.6 - - - +
90A THR* 4.1 8.7 - - + -
91A ILE* 1.3 73.6 - - - +
93A ASN* 1.3 65.5 + - - +
107A ILE* 2.7 53.4 + - + +
109A LEU* 4.1 19.1 - - + -
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Residues in contact with ASN 93 (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 3.9 0.3 - - - +
48A TRP* 3.6 6.9 - - - -
49A SER* 2.8 50.8 + - - +
50A TRP 4.6 5.4 + - - +
91A ILE* 3.4 22.0 + - - +
92A TYR* 1.3 88.8 + - - +
94A CYS* 1.3 61.1 + - - +
95A THR* 3.9 1.2 + - - +
104A THR* 3.6 15.7 - - + +
105A GLU 3.0 8.6 - - - +
106A ILE* 2.9 35.6 - - - +
107A ILE* 4.4 0.7 - - - -
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Residues in contact with CYS 94 (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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17A ILE* 3.4 12.9 - - + +
35A CYS* 4.5 12.1 - - - -
37A ILE* 4.6 10.5 - - - -
46A ILE* 3.7 19.7 - - - -
47A ALA 3.7 2.9 - - - -
48A TRP* 3.6 45.9 - - + -
76A SER* 4.5 7.2 - - - -
93A ASN* 1.3 72.6 - - - +
95A THR* 1.3 64.9 + - - +
96A ALA* 4.7 1.3 - - - -
104A THR* 3.3 21.2 - - - -
105A GLU 3.3 12.8 + - - +
107A ILE* 4.5 1.9 - - + +
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Residues in contact with THR 95 (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 ILE* 4.6 1.3 - - - -
47A ALA* 2.9 24.3 + - - -
49A SER* 4.6 10.4 + - - -
93A ASN* 3.9 1.6 + - - +
94A CYS* 1.3 71.7 - - - +
96A ALA* 1.3 62.1 + - - +
97A TRP* 2.9 55.9 - - + +
102A SER* 5.4 1.6 - - - -
103A ASP 3.4 7.0 - - - +
104A THR* 3.1 30.4 + - - +
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Residues in contact with ALA 96 (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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15A PRO* 4.1 15.7 - - + -
17A ILE* 4.6 9.6 - - + +
37A ILE* 5.1 6.3 - - + -
43A PRO* 3.8 15.7 - - + -
45A ARG 3.4 5.2 - - - -
46A ILE* 3.7 23.1 - - + -
94A CYS* 4.0 2.9 + - - -
95A THR* 1.3 74.6 - - - +
97A TRP* 1.3 68.8 + - - +
102A SER* 3.4 17.7 - - - -
103A ASP 3.3 12.5 + - - +
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Residues in contact with TRP 97 (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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15A PRO* 4.6 0.7 - - - -
43A PRO* 2.8 10.5 - - - +
44A ASP* 2.6 33.8 + - + -
45A ARG* 2.7 63.9 + - + +
47A ALA* 3.8 23.6 - - + -
95A THR* 2.9 51.5 - - + +
96A ALA* 1.3 73.0 - - - +
98A ASN* 1.3 53.9 + - - +
101A GLY 3.8 3.8 - - - -
102A SER* 3.6 23.3 + - - +
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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