Contacts of the strand formed by residues 93 - 98 (chain A) in PDB entry 2C0O
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 TRP 93 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A TYR* 3.3 23.3 - + - -
72A HIS* 4.1 17.3 - + - -
75A ASP* 3.8 23.8 - - + -
90A SER* 3.3 29.9 + - - +
92A GLU* 1.3 86.7 - - + +
94A TRP* 1.3 66.6 + - - +
106A TYR* 3.8 17.4 - - + -
107A ILE* 3.4 25.4 - - - -
108A PRO* 3.7 24.7 - - + -
227A LYS* 5.6 1.8 - - + -
228A PRO* 3.7 29.7 - - + +
229A TRP 2.7 25.6 + - - -
230A GLU* 4.8 0.7 - - - -
231A LYS* 3.6 41.6 + - + +
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Residues in contact with TRP 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A ILE* 5.9 2.0 - - + -
62A VAL* 4.6 12.3 - - + -
86A VAL* 3.5 32.1 - - + -
88A GLU 3.4 8.7 - - - +
89A GLU* 3.2 41.8 - - + +
90A SER 3.7 10.0 - - - +
91A GLY* 2.9 29.1 + - - +
92A GLU 4.2 0.2 - - - -
93A TRP* 1.3 77.7 - - - +
95A LYS* 1.3 64.4 + - - +
106A TYR* 3.3 8.8 - - - -
107A ILE* 2.9 47.5 + - + +
109A SER* 3.5 25.7 - - - -
112A VAL* 5.1 8.1 - - + -
114A ARG* 5.9 7.2 - - + -
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Residues in contact with LYS 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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86A VAL* 3.8 2.3 - - - -
87A LEU* 2.8 40.4 + - + +
88A GLU* 3.3 43.0 + - + +
90A SER* 4.7 0.2 + - - -
94A TRP* 1.3 74.3 - - - +
96A ALA* 1.3 61.5 + - - +
104A GLU* 4.4 23.0 + - - -
105A GLY* 3.4 9.9 - - - +
106A TYR* 3.6 35.2 - - + +
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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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76A LEU* 3.4 6.3 - - - +
84A MET* 4.1 15.9 - - + -
85A VAL 3.1 14.8 - - - +
86A VAL* 4.5 3.1 - - + -
87A LEU* 4.1 9.7 - - - +
95A LYS* 1.3 76.4 - - - +
97A ARG* 1.3 60.6 + - - +
98A SER 4.1 0.2 - - - -
104A GLU* 3.5 0.9 - - - -
105A GLY 2.8 33.8 + - - +
107A ILE* 3.6 30.5 - - + -
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Residues in contact with ARG 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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59A ARG* 4.9 9.7 - - - +
84A MET* 3.2 4.0 - - - -
85A VAL* 2.9 60.2 + - + +
87A LEU* 3.8 23.6 - - + +
96A ALA* 1.3 73.3 - - - +
98A SER* 1.3 65.6 + - - +
99A LEU* 3.4 1.4 + - + -
102A ARG* 3.8 49.5 - - - +
103A LYS 3.3 10.3 - - - +
104A GLU* 3.0 32.3 + - + -
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Residues in contact with SER 98 (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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76A LEU* 4.6 3.4 - - - -
77A SER 5.6 4.4 + - - -
78A PHE* 5.7 2.2 - - - +
82A ASP* 4.8 3.7 + - - -
83A GLN 3.8 3.1 + - - -
84A MET* 3.4 24.4 - - - +
97A ARG* 1.3 70.2 - - - +
99A LEU* 1.3 57.8 - - - +
100A ALA* 3.2 10.9 + - - +
101A THR* 2.6 40.7 + - - +
102A ARG* 2.7 32.7 + - - -
103A LYS 3.1 11.1 + - - -
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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