Contacts of the strand formed by residues 65 - 69 (chain A) in PDB entry 2EX4
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 CYS 65 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A THR 3.7 0.8 - - - -
64A SER* 1.3 79.6 - - - +
66A ALA* 1.3 65.8 + - - +
85A PHE* 3.9 4.5 - - - -
87A GLU* 3.3 20.6 - - + +
88A VAL 4.8 0.7 - - - -
89A ASP* 4.7 2.0 - - - -
113A ARG* 3.7 24.9 - - - -
129A SER 3.5 16.6 - - - +
130A TYR* 3.6 26.2 - - - -
131A ASP* 2.8 36.2 + - - +
132A VAL 3.5 1.0 + - - -
159A ARG* 3.7 9.2 - - - +
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Residues in contact with ALA 66 (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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65A CYS* 1.3 75.0 - - - +
67A LEU* 1.3 60.4 + - - +
68A ASP 4.1 0.4 - - - -
81A LEU* 4.2 21.5 - - + -
85A PHE* 3.8 28.9 - - + +
87A GLU 3.1 6.7 + - - -
88A VAL* 3.3 7.2 - - + -
89A ASP* 2.8 26.0 + - - +
130A TYR* 3.8 9.1 - - - -
132A VAL* 3.1 16.2 - - + +
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Residues in contact with LEU 67 (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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66A ALA* 1.3 72.9 - - - +
68A ASP* 1.3 56.0 + - - +
69A CYS* 3.7 24.2 + - - -
81A LEU* 4.7 2.6 - - - +
89A ASP* 3.4 30.5 - - + +
90A MET 4.4 0.7 - - - +
91A VAL* 4.0 17.9 - - + +
116A PHE* 4.8 0.4 - - + -
123A PHE* 3.8 25.8 - - + -
125A PRO* 4.2 8.5 - - + -
130A TYR* 3.8 35.8 - - + +
132A VAL 2.8 5.9 + - - +
133A ILE* 3.4 15.6 - - + +
134A TRP* 2.8 33.1 + - - +
150A PHE* 5.3 1.3 - - + -
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Residues in contact with ASP 68 (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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66A ALA 4.1 0.4 - - - -
67A LEU* 1.3 70.2 - - - +
69A CYS* 1.3 65.9 + - - +
70A GLY 4.6 0.2 - - - -
71A ALA* 3.4 32.9 - - + +
76A ILE* 3.8 19.5 + - - +
77A THR* 2.6 43.0 + - - +
81A LEU* 3.7 17.4 - - + +
88A VAL* 4.5 0.4 - - + +
89A ASP 2.8 15.0 + - - +
90A MET* 4.4 0.2 - - + -
91A VAL* 2.9 28.3 + - - +
134A TRP* 3.9 7.3 - - - +
1401A SAH 4.8 0.2 + - - -
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Residues in contact with CYS 69 (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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67A LEU* 3.7 20.2 - - - -
68A ASP* 1.3 74.5 + - - +
70A GLY* 1.3 68.2 + - - +
71A ALA 3.2 0.4 + - - -
91A VAL* 3.8 7.6 - - - -
120A LEU* 4.1 14.6 - - + -
133A ILE* 3.7 30.3 - - - -
134A TRP 2.9 19.2 + - - +
135A ILE* 3.9 13.0 - - + -
136A GLN 4.0 6.9 + - - -
138A VAL* 3.7 12.0 - - - +
150A PHE* 3.8 18.6 - - - -
1401A SAH 4.2 1.0 + - - -
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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