Contacts of the strand formed by residues 152 - 156 (chain A) in PDB entry 2A7P
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 THR 152 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67A LEU* 4.4 6.0 - - + +
69A LYS* 5.3 2.9 + - - -
126A LEU 4.0 2.2 + - - +
127A TRP* 3.3 48.5 + - + +
128A PHE* 2.8 28.1 + - - +
150A TYR* 3.5 2.0 - - - +
151A THR* 1.3 94.2 + - - +
153A LEU* 1.3 70.1 + - - +
224A TRP* 3.8 5.8 - - - -
227A LYS* 3.3 30.4 - - + +
229A LEU* 4.4 5.4 - - + -
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Residues in contact with LEU 153 (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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128A PHE* 3.4 36.6 - - + +
130A LEU* 4.0 14.6 - - + -
142A VAL* 4.2 12.8 - - + -
152A THR* 1.3 74.2 - - - +
154A VAL* 1.3 65.6 + - - +
220A LEU* 3.6 33.9 - - + -
224A TRP* 3.5 47.0 - - + +
227A LYS 3.0 6.1 + - - -
228A LEU* 3.4 14.8 - - + +
229A LEU 2.9 25.5 + - - -
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Residues in contact with VAL 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A PRO* 5.4 1.8 - - + -
106A VAL* 4.8 9.0 - - + -
127A TRP* 4.0 27.1 - - + -
128A PHE 2.8 14.3 + - - +
129A GLN* 3.2 11.2 - - + +
130A LEU* 2.6 33.8 + - - -
152A THR* 4.6 0.9 - - + -
153A LEU* 1.3 81.5 - - - +
155A LEU* 1.3 59.6 + - - +
156A THR* 3.6 3.0 + - - +
229A LEU* 3.3 18.4 - - + +
231A LYS* 3.6 38.8 - - + -
251A ILE* 4.2 11.4 - - + -
305A LEU* 6.2 0.2 - - + -
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Residues in contact with LEU 155 (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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130A LEU* 3.7 18.4 - - + +
132A VAL* 4.2 23.6 - - + +
153A LEU 4.2 0.4 - - - -
154A VAL* 1.3 71.4 - - - +
156A THR* 1.3 62.3 + - - +
157A THR* 3.7 19.1 + - + +
212A PHE* 3.5 29.8 - - + -
217A LEU* 4.1 16.6 - - + -
220A LEU* 3.8 29.4 - - + -
228A LEU* 4.7 4.1 - - + +
229A LEU 2.9 12.4 + - - +
230A VAL* 3.5 7.7 - - + -
231A LYS 2.7 32.2 + - - +
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Residues in contact with THR 156 (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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129A GLN* 3.1 23.4 - - - +
130A LEU 3.3 9.3 + - - +
131A TYR* 3.3 35.9 - - + +
132A VAL 5.6 0.3 + - - -
154A VAL 3.6 0.2 + - - -
155A LEU* 1.3 74.6 - - - +
157A THR* 1.3 61.7 + - - +
158A ASP* 3.4 25.1 - - - +
159A VAL 5.1 0.5 + - - -
208A MET* 5.6 0.9 - - - +
231A LYS* 3.6 19.6 - - + +
255A HIS* 4.0 2.7 - - + +
390A FMN 2.7 25.4 + - - +
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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