Contacts of the strand formed by residues 230 - 236 (chain A) in PDB entry 4LOF
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 230 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143A VAL 3.7 0.2 - - - +
144A GLN* 3.2 4.5 - - - -
145A LEU* 2.6 55.4 + - + -
157A PHE* 3.9 17.2 - - + -
200A ASN* 6.1 2.9 - - - +
218A VAL* 5.8 1.8 - - + -
219A PRO 5.6 3.4 - - - +
220A TYR* 4.7 5.2 - - - -
221A GLU 4.2 16.5 + - - +
223A PRO* 4.8 2.3 - - - +
229A CYS* 1.3 76.5 - - - +
231A THR* 1.3 66.6 + - - +
232A ILE* 4.1 20.6 - - + -
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Residues in contact with THR 231 (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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114A LEU* 6.0 1.8 - - + -
142A PRO* 3.8 22.4 - - + -
143A VAL 3.5 9.4 - - - +
144A GLN* 4.1 14.5 + - + +
229A CYS* 4.0 8.5 + - - -
230A THR* 1.3 79.4 + - - +
232A ILE* 1.3 63.9 + - - +
233A HIS* 3.8 28.3 + - + +
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Residues in contact with ILE 232 (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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141A CYS 3.3 2.9 - - - +
142A PRO* 3.4 0.7 - - - +
143A VAL* 2.9 31.8 + - - +
145A LEU* 3.3 27.1 - - + -
157A PHE* 4.5 1.8 - - + -
197A VAL* 3.7 26.9 - - + -
200A ASN* 5.5 5.2 - - + +
218A VAL* 3.3 33.4 - - + -
230A THR* 4.2 7.0 - - + -
231A THR* 1.3 75.6 - - - +
233A HIS* 1.3 65.2 + - - +
234A TYR* 3.1 49.1 + - + +
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Residues in contact with HIS 233 (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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140A THR* 3.2 33.1 + - + +
141A CYS 3.7 4.7 - - - -
142A PRO* 4.1 17.3 - - + +
197A VAL* 3.5 1.0 - - - -
198A GLU* 2.9 46.9 + - + +
199A GLY* 5.8 4.0 - - - -
231A THR* 3.8 24.8 + - + +
232A ILE* 1.3 80.1 - - - +
234A TYR* 1.3 63.9 + - - +
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Residues in contact with TYR 234 (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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140A THR* 3.3 5.0 - - - -
141A CYS* 2.6 43.4 + - + +
143A VAL* 3.9 26.2 - - + -
145A LEU* 4.7 0.8 - - + +
157A PHE* 4.8 4.0 + - - +
159A ALA* 3.5 31.9 + - + +
195A ILE* 3.9 17.5 - - + -
196A ARG 3.2 2.9 - - - +
197A VAL* 3.5 28.9 - - + -
216A VAL* 4.3 2.6 + - + -
232A ILE* 3.1 38.0 - - + +
233A HIS* 1.3 73.8 - - - +
235A LYS* 1.3 57.5 + - - +
236A TYR* 4.5 20.9 - - + +
253A THR* 5.9 0.4 - - + -
255A ILE* 3.8 32.6 - - + +
270A PHE* 5.4 1.3 - + - -
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Residues in contact with LYS 235 (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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138A ALA* 3.7 28.1 + - - +
139A LYS 3.8 8.5 - - - +
140A THR* 3.8 23.1 - - - +
194A LEU 3.4 2.3 - - - +
195A ILE* 3.5 4.2 - - - +
196A ARG* 2.7 55.9 + - + +
198A GLU* 2.9 40.9 + - + +
233A HIS 4.6 1.1 - - - +
234A TYR* 1.3 79.0 - - - +
236A TYR* 1.3 65.1 + - - +
237A MET* 4.2 23.7 - - - +
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Residues in contact with TYR 236 (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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133A MET* 5.2 1.6 - - + -
135A CYS* 3.7 17.9 - - - -
136A GLN 4.3 0.9 + - - +
137A LEU* 3.5 8.1 - - - +
138A ALA 2.9 22.6 + - - -
139A LYS 4.4 4.0 + - - -
141A CYS* 4.1 19.7 - - + -
194A LEU* 3.4 16.6 - - + -
195A ILE* 3.7 29.2 - - + +
234A TYR* 4.5 19.3 - - + +
235A LYS* 1.3 74.4 - - - +
237A MET* 1.3 60.5 + - - +
238A CYS 3.5 2.9 + - - +
251A ILE* 4.5 4.7 - - + -
253A THR* 2.8 33.9 + - - +
270A PHE* 3.6 20.3 - + - -
272A VAL* 3.9 20.6 - - + -
274A VAL* 3.4 25.2 - - + +
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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